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Transcript of Planning for optimal conservation of geographical genetic variability within species
1 23
Conservation Genetics ISSN 1566-0621Volume 13Number 4 Conserv Genet (2012) 131085-1093DOI 101007s10592-012-0356-8
Planning for optimal conservation ofgeographical genetic variability withinspecies
Joseacute Alexandre Felizola Diniz-FilhoDayane Borges Melo Guilherme deOliveira Rosane Garcia CollevattiThannya Nascimento Soares et al
1 23
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RESEARCH ARTICLE
Planning for optimal conservation of geographical geneticvariability within species
Jose Alexandre Felizola Diniz-Filho bull Dayane Borges Melo bull Guilherme de Oliveira bull
Rosane Garcia Collevatti bull Thannya Nascimento Soares bull Joao Carlos Nabout bull
Jacqueline de Souza Lima bull Ricardo Dobrovolski bull Lazaro Jose Chaves bull
Ronaldo Veloso Naves bull Rafael Dias Loyola bull Mariana Pires de Campos Telles
Received 15 November 2011 Accepted 14 April 2012 Published online 3 May 2012
Springer Science+Business Media BV 2012
Abstract Systematic Conservation Planning (SCP)
involves a series of steps that should be accomplished to
determine the most cost-effective way to invest in con-
servation action Although SCP has been usually applied at
the species level (or hierarchically higher) it is possible to
use alleles from molecular analyses at the population level
as basic units for analyses Here we demonstrate how SCP
procedures can be used to establish optimum strategies for
in situ and ex situ conservation of a single species using
Dipteryx alata (a Fabaceae tree species widely distributed
and endemics to Brazilian Cerrado) as a case study Data
for the analyses consisted in 52 alleles from eight micro-
satellite loci coded for a total of 644 individual trees
sampled in 25 local populations throughout speciesrsquo geo-
graphic range We found optimal solutions in which seven
local populations are the smallest set of local populations
of D alata that should be conserved to represent the known
genetic diversity Combining these several solutions
allowed estimating the relative importance of the local
populations for conserving all known alleles taking into
account the current land-use patterns in the region A
germplasm collection for this species already exists so we
also used SCP approach to identify the smallest number of
populations that should be further collected in the field to
complement the existing collection showing that only four
local populations should be sampled for optimizing the
species ex situ representation The initial application of the
SCP methods to genetic data showed here can be a useful
starting point for methodological and conceptual
improvements and may be a first important step towards a
comprehensive and balanced quantitative definition of
conservation goals shedding light to new possibilities for
in situ and ex situ designs within species
Keywords Complementarity Conservation planning Optimization Cerrado Hotspot Dipteryx alata
Introduction
The current biodiversity crisis has forced scientists to
develop systematic strategies to effectively achieve con-
servation goals aimed at solving potential conflicts between
conservation and human development (sensu Araujo 2003
J A F Diniz-Filho (amp) R D Loyola
Departamento de Ecologia ICB Universidade Federal de Goias
CxP 131 Goiania GO 74001-970 Brazil
e-mail dinizicbufgbr
D B Melo
Programa de Pos-Graduacao em Agronomia Escola de
Agronomia e Engenharia de Alimentos Universidade Federal de
Goias Goiania GO 74001-970 Brazil
G de Oliveira
Programa DTI Universidade Federal de Goias Campus Jataı
Rod BR-364 KM 192 Jataı GO 75800-970 Brazil
R G Collevatti T N Soares M P C Telles
Departamento de Biologia Geral ICB Universidade Federal de
Goias CxP 131 Goiania GO 74001-970 Brazil
J C Nabout
Unidade de Ciencias Exatas e da Terra Universidade Estadual
de Goias Anapolis GO 75132-400 Brazil
Jacqueline de S Lima R Dobrovolski
Programa de Pos-Graduacao em Ecologia amp Evolucao ICB
Universidade Federal de Goias CxP 131 Goiania GO 74001-
970 Brazil
L J Chaves R V Naves
Escola de Agronomia e Engenharia de Alimentos Universidade
Federal de Goias Goiania GO 74001-970 Brazil
123
Conserv Genet (2012) 131085ndash1093
DOI 101007s10592-012-0356-8
Authors personal copy
Balmford et al 2001) The overall underlying principle of
this strategy lies in the science of systematic conservation
planning (SCP) which involves a series of steps that
should be accomplished to determine the most cost-effec-
tive way to invest in conservation actions (Margules and
Pressey 2000 see also Sarkar and Illoldi-Rangel 2010 for a
recent update) Ultimately SCP allows better planning for
conservation actions and land use at different spatial scales
It has been applied to a series of datasets to test and
improve its methodological details and used in practical
conservation actions in some parts of the world (see
Margules and Sarkar 2007)
The core of SCP is the principle of complementarity
in which a set of sites (among several available ones) are
selected so as to minimize the overall cost of conservation
action (ie the minimum set coverage problem) or to
maximize the level of feature representation given a
limited budget (ie the maximal coverage problem)
(Cabeza and Moilanen 2001) While resolving such
optimization problems using several possible mathemati-
cal and computational methods SCP always maximizes
the dissimilarities among biodiversity features being
considered (ie conservation targets such as species
vegetation types genes see Diniz-Filho and Bini 2011)
More complexity is usually included to these general
problems by adding socio-economical costs to the areas or
minimizing their spatial aggregation (Abbitt et al 2000
Balmford et al 2001 Diniz-Filho et al 2007a Loyola
et al 2009)
Traditionally SCP has been applied to more graspable
conservation goals such as species or vegetation types (see
Brooks et al 2004 Grelle et al 2010 Pressey 2004)
However it is possible to apply the same framework to
solve a series of problems at much lower hierarchical
levels allowing the definition of conservation strategies at
the intra-specific level (see Diniz-Filho and Telles 2006)
The geographical variation of both phenotypic and genetic
data within species have been known for some time and
used in many cases to understand the evolutionary drivers
of population differentiation (Epperson 2003) In a con-
servation context the conservation of intraspecific varia-
tion has been dominated by the debate among how to
define evolutionary significant units (ESUs) or manage-
ment units (MUs) (eg Fraser and Bernatchez 2001 see
also Diniz-Filho and Telles 2002 for a proposal to define
operational units to be used with continuous variation in
the geographical space) or meta-population dynamic pro-
cesses related to persistence (eg McCarthy et al 2005) It
is important however to generalize this to a more basic
representation of the genetic variability throughout geo-
graphical space and in this context SCP procedures may
be quite useful as well (eg see Diniz-Filho and Bini 2011
Loyola et al 2011 Neel and Cummings 2003)
Here we applied the systematic conservation planning
protocol to define conservation priorities for Dipteryx alata
(Fabaceae) This species is endemic to the Brazilian
Cerrado one of the global Biodiversity Hotspots (Myers
et al 2000) where it is commonly known as the lsquolsquoBarursquorsquo
tree Despite endemics to the biome it is a widely dis-
tributed tree species in the Cerrado found in eutrophic and
drained soils of seasonal savannas The edible nuts are also
important for local economies and are now used for several
natural goods or products (eg Felfili et al 2004) Previous
studies showed a significant amount of spatial genetic
differentiation among and within local populations
(Collevatti et al 2010 Soares et al 2008) and broad-scale
geographical structure is apparently associated with pat-
terns of historical habitat fragmentation in the Cerrado
More specifically we found here optimal solutions
indicating the smallest set of local populations of D alata
that should be conserved to represent the known genetic
diversity of the species in the Cerrado aiming at in situ
conservation of the species We also took into account the
current land-use patterns found in the Cerrado (expressed
as the proportion of natural remnants in a buffer zone
around local populations) to weight final solutions and thus
increase the chance of long-term persistence of these
populations by protecting them from human impacts A
germplasm collection for this species already exists so we
also used SCP in a different analysis to identify
the smallest number of samples that should be collected
in the field to complement the existing collection aiming at
the species ex situ conservation
Methods and materials
Genetic data
Genetic data for D alata consisted of microsatellite
markers analyzed for 25 widely distributed local popula-
tions encompassing most of speciesrsquo geographical range
(Fig 1) A total of 644 individual trees were genotyped for
eight microsatellite loci (see Soares et al 2012 for meth-
odological details) with sample sizes within each locality
ranging from 12 to 32 (15 out of the 25 local populations
had 32 individuals analyzed) Details of sample size pri-
vate alleles and genetic characteristics of each local pop-
ulation are given in Table 1 We also calculated standard
population genetics statistics such as observed and
expected heterozygosity as well as an estimate of FST
obtained from an analysis of variance of allele frequencies
(Weir and Cockerham 1984) to provide an overall
description of genetic population structure of D alata The
genetic analyses were conducted with the software FSTAT
2932 (Goudet 2002)
1086 Conserv Genet (2012) 131085ndash1093
123
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Systematic conservation planning
We produced an allele-by-site (local populations) presence-
absence matrix to solve the so-called minimum set coverage
problem in optimization theory (Kirkpatrick 1983) We
defined alleles as our conservation goal and used an algo-
rithm to achieve the initial conservation target of finding the
smallest number of local populations in which all alleles are
represented at least once Even though genetic diversity
would be a best goal from a conservation viewpoint due to its
relationship with inbreeding depression (Charlesworth and
Charlesworth 1987 Frankham 2003) allele presence-
absence is a best choice in this case because D alata popu-
lations are highly genetic differentiated mainly because of
differences in allele composition Further it allows an easy
solution to SCP because alleles can be directly analogous to
species (or other goals at higher organizational level)
Because there are several feasible solutions for this mini-
mization problem we used the selection frequency ie the
frequency at which each local population appears in 100
analyzed solutions as an indicator of site importance for
achieving the conservation target
The SCP problems are solved using several possible
computational and mathematical methods based on exact
optimization algorithms (eg branch-and-bound algorithm
implemented in linear programming) or approximate
algorithms that generate near-optimum solutions (eg
simulated annealing) (see Cabeza and Moilanen 2001
Williams et al 2004) Here we applied the simulated
annealing algorithm which is a computer-intensive search
method (see Possingham et al 2000) to find the smallest
number of local populations that represent all alleles at
least once and that at the same time maximize the amount
of natural habitat remnants around local populations taking
into account broad-scale properties of landscape (see
Segelbacher et al 2010) We obtained this variable for each
local population by analyzing land use data from vegeta-
tion cover maps of the Brazilian biomes at the 1250000
spatial scale We reclassified the maps into natural vege-
tation or anthropogenic land cover classes (this last clas-
sification includes agriculture pasture lands urban areas
and mining regions) and then created 10 km-size buffers
around the geographical position of each population The
proportion of the buffer areas covered by natural vegetation
Fig 1 Geographic location of
the 25 local populations of
Dipteryx alata in Central Brazil
analyzed using SCP methods
based on microsatellite allelic
variation The region shown in
dark tone is still covered by
natural remnants of Cerrado
vegetation
Conserv Genet (2012) 131085ndash1093 1087
123
Authors personal copy
were then calculated and used as a surrogate for regional
level of habitat conservation (see Fig 1 for the overall
patterns of natural remnants in the region) We also used a
randomization procedure to evaluate if the amount of mean
proportion of natural remnants in the best solution differs
from random solutions with the same number of local
populations
Finally there is a large accessible germplasm collection
for D alata composed by 178 fully growth adult trees
located at the Agronomy School of the Federal University
of Goias Brazil These 178 individuals came from several
locations in the state of Goias and were also genotyped for
the eight microsatellite loci A different analysis was
conducted in which the individuals in the germplasm bank
were included as another lsquolsquolocal populationrsquorsquo We then
repeated the SCP analysis by assuming that this germplasm
bank was already protected (ie we included this
population in the initial and final portfolios when running
the algorithm) In that case the optimization problem was
to find the smallest number of local populations that better
complement the genetic variability already preserved in the
germplasm bank This is thus equivalent to running a gap
analysis in which a single reserve (the germplasm bank) is
already established We also calculated the SCP solutions
by minimizing the geographic distance to Goiania (ie
using this distance as a cost variable) so that overall costs
of sampling and transporting material to the locality where
the germplasm collection is maintained are minimum
Results
After coding the eight microsatellites a total of 52 alleles
were recorded out of which only six were found in a
Table 1 Genetic characterization for 25 populations of D alata based on eight microsatellite loci
Population N A Ar Ap Ho He f Habitata
ABMT 32 2375 2223 0 0291 0382 0238 2
AMG 32 2250 1973 0 0293 0310 0055ns 3
AMS 32 4250 3609 1 0349 0476 0267 3
AQMS 31 3375 2817 0 0442 0459 0038ns 1
ARTO 15 2250 2205 0 0381 0372 -0025ns 3
ATO 32 3000 2747 0 0382 0488 0217 1
CAMT 30 3750 3152 2 0278 0466 0405 2
CMS 13 2875 2861 0 0466 0480 0029ns 4
CMT 32 2625 2502 1 0249 0322 0229 1
ENGO 12 2500 2478 0 0408 0474 0139 1
IGO 13 2500 2447 0 0350 0453 0226 1
ISP 32 2375 2212 0 0322 0455 0291 3
JGO 32 2625 2480 0 0638 0599 -0065ns 1
LGO 32 2500 2425 0 0424 0509 0166 1
MAMG 32 2875 2582 0 0448 0514 0128 4
NTO 12 2000 2093 0 0458 0393 -0165ns 3
PCMS 13 2875 2808 0 0169 0345 0509 1
PGO 32 2500 2164 0 0259 0426 0336 3
PMG 32 2375 2103 0 0176 0257 0314 1
PMS 13 3125 3059 0 0215 0410 0476 1
RAGO 32 3250 2865 0 0473 0462 -0024ns 3
RAMT 32 3375 2976 2 0308 0462 0333 3
SMGO 32 2625 2409 0 0354 0336 -0052ns 1
SMS 32 3625 3213 0 0422 0482 0125 2
STGO 12 2875 2823 0 0356 0387 0080ns 1
Overall 644 2835 2609 6 0356 0429 0171 ndash
P [ 005
N sample size A total number of alleles Ar Allelic richness Ap private alleles Ho observed heterozygosity He expected heterozygosity
f inbreeding coefficient ns not significanta 1mdashIsolated adult individuals in pasture or crop field 2mdashisolated adult individuals in remnant of savanna at roadsides 3mdashsavanna remnant
surrounded by pasture 4mdashfragment of savanna
1088 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
unique population Observed heterozygosity was low in all
populations and most populations show deviations from
HardyndashWeinberg equilibrium with f-values significantly
different from zero for most local populations (Table 1) A
significant amount of divergence among these local popu-
lations was also observed (FST = 0267 SD = 0036
P 00001) indicating that several local populations
should be conserved to maintain all genetic diversity
Optimization solutions revealed that a minimum of
seven local populations are necessary to represent all 52
alleles at least once Several solutions for this problem
were reached and after considering a total of 100 minimum
solutions four local populations were extremely important
for achieving this goal (ie they were found in 100 of
solutions and a fiftieth additional one appeared in 95 of
the solutions) Further a total of ten populations had fre-
quencies of selection higher than 0 indicating that the
solutions are not always the same (Fig 2)
There was no significant relationship between selection
frequency and genetic parameters within local populations
except for Ar (r = 0488 P = 0013) but this is someway
tautological because optimization works to maximize
number of alleles (unique in each local population) Even
so it is important to note that these data could be also used
as covariates if one is interested for example in conserv-
ing the populations with higher selection frequency that
have more expected heterozygosity
Given the distribution of alleles in local populations (ie
many rare alleles are found in one or two populations
only) the mean amount of proportional remaining habitat
around the seven local populations selected (equal to 022)
was not significantly different from a 1000 random sam-
ples with same size (032 plusmn 014 P = 0265) However in
none of these random samples were the total number of
alleles represented (the mean number of alleles represented
in random samples of seven populations is 385 plusmn 33)
(Fig 3) This supports the idea that although human
actions cannot be minimized because of data constraints
random solutions are much less efficient than the optimized
one as expected
For the alternative analysis for an ex situ SCP strategy
samples of only four additional local populations would be
necessary to optimally complement the genetic variability
currently represented in the germplasm bank (Fig 4) Only
these four populations have maximum frequency of
selection (ie because only they appeared in all solutions)
Minimizing distances to Goiania did not change this
solution in this particular case because of the rare variants
found in the state of Mato Grosso are unique and conse-
quently they have maximum frequencies of selection (ie
appear in all solutions)
Discussion
Here we showed that it is possible to design optimal con-
servation strategies for the conservation of genetic diver-
sity under the framework of SCP Moreover alternative
applications of SCP for in situ and ex situ conservation
strategies were done based on the same dataset although
using distinct weights revealing their distinct purposes
We understand that these ex situ and in situ strategies can
Fig 2 Frequency of solutions
from SCP maximizing the total
number of alleles represented
minimizing the number of local
populations and maximizing the
amount of natural remnants
This count if based on
combination of several solutions
with seven local populations
that we found for optimizing the
in situ conservation Local
populations with frequencies
tending to 100 tend to be
irreplaceable so that losing
them will not allow one to
achieve the conservation goal
Conserv Genet (2012) 131085ndash1093 1089
123
Authors personal copy
be implemented together so as to maximize the effective-
ness of conservation planning In our case study dealing
with the genetic variability of D alata natural populations
we showed that it is possible to represent all known alleles
at least once by strategically conserving (in situ) seven
local populations distributed in the Cerrado biome
Because of the analytical constraints imposed by the dis-
tribution of alleles in different local population and the
predetermined targets trying to define a solution that
minimizes the human impacts of these local populations
(ie by selecting local population in regions with more
natural cover remnants) did not change the selected pop-
ulations although it may help to define priorities among
the populations studied (eg planning a schedule for con-
servation interventions) Further assuming that the germ-
plasm bank is a fully protected lsquolsquopopulationrsquorsquo we also
showed that even fewer local populations need to be
sampled to represent the known genetic variability of the
species aiming at its ex situ conservation
Systematic conservation planning is usually applied to
species conservation building conservation priority
regions based on several goals with different conservation
targets (Sarkar and Illoldi-Rangel 2010) This initial
application with genetic data represents a step further to the
theoretical ideas originally presented by Diniz-Filho and
Telles (2006) who proposed how different algorithms
could be used to represent genetic diversity under distinct
spatial population structures The analysis shown here for
D alata indeed suggests that systematic conservation
planning can be a quite useful and objective tool to guide
actions for within-species conservation although of course
further improvements may be important and more work is
needed to expand the framework
A first important issue to be discussed is that our
application is focused on neutral molecular markers which
represents the overall variability of the species that have
been accumulated throughout its evolutionary history Of
course this does not necessarily reflect adaptive traits that
must be important for population persistence or the traits
(ie fruit production and quality) that may be important for
000 015 030 045 060 075
Mean proportion of natural remnants
25
35
45
55N
umbe
r of
alle
les
repr
esen
ted
Best solution
Fig 3 Relationship between number of alleles represented and
proportion of natural remnants in the conserved populations under a
null model in which the seven local populations are randomly
sampled from the pool of 25 and combined in a reserve network The
optimum solution obtained by SCP is highlighted
Fig 4 Local populations
defined by SCP necessary to
better complement the
germplasm collection in the exsitu conservation program The
four local populations are
connected by arrows to Goiania
the locality where the
germplasm of D alata is
maintained
1090 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
1 23
Your article is protected by copyright and
all rights are held exclusively by Springer
Science+Business Media BV This e-offprint
is for personal use only and shall not be self-
archived in electronic repositories If you
wish to self-archive your work please use the
accepted authorrsquos version for posting to your
own website or your institutionrsquos repository
You may further deposit the accepted authorrsquos
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request provided it is not made publicly
available until 12 months after publication
RESEARCH ARTICLE
Planning for optimal conservation of geographical geneticvariability within species
Jose Alexandre Felizola Diniz-Filho bull Dayane Borges Melo bull Guilherme de Oliveira bull
Rosane Garcia Collevatti bull Thannya Nascimento Soares bull Joao Carlos Nabout bull
Jacqueline de Souza Lima bull Ricardo Dobrovolski bull Lazaro Jose Chaves bull
Ronaldo Veloso Naves bull Rafael Dias Loyola bull Mariana Pires de Campos Telles
Received 15 November 2011 Accepted 14 April 2012 Published online 3 May 2012
Springer Science+Business Media BV 2012
Abstract Systematic Conservation Planning (SCP)
involves a series of steps that should be accomplished to
determine the most cost-effective way to invest in con-
servation action Although SCP has been usually applied at
the species level (or hierarchically higher) it is possible to
use alleles from molecular analyses at the population level
as basic units for analyses Here we demonstrate how SCP
procedures can be used to establish optimum strategies for
in situ and ex situ conservation of a single species using
Dipteryx alata (a Fabaceae tree species widely distributed
and endemics to Brazilian Cerrado) as a case study Data
for the analyses consisted in 52 alleles from eight micro-
satellite loci coded for a total of 644 individual trees
sampled in 25 local populations throughout speciesrsquo geo-
graphic range We found optimal solutions in which seven
local populations are the smallest set of local populations
of D alata that should be conserved to represent the known
genetic diversity Combining these several solutions
allowed estimating the relative importance of the local
populations for conserving all known alleles taking into
account the current land-use patterns in the region A
germplasm collection for this species already exists so we
also used SCP approach to identify the smallest number of
populations that should be further collected in the field to
complement the existing collection showing that only four
local populations should be sampled for optimizing the
species ex situ representation The initial application of the
SCP methods to genetic data showed here can be a useful
starting point for methodological and conceptual
improvements and may be a first important step towards a
comprehensive and balanced quantitative definition of
conservation goals shedding light to new possibilities for
in situ and ex situ designs within species
Keywords Complementarity Conservation planning Optimization Cerrado Hotspot Dipteryx alata
Introduction
The current biodiversity crisis has forced scientists to
develop systematic strategies to effectively achieve con-
servation goals aimed at solving potential conflicts between
conservation and human development (sensu Araujo 2003
J A F Diniz-Filho (amp) R D Loyola
Departamento de Ecologia ICB Universidade Federal de Goias
CxP 131 Goiania GO 74001-970 Brazil
e-mail dinizicbufgbr
D B Melo
Programa de Pos-Graduacao em Agronomia Escola de
Agronomia e Engenharia de Alimentos Universidade Federal de
Goias Goiania GO 74001-970 Brazil
G de Oliveira
Programa DTI Universidade Federal de Goias Campus Jataı
Rod BR-364 KM 192 Jataı GO 75800-970 Brazil
R G Collevatti T N Soares M P C Telles
Departamento de Biologia Geral ICB Universidade Federal de
Goias CxP 131 Goiania GO 74001-970 Brazil
J C Nabout
Unidade de Ciencias Exatas e da Terra Universidade Estadual
de Goias Anapolis GO 75132-400 Brazil
Jacqueline de S Lima R Dobrovolski
Programa de Pos-Graduacao em Ecologia amp Evolucao ICB
Universidade Federal de Goias CxP 131 Goiania GO 74001-
970 Brazil
L J Chaves R V Naves
Escola de Agronomia e Engenharia de Alimentos Universidade
Federal de Goias Goiania GO 74001-970 Brazil
123
Conserv Genet (2012) 131085ndash1093
DOI 101007s10592-012-0356-8
Authors personal copy
Balmford et al 2001) The overall underlying principle of
this strategy lies in the science of systematic conservation
planning (SCP) which involves a series of steps that
should be accomplished to determine the most cost-effec-
tive way to invest in conservation actions (Margules and
Pressey 2000 see also Sarkar and Illoldi-Rangel 2010 for a
recent update) Ultimately SCP allows better planning for
conservation actions and land use at different spatial scales
It has been applied to a series of datasets to test and
improve its methodological details and used in practical
conservation actions in some parts of the world (see
Margules and Sarkar 2007)
The core of SCP is the principle of complementarity
in which a set of sites (among several available ones) are
selected so as to minimize the overall cost of conservation
action (ie the minimum set coverage problem) or to
maximize the level of feature representation given a
limited budget (ie the maximal coverage problem)
(Cabeza and Moilanen 2001) While resolving such
optimization problems using several possible mathemati-
cal and computational methods SCP always maximizes
the dissimilarities among biodiversity features being
considered (ie conservation targets such as species
vegetation types genes see Diniz-Filho and Bini 2011)
More complexity is usually included to these general
problems by adding socio-economical costs to the areas or
minimizing their spatial aggregation (Abbitt et al 2000
Balmford et al 2001 Diniz-Filho et al 2007a Loyola
et al 2009)
Traditionally SCP has been applied to more graspable
conservation goals such as species or vegetation types (see
Brooks et al 2004 Grelle et al 2010 Pressey 2004)
However it is possible to apply the same framework to
solve a series of problems at much lower hierarchical
levels allowing the definition of conservation strategies at
the intra-specific level (see Diniz-Filho and Telles 2006)
The geographical variation of both phenotypic and genetic
data within species have been known for some time and
used in many cases to understand the evolutionary drivers
of population differentiation (Epperson 2003) In a con-
servation context the conservation of intraspecific varia-
tion has been dominated by the debate among how to
define evolutionary significant units (ESUs) or manage-
ment units (MUs) (eg Fraser and Bernatchez 2001 see
also Diniz-Filho and Telles 2002 for a proposal to define
operational units to be used with continuous variation in
the geographical space) or meta-population dynamic pro-
cesses related to persistence (eg McCarthy et al 2005) It
is important however to generalize this to a more basic
representation of the genetic variability throughout geo-
graphical space and in this context SCP procedures may
be quite useful as well (eg see Diniz-Filho and Bini 2011
Loyola et al 2011 Neel and Cummings 2003)
Here we applied the systematic conservation planning
protocol to define conservation priorities for Dipteryx alata
(Fabaceae) This species is endemic to the Brazilian
Cerrado one of the global Biodiversity Hotspots (Myers
et al 2000) where it is commonly known as the lsquolsquoBarursquorsquo
tree Despite endemics to the biome it is a widely dis-
tributed tree species in the Cerrado found in eutrophic and
drained soils of seasonal savannas The edible nuts are also
important for local economies and are now used for several
natural goods or products (eg Felfili et al 2004) Previous
studies showed a significant amount of spatial genetic
differentiation among and within local populations
(Collevatti et al 2010 Soares et al 2008) and broad-scale
geographical structure is apparently associated with pat-
terns of historical habitat fragmentation in the Cerrado
More specifically we found here optimal solutions
indicating the smallest set of local populations of D alata
that should be conserved to represent the known genetic
diversity of the species in the Cerrado aiming at in situ
conservation of the species We also took into account the
current land-use patterns found in the Cerrado (expressed
as the proportion of natural remnants in a buffer zone
around local populations) to weight final solutions and thus
increase the chance of long-term persistence of these
populations by protecting them from human impacts A
germplasm collection for this species already exists so we
also used SCP in a different analysis to identify
the smallest number of samples that should be collected
in the field to complement the existing collection aiming at
the species ex situ conservation
Methods and materials
Genetic data
Genetic data for D alata consisted of microsatellite
markers analyzed for 25 widely distributed local popula-
tions encompassing most of speciesrsquo geographical range
(Fig 1) A total of 644 individual trees were genotyped for
eight microsatellite loci (see Soares et al 2012 for meth-
odological details) with sample sizes within each locality
ranging from 12 to 32 (15 out of the 25 local populations
had 32 individuals analyzed) Details of sample size pri-
vate alleles and genetic characteristics of each local pop-
ulation are given in Table 1 We also calculated standard
population genetics statistics such as observed and
expected heterozygosity as well as an estimate of FST
obtained from an analysis of variance of allele frequencies
(Weir and Cockerham 1984) to provide an overall
description of genetic population structure of D alata The
genetic analyses were conducted with the software FSTAT
2932 (Goudet 2002)
1086 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
Systematic conservation planning
We produced an allele-by-site (local populations) presence-
absence matrix to solve the so-called minimum set coverage
problem in optimization theory (Kirkpatrick 1983) We
defined alleles as our conservation goal and used an algo-
rithm to achieve the initial conservation target of finding the
smallest number of local populations in which all alleles are
represented at least once Even though genetic diversity
would be a best goal from a conservation viewpoint due to its
relationship with inbreeding depression (Charlesworth and
Charlesworth 1987 Frankham 2003) allele presence-
absence is a best choice in this case because D alata popu-
lations are highly genetic differentiated mainly because of
differences in allele composition Further it allows an easy
solution to SCP because alleles can be directly analogous to
species (or other goals at higher organizational level)
Because there are several feasible solutions for this mini-
mization problem we used the selection frequency ie the
frequency at which each local population appears in 100
analyzed solutions as an indicator of site importance for
achieving the conservation target
The SCP problems are solved using several possible
computational and mathematical methods based on exact
optimization algorithms (eg branch-and-bound algorithm
implemented in linear programming) or approximate
algorithms that generate near-optimum solutions (eg
simulated annealing) (see Cabeza and Moilanen 2001
Williams et al 2004) Here we applied the simulated
annealing algorithm which is a computer-intensive search
method (see Possingham et al 2000) to find the smallest
number of local populations that represent all alleles at
least once and that at the same time maximize the amount
of natural habitat remnants around local populations taking
into account broad-scale properties of landscape (see
Segelbacher et al 2010) We obtained this variable for each
local population by analyzing land use data from vegeta-
tion cover maps of the Brazilian biomes at the 1250000
spatial scale We reclassified the maps into natural vege-
tation or anthropogenic land cover classes (this last clas-
sification includes agriculture pasture lands urban areas
and mining regions) and then created 10 km-size buffers
around the geographical position of each population The
proportion of the buffer areas covered by natural vegetation
Fig 1 Geographic location of
the 25 local populations of
Dipteryx alata in Central Brazil
analyzed using SCP methods
based on microsatellite allelic
variation The region shown in
dark tone is still covered by
natural remnants of Cerrado
vegetation
Conserv Genet (2012) 131085ndash1093 1087
123
Authors personal copy
were then calculated and used as a surrogate for regional
level of habitat conservation (see Fig 1 for the overall
patterns of natural remnants in the region) We also used a
randomization procedure to evaluate if the amount of mean
proportion of natural remnants in the best solution differs
from random solutions with the same number of local
populations
Finally there is a large accessible germplasm collection
for D alata composed by 178 fully growth adult trees
located at the Agronomy School of the Federal University
of Goias Brazil These 178 individuals came from several
locations in the state of Goias and were also genotyped for
the eight microsatellite loci A different analysis was
conducted in which the individuals in the germplasm bank
were included as another lsquolsquolocal populationrsquorsquo We then
repeated the SCP analysis by assuming that this germplasm
bank was already protected (ie we included this
population in the initial and final portfolios when running
the algorithm) In that case the optimization problem was
to find the smallest number of local populations that better
complement the genetic variability already preserved in the
germplasm bank This is thus equivalent to running a gap
analysis in which a single reserve (the germplasm bank) is
already established We also calculated the SCP solutions
by minimizing the geographic distance to Goiania (ie
using this distance as a cost variable) so that overall costs
of sampling and transporting material to the locality where
the germplasm collection is maintained are minimum
Results
After coding the eight microsatellites a total of 52 alleles
were recorded out of which only six were found in a
Table 1 Genetic characterization for 25 populations of D alata based on eight microsatellite loci
Population N A Ar Ap Ho He f Habitata
ABMT 32 2375 2223 0 0291 0382 0238 2
AMG 32 2250 1973 0 0293 0310 0055ns 3
AMS 32 4250 3609 1 0349 0476 0267 3
AQMS 31 3375 2817 0 0442 0459 0038ns 1
ARTO 15 2250 2205 0 0381 0372 -0025ns 3
ATO 32 3000 2747 0 0382 0488 0217 1
CAMT 30 3750 3152 2 0278 0466 0405 2
CMS 13 2875 2861 0 0466 0480 0029ns 4
CMT 32 2625 2502 1 0249 0322 0229 1
ENGO 12 2500 2478 0 0408 0474 0139 1
IGO 13 2500 2447 0 0350 0453 0226 1
ISP 32 2375 2212 0 0322 0455 0291 3
JGO 32 2625 2480 0 0638 0599 -0065ns 1
LGO 32 2500 2425 0 0424 0509 0166 1
MAMG 32 2875 2582 0 0448 0514 0128 4
NTO 12 2000 2093 0 0458 0393 -0165ns 3
PCMS 13 2875 2808 0 0169 0345 0509 1
PGO 32 2500 2164 0 0259 0426 0336 3
PMG 32 2375 2103 0 0176 0257 0314 1
PMS 13 3125 3059 0 0215 0410 0476 1
RAGO 32 3250 2865 0 0473 0462 -0024ns 3
RAMT 32 3375 2976 2 0308 0462 0333 3
SMGO 32 2625 2409 0 0354 0336 -0052ns 1
SMS 32 3625 3213 0 0422 0482 0125 2
STGO 12 2875 2823 0 0356 0387 0080ns 1
Overall 644 2835 2609 6 0356 0429 0171 ndash
P [ 005
N sample size A total number of alleles Ar Allelic richness Ap private alleles Ho observed heterozygosity He expected heterozygosity
f inbreeding coefficient ns not significanta 1mdashIsolated adult individuals in pasture or crop field 2mdashisolated adult individuals in remnant of savanna at roadsides 3mdashsavanna remnant
surrounded by pasture 4mdashfragment of savanna
1088 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
unique population Observed heterozygosity was low in all
populations and most populations show deviations from
HardyndashWeinberg equilibrium with f-values significantly
different from zero for most local populations (Table 1) A
significant amount of divergence among these local popu-
lations was also observed (FST = 0267 SD = 0036
P 00001) indicating that several local populations
should be conserved to maintain all genetic diversity
Optimization solutions revealed that a minimum of
seven local populations are necessary to represent all 52
alleles at least once Several solutions for this problem
were reached and after considering a total of 100 minimum
solutions four local populations were extremely important
for achieving this goal (ie they were found in 100 of
solutions and a fiftieth additional one appeared in 95 of
the solutions) Further a total of ten populations had fre-
quencies of selection higher than 0 indicating that the
solutions are not always the same (Fig 2)
There was no significant relationship between selection
frequency and genetic parameters within local populations
except for Ar (r = 0488 P = 0013) but this is someway
tautological because optimization works to maximize
number of alleles (unique in each local population) Even
so it is important to note that these data could be also used
as covariates if one is interested for example in conserv-
ing the populations with higher selection frequency that
have more expected heterozygosity
Given the distribution of alleles in local populations (ie
many rare alleles are found in one or two populations
only) the mean amount of proportional remaining habitat
around the seven local populations selected (equal to 022)
was not significantly different from a 1000 random sam-
ples with same size (032 plusmn 014 P = 0265) However in
none of these random samples were the total number of
alleles represented (the mean number of alleles represented
in random samples of seven populations is 385 plusmn 33)
(Fig 3) This supports the idea that although human
actions cannot be minimized because of data constraints
random solutions are much less efficient than the optimized
one as expected
For the alternative analysis for an ex situ SCP strategy
samples of only four additional local populations would be
necessary to optimally complement the genetic variability
currently represented in the germplasm bank (Fig 4) Only
these four populations have maximum frequency of
selection (ie because only they appeared in all solutions)
Minimizing distances to Goiania did not change this
solution in this particular case because of the rare variants
found in the state of Mato Grosso are unique and conse-
quently they have maximum frequencies of selection (ie
appear in all solutions)
Discussion
Here we showed that it is possible to design optimal con-
servation strategies for the conservation of genetic diver-
sity under the framework of SCP Moreover alternative
applications of SCP for in situ and ex situ conservation
strategies were done based on the same dataset although
using distinct weights revealing their distinct purposes
We understand that these ex situ and in situ strategies can
Fig 2 Frequency of solutions
from SCP maximizing the total
number of alleles represented
minimizing the number of local
populations and maximizing the
amount of natural remnants
This count if based on
combination of several solutions
with seven local populations
that we found for optimizing the
in situ conservation Local
populations with frequencies
tending to 100 tend to be
irreplaceable so that losing
them will not allow one to
achieve the conservation goal
Conserv Genet (2012) 131085ndash1093 1089
123
Authors personal copy
be implemented together so as to maximize the effective-
ness of conservation planning In our case study dealing
with the genetic variability of D alata natural populations
we showed that it is possible to represent all known alleles
at least once by strategically conserving (in situ) seven
local populations distributed in the Cerrado biome
Because of the analytical constraints imposed by the dis-
tribution of alleles in different local population and the
predetermined targets trying to define a solution that
minimizes the human impacts of these local populations
(ie by selecting local population in regions with more
natural cover remnants) did not change the selected pop-
ulations although it may help to define priorities among
the populations studied (eg planning a schedule for con-
servation interventions) Further assuming that the germ-
plasm bank is a fully protected lsquolsquopopulationrsquorsquo we also
showed that even fewer local populations need to be
sampled to represent the known genetic variability of the
species aiming at its ex situ conservation
Systematic conservation planning is usually applied to
species conservation building conservation priority
regions based on several goals with different conservation
targets (Sarkar and Illoldi-Rangel 2010) This initial
application with genetic data represents a step further to the
theoretical ideas originally presented by Diniz-Filho and
Telles (2006) who proposed how different algorithms
could be used to represent genetic diversity under distinct
spatial population structures The analysis shown here for
D alata indeed suggests that systematic conservation
planning can be a quite useful and objective tool to guide
actions for within-species conservation although of course
further improvements may be important and more work is
needed to expand the framework
A first important issue to be discussed is that our
application is focused on neutral molecular markers which
represents the overall variability of the species that have
been accumulated throughout its evolutionary history Of
course this does not necessarily reflect adaptive traits that
must be important for population persistence or the traits
(ie fruit production and quality) that may be important for
000 015 030 045 060 075
Mean proportion of natural remnants
25
35
45
55N
umbe
r of
alle
les
repr
esen
ted
Best solution
Fig 3 Relationship between number of alleles represented and
proportion of natural remnants in the conserved populations under a
null model in which the seven local populations are randomly
sampled from the pool of 25 and combined in a reserve network The
optimum solution obtained by SCP is highlighted
Fig 4 Local populations
defined by SCP necessary to
better complement the
germplasm collection in the exsitu conservation program The
four local populations are
connected by arrows to Goiania
the locality where the
germplasm of D alata is
maintained
1090 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
RESEARCH ARTICLE
Planning for optimal conservation of geographical geneticvariability within species
Jose Alexandre Felizola Diniz-Filho bull Dayane Borges Melo bull Guilherme de Oliveira bull
Rosane Garcia Collevatti bull Thannya Nascimento Soares bull Joao Carlos Nabout bull
Jacqueline de Souza Lima bull Ricardo Dobrovolski bull Lazaro Jose Chaves bull
Ronaldo Veloso Naves bull Rafael Dias Loyola bull Mariana Pires de Campos Telles
Received 15 November 2011 Accepted 14 April 2012 Published online 3 May 2012
Springer Science+Business Media BV 2012
Abstract Systematic Conservation Planning (SCP)
involves a series of steps that should be accomplished to
determine the most cost-effective way to invest in con-
servation action Although SCP has been usually applied at
the species level (or hierarchically higher) it is possible to
use alleles from molecular analyses at the population level
as basic units for analyses Here we demonstrate how SCP
procedures can be used to establish optimum strategies for
in situ and ex situ conservation of a single species using
Dipteryx alata (a Fabaceae tree species widely distributed
and endemics to Brazilian Cerrado) as a case study Data
for the analyses consisted in 52 alleles from eight micro-
satellite loci coded for a total of 644 individual trees
sampled in 25 local populations throughout speciesrsquo geo-
graphic range We found optimal solutions in which seven
local populations are the smallest set of local populations
of D alata that should be conserved to represent the known
genetic diversity Combining these several solutions
allowed estimating the relative importance of the local
populations for conserving all known alleles taking into
account the current land-use patterns in the region A
germplasm collection for this species already exists so we
also used SCP approach to identify the smallest number of
populations that should be further collected in the field to
complement the existing collection showing that only four
local populations should be sampled for optimizing the
species ex situ representation The initial application of the
SCP methods to genetic data showed here can be a useful
starting point for methodological and conceptual
improvements and may be a first important step towards a
comprehensive and balanced quantitative definition of
conservation goals shedding light to new possibilities for
in situ and ex situ designs within species
Keywords Complementarity Conservation planning Optimization Cerrado Hotspot Dipteryx alata
Introduction
The current biodiversity crisis has forced scientists to
develop systematic strategies to effectively achieve con-
servation goals aimed at solving potential conflicts between
conservation and human development (sensu Araujo 2003
J A F Diniz-Filho (amp) R D Loyola
Departamento de Ecologia ICB Universidade Federal de Goias
CxP 131 Goiania GO 74001-970 Brazil
e-mail dinizicbufgbr
D B Melo
Programa de Pos-Graduacao em Agronomia Escola de
Agronomia e Engenharia de Alimentos Universidade Federal de
Goias Goiania GO 74001-970 Brazil
G de Oliveira
Programa DTI Universidade Federal de Goias Campus Jataı
Rod BR-364 KM 192 Jataı GO 75800-970 Brazil
R G Collevatti T N Soares M P C Telles
Departamento de Biologia Geral ICB Universidade Federal de
Goias CxP 131 Goiania GO 74001-970 Brazil
J C Nabout
Unidade de Ciencias Exatas e da Terra Universidade Estadual
de Goias Anapolis GO 75132-400 Brazil
Jacqueline de S Lima R Dobrovolski
Programa de Pos-Graduacao em Ecologia amp Evolucao ICB
Universidade Federal de Goias CxP 131 Goiania GO 74001-
970 Brazil
L J Chaves R V Naves
Escola de Agronomia e Engenharia de Alimentos Universidade
Federal de Goias Goiania GO 74001-970 Brazil
123
Conserv Genet (2012) 131085ndash1093
DOI 101007s10592-012-0356-8
Authors personal copy
Balmford et al 2001) The overall underlying principle of
this strategy lies in the science of systematic conservation
planning (SCP) which involves a series of steps that
should be accomplished to determine the most cost-effec-
tive way to invest in conservation actions (Margules and
Pressey 2000 see also Sarkar and Illoldi-Rangel 2010 for a
recent update) Ultimately SCP allows better planning for
conservation actions and land use at different spatial scales
It has been applied to a series of datasets to test and
improve its methodological details and used in practical
conservation actions in some parts of the world (see
Margules and Sarkar 2007)
The core of SCP is the principle of complementarity
in which a set of sites (among several available ones) are
selected so as to minimize the overall cost of conservation
action (ie the minimum set coverage problem) or to
maximize the level of feature representation given a
limited budget (ie the maximal coverage problem)
(Cabeza and Moilanen 2001) While resolving such
optimization problems using several possible mathemati-
cal and computational methods SCP always maximizes
the dissimilarities among biodiversity features being
considered (ie conservation targets such as species
vegetation types genes see Diniz-Filho and Bini 2011)
More complexity is usually included to these general
problems by adding socio-economical costs to the areas or
minimizing their spatial aggregation (Abbitt et al 2000
Balmford et al 2001 Diniz-Filho et al 2007a Loyola
et al 2009)
Traditionally SCP has been applied to more graspable
conservation goals such as species or vegetation types (see
Brooks et al 2004 Grelle et al 2010 Pressey 2004)
However it is possible to apply the same framework to
solve a series of problems at much lower hierarchical
levels allowing the definition of conservation strategies at
the intra-specific level (see Diniz-Filho and Telles 2006)
The geographical variation of both phenotypic and genetic
data within species have been known for some time and
used in many cases to understand the evolutionary drivers
of population differentiation (Epperson 2003) In a con-
servation context the conservation of intraspecific varia-
tion has been dominated by the debate among how to
define evolutionary significant units (ESUs) or manage-
ment units (MUs) (eg Fraser and Bernatchez 2001 see
also Diniz-Filho and Telles 2002 for a proposal to define
operational units to be used with continuous variation in
the geographical space) or meta-population dynamic pro-
cesses related to persistence (eg McCarthy et al 2005) It
is important however to generalize this to a more basic
representation of the genetic variability throughout geo-
graphical space and in this context SCP procedures may
be quite useful as well (eg see Diniz-Filho and Bini 2011
Loyola et al 2011 Neel and Cummings 2003)
Here we applied the systematic conservation planning
protocol to define conservation priorities for Dipteryx alata
(Fabaceae) This species is endemic to the Brazilian
Cerrado one of the global Biodiversity Hotspots (Myers
et al 2000) where it is commonly known as the lsquolsquoBarursquorsquo
tree Despite endemics to the biome it is a widely dis-
tributed tree species in the Cerrado found in eutrophic and
drained soils of seasonal savannas The edible nuts are also
important for local economies and are now used for several
natural goods or products (eg Felfili et al 2004) Previous
studies showed a significant amount of spatial genetic
differentiation among and within local populations
(Collevatti et al 2010 Soares et al 2008) and broad-scale
geographical structure is apparently associated with pat-
terns of historical habitat fragmentation in the Cerrado
More specifically we found here optimal solutions
indicating the smallest set of local populations of D alata
that should be conserved to represent the known genetic
diversity of the species in the Cerrado aiming at in situ
conservation of the species We also took into account the
current land-use patterns found in the Cerrado (expressed
as the proportion of natural remnants in a buffer zone
around local populations) to weight final solutions and thus
increase the chance of long-term persistence of these
populations by protecting them from human impacts A
germplasm collection for this species already exists so we
also used SCP in a different analysis to identify
the smallest number of samples that should be collected
in the field to complement the existing collection aiming at
the species ex situ conservation
Methods and materials
Genetic data
Genetic data for D alata consisted of microsatellite
markers analyzed for 25 widely distributed local popula-
tions encompassing most of speciesrsquo geographical range
(Fig 1) A total of 644 individual trees were genotyped for
eight microsatellite loci (see Soares et al 2012 for meth-
odological details) with sample sizes within each locality
ranging from 12 to 32 (15 out of the 25 local populations
had 32 individuals analyzed) Details of sample size pri-
vate alleles and genetic characteristics of each local pop-
ulation are given in Table 1 We also calculated standard
population genetics statistics such as observed and
expected heterozygosity as well as an estimate of FST
obtained from an analysis of variance of allele frequencies
(Weir and Cockerham 1984) to provide an overall
description of genetic population structure of D alata The
genetic analyses were conducted with the software FSTAT
2932 (Goudet 2002)
1086 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
Systematic conservation planning
We produced an allele-by-site (local populations) presence-
absence matrix to solve the so-called minimum set coverage
problem in optimization theory (Kirkpatrick 1983) We
defined alleles as our conservation goal and used an algo-
rithm to achieve the initial conservation target of finding the
smallest number of local populations in which all alleles are
represented at least once Even though genetic diversity
would be a best goal from a conservation viewpoint due to its
relationship with inbreeding depression (Charlesworth and
Charlesworth 1987 Frankham 2003) allele presence-
absence is a best choice in this case because D alata popu-
lations are highly genetic differentiated mainly because of
differences in allele composition Further it allows an easy
solution to SCP because alleles can be directly analogous to
species (or other goals at higher organizational level)
Because there are several feasible solutions for this mini-
mization problem we used the selection frequency ie the
frequency at which each local population appears in 100
analyzed solutions as an indicator of site importance for
achieving the conservation target
The SCP problems are solved using several possible
computational and mathematical methods based on exact
optimization algorithms (eg branch-and-bound algorithm
implemented in linear programming) or approximate
algorithms that generate near-optimum solutions (eg
simulated annealing) (see Cabeza and Moilanen 2001
Williams et al 2004) Here we applied the simulated
annealing algorithm which is a computer-intensive search
method (see Possingham et al 2000) to find the smallest
number of local populations that represent all alleles at
least once and that at the same time maximize the amount
of natural habitat remnants around local populations taking
into account broad-scale properties of landscape (see
Segelbacher et al 2010) We obtained this variable for each
local population by analyzing land use data from vegeta-
tion cover maps of the Brazilian biomes at the 1250000
spatial scale We reclassified the maps into natural vege-
tation or anthropogenic land cover classes (this last clas-
sification includes agriculture pasture lands urban areas
and mining regions) and then created 10 km-size buffers
around the geographical position of each population The
proportion of the buffer areas covered by natural vegetation
Fig 1 Geographic location of
the 25 local populations of
Dipteryx alata in Central Brazil
analyzed using SCP methods
based on microsatellite allelic
variation The region shown in
dark tone is still covered by
natural remnants of Cerrado
vegetation
Conserv Genet (2012) 131085ndash1093 1087
123
Authors personal copy
were then calculated and used as a surrogate for regional
level of habitat conservation (see Fig 1 for the overall
patterns of natural remnants in the region) We also used a
randomization procedure to evaluate if the amount of mean
proportion of natural remnants in the best solution differs
from random solutions with the same number of local
populations
Finally there is a large accessible germplasm collection
for D alata composed by 178 fully growth adult trees
located at the Agronomy School of the Federal University
of Goias Brazil These 178 individuals came from several
locations in the state of Goias and were also genotyped for
the eight microsatellite loci A different analysis was
conducted in which the individuals in the germplasm bank
were included as another lsquolsquolocal populationrsquorsquo We then
repeated the SCP analysis by assuming that this germplasm
bank was already protected (ie we included this
population in the initial and final portfolios when running
the algorithm) In that case the optimization problem was
to find the smallest number of local populations that better
complement the genetic variability already preserved in the
germplasm bank This is thus equivalent to running a gap
analysis in which a single reserve (the germplasm bank) is
already established We also calculated the SCP solutions
by minimizing the geographic distance to Goiania (ie
using this distance as a cost variable) so that overall costs
of sampling and transporting material to the locality where
the germplasm collection is maintained are minimum
Results
After coding the eight microsatellites a total of 52 alleles
were recorded out of which only six were found in a
Table 1 Genetic characterization for 25 populations of D alata based on eight microsatellite loci
Population N A Ar Ap Ho He f Habitata
ABMT 32 2375 2223 0 0291 0382 0238 2
AMG 32 2250 1973 0 0293 0310 0055ns 3
AMS 32 4250 3609 1 0349 0476 0267 3
AQMS 31 3375 2817 0 0442 0459 0038ns 1
ARTO 15 2250 2205 0 0381 0372 -0025ns 3
ATO 32 3000 2747 0 0382 0488 0217 1
CAMT 30 3750 3152 2 0278 0466 0405 2
CMS 13 2875 2861 0 0466 0480 0029ns 4
CMT 32 2625 2502 1 0249 0322 0229 1
ENGO 12 2500 2478 0 0408 0474 0139 1
IGO 13 2500 2447 0 0350 0453 0226 1
ISP 32 2375 2212 0 0322 0455 0291 3
JGO 32 2625 2480 0 0638 0599 -0065ns 1
LGO 32 2500 2425 0 0424 0509 0166 1
MAMG 32 2875 2582 0 0448 0514 0128 4
NTO 12 2000 2093 0 0458 0393 -0165ns 3
PCMS 13 2875 2808 0 0169 0345 0509 1
PGO 32 2500 2164 0 0259 0426 0336 3
PMG 32 2375 2103 0 0176 0257 0314 1
PMS 13 3125 3059 0 0215 0410 0476 1
RAGO 32 3250 2865 0 0473 0462 -0024ns 3
RAMT 32 3375 2976 2 0308 0462 0333 3
SMGO 32 2625 2409 0 0354 0336 -0052ns 1
SMS 32 3625 3213 0 0422 0482 0125 2
STGO 12 2875 2823 0 0356 0387 0080ns 1
Overall 644 2835 2609 6 0356 0429 0171 ndash
P [ 005
N sample size A total number of alleles Ar Allelic richness Ap private alleles Ho observed heterozygosity He expected heterozygosity
f inbreeding coefficient ns not significanta 1mdashIsolated adult individuals in pasture or crop field 2mdashisolated adult individuals in remnant of savanna at roadsides 3mdashsavanna remnant
surrounded by pasture 4mdashfragment of savanna
1088 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
unique population Observed heterozygosity was low in all
populations and most populations show deviations from
HardyndashWeinberg equilibrium with f-values significantly
different from zero for most local populations (Table 1) A
significant amount of divergence among these local popu-
lations was also observed (FST = 0267 SD = 0036
P 00001) indicating that several local populations
should be conserved to maintain all genetic diversity
Optimization solutions revealed that a minimum of
seven local populations are necessary to represent all 52
alleles at least once Several solutions for this problem
were reached and after considering a total of 100 minimum
solutions four local populations were extremely important
for achieving this goal (ie they were found in 100 of
solutions and a fiftieth additional one appeared in 95 of
the solutions) Further a total of ten populations had fre-
quencies of selection higher than 0 indicating that the
solutions are not always the same (Fig 2)
There was no significant relationship between selection
frequency and genetic parameters within local populations
except for Ar (r = 0488 P = 0013) but this is someway
tautological because optimization works to maximize
number of alleles (unique in each local population) Even
so it is important to note that these data could be also used
as covariates if one is interested for example in conserv-
ing the populations with higher selection frequency that
have more expected heterozygosity
Given the distribution of alleles in local populations (ie
many rare alleles are found in one or two populations
only) the mean amount of proportional remaining habitat
around the seven local populations selected (equal to 022)
was not significantly different from a 1000 random sam-
ples with same size (032 plusmn 014 P = 0265) However in
none of these random samples were the total number of
alleles represented (the mean number of alleles represented
in random samples of seven populations is 385 plusmn 33)
(Fig 3) This supports the idea that although human
actions cannot be minimized because of data constraints
random solutions are much less efficient than the optimized
one as expected
For the alternative analysis for an ex situ SCP strategy
samples of only four additional local populations would be
necessary to optimally complement the genetic variability
currently represented in the germplasm bank (Fig 4) Only
these four populations have maximum frequency of
selection (ie because only they appeared in all solutions)
Minimizing distances to Goiania did not change this
solution in this particular case because of the rare variants
found in the state of Mato Grosso are unique and conse-
quently they have maximum frequencies of selection (ie
appear in all solutions)
Discussion
Here we showed that it is possible to design optimal con-
servation strategies for the conservation of genetic diver-
sity under the framework of SCP Moreover alternative
applications of SCP for in situ and ex situ conservation
strategies were done based on the same dataset although
using distinct weights revealing their distinct purposes
We understand that these ex situ and in situ strategies can
Fig 2 Frequency of solutions
from SCP maximizing the total
number of alleles represented
minimizing the number of local
populations and maximizing the
amount of natural remnants
This count if based on
combination of several solutions
with seven local populations
that we found for optimizing the
in situ conservation Local
populations with frequencies
tending to 100 tend to be
irreplaceable so that losing
them will not allow one to
achieve the conservation goal
Conserv Genet (2012) 131085ndash1093 1089
123
Authors personal copy
be implemented together so as to maximize the effective-
ness of conservation planning In our case study dealing
with the genetic variability of D alata natural populations
we showed that it is possible to represent all known alleles
at least once by strategically conserving (in situ) seven
local populations distributed in the Cerrado biome
Because of the analytical constraints imposed by the dis-
tribution of alleles in different local population and the
predetermined targets trying to define a solution that
minimizes the human impacts of these local populations
(ie by selecting local population in regions with more
natural cover remnants) did not change the selected pop-
ulations although it may help to define priorities among
the populations studied (eg planning a schedule for con-
servation interventions) Further assuming that the germ-
plasm bank is a fully protected lsquolsquopopulationrsquorsquo we also
showed that even fewer local populations need to be
sampled to represent the known genetic variability of the
species aiming at its ex situ conservation
Systematic conservation planning is usually applied to
species conservation building conservation priority
regions based on several goals with different conservation
targets (Sarkar and Illoldi-Rangel 2010) This initial
application with genetic data represents a step further to the
theoretical ideas originally presented by Diniz-Filho and
Telles (2006) who proposed how different algorithms
could be used to represent genetic diversity under distinct
spatial population structures The analysis shown here for
D alata indeed suggests that systematic conservation
planning can be a quite useful and objective tool to guide
actions for within-species conservation although of course
further improvements may be important and more work is
needed to expand the framework
A first important issue to be discussed is that our
application is focused on neutral molecular markers which
represents the overall variability of the species that have
been accumulated throughout its evolutionary history Of
course this does not necessarily reflect adaptive traits that
must be important for population persistence or the traits
(ie fruit production and quality) that may be important for
000 015 030 045 060 075
Mean proportion of natural remnants
25
35
45
55N
umbe
r of
alle
les
repr
esen
ted
Best solution
Fig 3 Relationship between number of alleles represented and
proportion of natural remnants in the conserved populations under a
null model in which the seven local populations are randomly
sampled from the pool of 25 and combined in a reserve network The
optimum solution obtained by SCP is highlighted
Fig 4 Local populations
defined by SCP necessary to
better complement the
germplasm collection in the exsitu conservation program The
four local populations are
connected by arrows to Goiania
the locality where the
germplasm of D alata is
maintained
1090 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
Balmford et al 2001) The overall underlying principle of
this strategy lies in the science of systematic conservation
planning (SCP) which involves a series of steps that
should be accomplished to determine the most cost-effec-
tive way to invest in conservation actions (Margules and
Pressey 2000 see also Sarkar and Illoldi-Rangel 2010 for a
recent update) Ultimately SCP allows better planning for
conservation actions and land use at different spatial scales
It has been applied to a series of datasets to test and
improve its methodological details and used in practical
conservation actions in some parts of the world (see
Margules and Sarkar 2007)
The core of SCP is the principle of complementarity
in which a set of sites (among several available ones) are
selected so as to minimize the overall cost of conservation
action (ie the minimum set coverage problem) or to
maximize the level of feature representation given a
limited budget (ie the maximal coverage problem)
(Cabeza and Moilanen 2001) While resolving such
optimization problems using several possible mathemati-
cal and computational methods SCP always maximizes
the dissimilarities among biodiversity features being
considered (ie conservation targets such as species
vegetation types genes see Diniz-Filho and Bini 2011)
More complexity is usually included to these general
problems by adding socio-economical costs to the areas or
minimizing their spatial aggregation (Abbitt et al 2000
Balmford et al 2001 Diniz-Filho et al 2007a Loyola
et al 2009)
Traditionally SCP has been applied to more graspable
conservation goals such as species or vegetation types (see
Brooks et al 2004 Grelle et al 2010 Pressey 2004)
However it is possible to apply the same framework to
solve a series of problems at much lower hierarchical
levels allowing the definition of conservation strategies at
the intra-specific level (see Diniz-Filho and Telles 2006)
The geographical variation of both phenotypic and genetic
data within species have been known for some time and
used in many cases to understand the evolutionary drivers
of population differentiation (Epperson 2003) In a con-
servation context the conservation of intraspecific varia-
tion has been dominated by the debate among how to
define evolutionary significant units (ESUs) or manage-
ment units (MUs) (eg Fraser and Bernatchez 2001 see
also Diniz-Filho and Telles 2002 for a proposal to define
operational units to be used with continuous variation in
the geographical space) or meta-population dynamic pro-
cesses related to persistence (eg McCarthy et al 2005) It
is important however to generalize this to a more basic
representation of the genetic variability throughout geo-
graphical space and in this context SCP procedures may
be quite useful as well (eg see Diniz-Filho and Bini 2011
Loyola et al 2011 Neel and Cummings 2003)
Here we applied the systematic conservation planning
protocol to define conservation priorities for Dipteryx alata
(Fabaceae) This species is endemic to the Brazilian
Cerrado one of the global Biodiversity Hotspots (Myers
et al 2000) where it is commonly known as the lsquolsquoBarursquorsquo
tree Despite endemics to the biome it is a widely dis-
tributed tree species in the Cerrado found in eutrophic and
drained soils of seasonal savannas The edible nuts are also
important for local economies and are now used for several
natural goods or products (eg Felfili et al 2004) Previous
studies showed a significant amount of spatial genetic
differentiation among and within local populations
(Collevatti et al 2010 Soares et al 2008) and broad-scale
geographical structure is apparently associated with pat-
terns of historical habitat fragmentation in the Cerrado
More specifically we found here optimal solutions
indicating the smallest set of local populations of D alata
that should be conserved to represent the known genetic
diversity of the species in the Cerrado aiming at in situ
conservation of the species We also took into account the
current land-use patterns found in the Cerrado (expressed
as the proportion of natural remnants in a buffer zone
around local populations) to weight final solutions and thus
increase the chance of long-term persistence of these
populations by protecting them from human impacts A
germplasm collection for this species already exists so we
also used SCP in a different analysis to identify
the smallest number of samples that should be collected
in the field to complement the existing collection aiming at
the species ex situ conservation
Methods and materials
Genetic data
Genetic data for D alata consisted of microsatellite
markers analyzed for 25 widely distributed local popula-
tions encompassing most of speciesrsquo geographical range
(Fig 1) A total of 644 individual trees were genotyped for
eight microsatellite loci (see Soares et al 2012 for meth-
odological details) with sample sizes within each locality
ranging from 12 to 32 (15 out of the 25 local populations
had 32 individuals analyzed) Details of sample size pri-
vate alleles and genetic characteristics of each local pop-
ulation are given in Table 1 We also calculated standard
population genetics statistics such as observed and
expected heterozygosity as well as an estimate of FST
obtained from an analysis of variance of allele frequencies
(Weir and Cockerham 1984) to provide an overall
description of genetic population structure of D alata The
genetic analyses were conducted with the software FSTAT
2932 (Goudet 2002)
1086 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
Systematic conservation planning
We produced an allele-by-site (local populations) presence-
absence matrix to solve the so-called minimum set coverage
problem in optimization theory (Kirkpatrick 1983) We
defined alleles as our conservation goal and used an algo-
rithm to achieve the initial conservation target of finding the
smallest number of local populations in which all alleles are
represented at least once Even though genetic diversity
would be a best goal from a conservation viewpoint due to its
relationship with inbreeding depression (Charlesworth and
Charlesworth 1987 Frankham 2003) allele presence-
absence is a best choice in this case because D alata popu-
lations are highly genetic differentiated mainly because of
differences in allele composition Further it allows an easy
solution to SCP because alleles can be directly analogous to
species (or other goals at higher organizational level)
Because there are several feasible solutions for this mini-
mization problem we used the selection frequency ie the
frequency at which each local population appears in 100
analyzed solutions as an indicator of site importance for
achieving the conservation target
The SCP problems are solved using several possible
computational and mathematical methods based on exact
optimization algorithms (eg branch-and-bound algorithm
implemented in linear programming) or approximate
algorithms that generate near-optimum solutions (eg
simulated annealing) (see Cabeza and Moilanen 2001
Williams et al 2004) Here we applied the simulated
annealing algorithm which is a computer-intensive search
method (see Possingham et al 2000) to find the smallest
number of local populations that represent all alleles at
least once and that at the same time maximize the amount
of natural habitat remnants around local populations taking
into account broad-scale properties of landscape (see
Segelbacher et al 2010) We obtained this variable for each
local population by analyzing land use data from vegeta-
tion cover maps of the Brazilian biomes at the 1250000
spatial scale We reclassified the maps into natural vege-
tation or anthropogenic land cover classes (this last clas-
sification includes agriculture pasture lands urban areas
and mining regions) and then created 10 km-size buffers
around the geographical position of each population The
proportion of the buffer areas covered by natural vegetation
Fig 1 Geographic location of
the 25 local populations of
Dipteryx alata in Central Brazil
analyzed using SCP methods
based on microsatellite allelic
variation The region shown in
dark tone is still covered by
natural remnants of Cerrado
vegetation
Conserv Genet (2012) 131085ndash1093 1087
123
Authors personal copy
were then calculated and used as a surrogate for regional
level of habitat conservation (see Fig 1 for the overall
patterns of natural remnants in the region) We also used a
randomization procedure to evaluate if the amount of mean
proportion of natural remnants in the best solution differs
from random solutions with the same number of local
populations
Finally there is a large accessible germplasm collection
for D alata composed by 178 fully growth adult trees
located at the Agronomy School of the Federal University
of Goias Brazil These 178 individuals came from several
locations in the state of Goias and were also genotyped for
the eight microsatellite loci A different analysis was
conducted in which the individuals in the germplasm bank
were included as another lsquolsquolocal populationrsquorsquo We then
repeated the SCP analysis by assuming that this germplasm
bank was already protected (ie we included this
population in the initial and final portfolios when running
the algorithm) In that case the optimization problem was
to find the smallest number of local populations that better
complement the genetic variability already preserved in the
germplasm bank This is thus equivalent to running a gap
analysis in which a single reserve (the germplasm bank) is
already established We also calculated the SCP solutions
by minimizing the geographic distance to Goiania (ie
using this distance as a cost variable) so that overall costs
of sampling and transporting material to the locality where
the germplasm collection is maintained are minimum
Results
After coding the eight microsatellites a total of 52 alleles
were recorded out of which only six were found in a
Table 1 Genetic characterization for 25 populations of D alata based on eight microsatellite loci
Population N A Ar Ap Ho He f Habitata
ABMT 32 2375 2223 0 0291 0382 0238 2
AMG 32 2250 1973 0 0293 0310 0055ns 3
AMS 32 4250 3609 1 0349 0476 0267 3
AQMS 31 3375 2817 0 0442 0459 0038ns 1
ARTO 15 2250 2205 0 0381 0372 -0025ns 3
ATO 32 3000 2747 0 0382 0488 0217 1
CAMT 30 3750 3152 2 0278 0466 0405 2
CMS 13 2875 2861 0 0466 0480 0029ns 4
CMT 32 2625 2502 1 0249 0322 0229 1
ENGO 12 2500 2478 0 0408 0474 0139 1
IGO 13 2500 2447 0 0350 0453 0226 1
ISP 32 2375 2212 0 0322 0455 0291 3
JGO 32 2625 2480 0 0638 0599 -0065ns 1
LGO 32 2500 2425 0 0424 0509 0166 1
MAMG 32 2875 2582 0 0448 0514 0128 4
NTO 12 2000 2093 0 0458 0393 -0165ns 3
PCMS 13 2875 2808 0 0169 0345 0509 1
PGO 32 2500 2164 0 0259 0426 0336 3
PMG 32 2375 2103 0 0176 0257 0314 1
PMS 13 3125 3059 0 0215 0410 0476 1
RAGO 32 3250 2865 0 0473 0462 -0024ns 3
RAMT 32 3375 2976 2 0308 0462 0333 3
SMGO 32 2625 2409 0 0354 0336 -0052ns 1
SMS 32 3625 3213 0 0422 0482 0125 2
STGO 12 2875 2823 0 0356 0387 0080ns 1
Overall 644 2835 2609 6 0356 0429 0171 ndash
P [ 005
N sample size A total number of alleles Ar Allelic richness Ap private alleles Ho observed heterozygosity He expected heterozygosity
f inbreeding coefficient ns not significanta 1mdashIsolated adult individuals in pasture or crop field 2mdashisolated adult individuals in remnant of savanna at roadsides 3mdashsavanna remnant
surrounded by pasture 4mdashfragment of savanna
1088 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
unique population Observed heterozygosity was low in all
populations and most populations show deviations from
HardyndashWeinberg equilibrium with f-values significantly
different from zero for most local populations (Table 1) A
significant amount of divergence among these local popu-
lations was also observed (FST = 0267 SD = 0036
P 00001) indicating that several local populations
should be conserved to maintain all genetic diversity
Optimization solutions revealed that a minimum of
seven local populations are necessary to represent all 52
alleles at least once Several solutions for this problem
were reached and after considering a total of 100 minimum
solutions four local populations were extremely important
for achieving this goal (ie they were found in 100 of
solutions and a fiftieth additional one appeared in 95 of
the solutions) Further a total of ten populations had fre-
quencies of selection higher than 0 indicating that the
solutions are not always the same (Fig 2)
There was no significant relationship between selection
frequency and genetic parameters within local populations
except for Ar (r = 0488 P = 0013) but this is someway
tautological because optimization works to maximize
number of alleles (unique in each local population) Even
so it is important to note that these data could be also used
as covariates if one is interested for example in conserv-
ing the populations with higher selection frequency that
have more expected heterozygosity
Given the distribution of alleles in local populations (ie
many rare alleles are found in one or two populations
only) the mean amount of proportional remaining habitat
around the seven local populations selected (equal to 022)
was not significantly different from a 1000 random sam-
ples with same size (032 plusmn 014 P = 0265) However in
none of these random samples were the total number of
alleles represented (the mean number of alleles represented
in random samples of seven populations is 385 plusmn 33)
(Fig 3) This supports the idea that although human
actions cannot be minimized because of data constraints
random solutions are much less efficient than the optimized
one as expected
For the alternative analysis for an ex situ SCP strategy
samples of only four additional local populations would be
necessary to optimally complement the genetic variability
currently represented in the germplasm bank (Fig 4) Only
these four populations have maximum frequency of
selection (ie because only they appeared in all solutions)
Minimizing distances to Goiania did not change this
solution in this particular case because of the rare variants
found in the state of Mato Grosso are unique and conse-
quently they have maximum frequencies of selection (ie
appear in all solutions)
Discussion
Here we showed that it is possible to design optimal con-
servation strategies for the conservation of genetic diver-
sity under the framework of SCP Moreover alternative
applications of SCP for in situ and ex situ conservation
strategies were done based on the same dataset although
using distinct weights revealing their distinct purposes
We understand that these ex situ and in situ strategies can
Fig 2 Frequency of solutions
from SCP maximizing the total
number of alleles represented
minimizing the number of local
populations and maximizing the
amount of natural remnants
This count if based on
combination of several solutions
with seven local populations
that we found for optimizing the
in situ conservation Local
populations with frequencies
tending to 100 tend to be
irreplaceable so that losing
them will not allow one to
achieve the conservation goal
Conserv Genet (2012) 131085ndash1093 1089
123
Authors personal copy
be implemented together so as to maximize the effective-
ness of conservation planning In our case study dealing
with the genetic variability of D alata natural populations
we showed that it is possible to represent all known alleles
at least once by strategically conserving (in situ) seven
local populations distributed in the Cerrado biome
Because of the analytical constraints imposed by the dis-
tribution of alleles in different local population and the
predetermined targets trying to define a solution that
minimizes the human impacts of these local populations
(ie by selecting local population in regions with more
natural cover remnants) did not change the selected pop-
ulations although it may help to define priorities among
the populations studied (eg planning a schedule for con-
servation interventions) Further assuming that the germ-
plasm bank is a fully protected lsquolsquopopulationrsquorsquo we also
showed that even fewer local populations need to be
sampled to represent the known genetic variability of the
species aiming at its ex situ conservation
Systematic conservation planning is usually applied to
species conservation building conservation priority
regions based on several goals with different conservation
targets (Sarkar and Illoldi-Rangel 2010) This initial
application with genetic data represents a step further to the
theoretical ideas originally presented by Diniz-Filho and
Telles (2006) who proposed how different algorithms
could be used to represent genetic diversity under distinct
spatial population structures The analysis shown here for
D alata indeed suggests that systematic conservation
planning can be a quite useful and objective tool to guide
actions for within-species conservation although of course
further improvements may be important and more work is
needed to expand the framework
A first important issue to be discussed is that our
application is focused on neutral molecular markers which
represents the overall variability of the species that have
been accumulated throughout its evolutionary history Of
course this does not necessarily reflect adaptive traits that
must be important for population persistence or the traits
(ie fruit production and quality) that may be important for
000 015 030 045 060 075
Mean proportion of natural remnants
25
35
45
55N
umbe
r of
alle
les
repr
esen
ted
Best solution
Fig 3 Relationship between number of alleles represented and
proportion of natural remnants in the conserved populations under a
null model in which the seven local populations are randomly
sampled from the pool of 25 and combined in a reserve network The
optimum solution obtained by SCP is highlighted
Fig 4 Local populations
defined by SCP necessary to
better complement the
germplasm collection in the exsitu conservation program The
four local populations are
connected by arrows to Goiania
the locality where the
germplasm of D alata is
maintained
1090 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
Systematic conservation planning
We produced an allele-by-site (local populations) presence-
absence matrix to solve the so-called minimum set coverage
problem in optimization theory (Kirkpatrick 1983) We
defined alleles as our conservation goal and used an algo-
rithm to achieve the initial conservation target of finding the
smallest number of local populations in which all alleles are
represented at least once Even though genetic diversity
would be a best goal from a conservation viewpoint due to its
relationship with inbreeding depression (Charlesworth and
Charlesworth 1987 Frankham 2003) allele presence-
absence is a best choice in this case because D alata popu-
lations are highly genetic differentiated mainly because of
differences in allele composition Further it allows an easy
solution to SCP because alleles can be directly analogous to
species (or other goals at higher organizational level)
Because there are several feasible solutions for this mini-
mization problem we used the selection frequency ie the
frequency at which each local population appears in 100
analyzed solutions as an indicator of site importance for
achieving the conservation target
The SCP problems are solved using several possible
computational and mathematical methods based on exact
optimization algorithms (eg branch-and-bound algorithm
implemented in linear programming) or approximate
algorithms that generate near-optimum solutions (eg
simulated annealing) (see Cabeza and Moilanen 2001
Williams et al 2004) Here we applied the simulated
annealing algorithm which is a computer-intensive search
method (see Possingham et al 2000) to find the smallest
number of local populations that represent all alleles at
least once and that at the same time maximize the amount
of natural habitat remnants around local populations taking
into account broad-scale properties of landscape (see
Segelbacher et al 2010) We obtained this variable for each
local population by analyzing land use data from vegeta-
tion cover maps of the Brazilian biomes at the 1250000
spatial scale We reclassified the maps into natural vege-
tation or anthropogenic land cover classes (this last clas-
sification includes agriculture pasture lands urban areas
and mining regions) and then created 10 km-size buffers
around the geographical position of each population The
proportion of the buffer areas covered by natural vegetation
Fig 1 Geographic location of
the 25 local populations of
Dipteryx alata in Central Brazil
analyzed using SCP methods
based on microsatellite allelic
variation The region shown in
dark tone is still covered by
natural remnants of Cerrado
vegetation
Conserv Genet (2012) 131085ndash1093 1087
123
Authors personal copy
were then calculated and used as a surrogate for regional
level of habitat conservation (see Fig 1 for the overall
patterns of natural remnants in the region) We also used a
randomization procedure to evaluate if the amount of mean
proportion of natural remnants in the best solution differs
from random solutions with the same number of local
populations
Finally there is a large accessible germplasm collection
for D alata composed by 178 fully growth adult trees
located at the Agronomy School of the Federal University
of Goias Brazil These 178 individuals came from several
locations in the state of Goias and were also genotyped for
the eight microsatellite loci A different analysis was
conducted in which the individuals in the germplasm bank
were included as another lsquolsquolocal populationrsquorsquo We then
repeated the SCP analysis by assuming that this germplasm
bank was already protected (ie we included this
population in the initial and final portfolios when running
the algorithm) In that case the optimization problem was
to find the smallest number of local populations that better
complement the genetic variability already preserved in the
germplasm bank This is thus equivalent to running a gap
analysis in which a single reserve (the germplasm bank) is
already established We also calculated the SCP solutions
by minimizing the geographic distance to Goiania (ie
using this distance as a cost variable) so that overall costs
of sampling and transporting material to the locality where
the germplasm collection is maintained are minimum
Results
After coding the eight microsatellites a total of 52 alleles
were recorded out of which only six were found in a
Table 1 Genetic characterization for 25 populations of D alata based on eight microsatellite loci
Population N A Ar Ap Ho He f Habitata
ABMT 32 2375 2223 0 0291 0382 0238 2
AMG 32 2250 1973 0 0293 0310 0055ns 3
AMS 32 4250 3609 1 0349 0476 0267 3
AQMS 31 3375 2817 0 0442 0459 0038ns 1
ARTO 15 2250 2205 0 0381 0372 -0025ns 3
ATO 32 3000 2747 0 0382 0488 0217 1
CAMT 30 3750 3152 2 0278 0466 0405 2
CMS 13 2875 2861 0 0466 0480 0029ns 4
CMT 32 2625 2502 1 0249 0322 0229 1
ENGO 12 2500 2478 0 0408 0474 0139 1
IGO 13 2500 2447 0 0350 0453 0226 1
ISP 32 2375 2212 0 0322 0455 0291 3
JGO 32 2625 2480 0 0638 0599 -0065ns 1
LGO 32 2500 2425 0 0424 0509 0166 1
MAMG 32 2875 2582 0 0448 0514 0128 4
NTO 12 2000 2093 0 0458 0393 -0165ns 3
PCMS 13 2875 2808 0 0169 0345 0509 1
PGO 32 2500 2164 0 0259 0426 0336 3
PMG 32 2375 2103 0 0176 0257 0314 1
PMS 13 3125 3059 0 0215 0410 0476 1
RAGO 32 3250 2865 0 0473 0462 -0024ns 3
RAMT 32 3375 2976 2 0308 0462 0333 3
SMGO 32 2625 2409 0 0354 0336 -0052ns 1
SMS 32 3625 3213 0 0422 0482 0125 2
STGO 12 2875 2823 0 0356 0387 0080ns 1
Overall 644 2835 2609 6 0356 0429 0171 ndash
P [ 005
N sample size A total number of alleles Ar Allelic richness Ap private alleles Ho observed heterozygosity He expected heterozygosity
f inbreeding coefficient ns not significanta 1mdashIsolated adult individuals in pasture or crop field 2mdashisolated adult individuals in remnant of savanna at roadsides 3mdashsavanna remnant
surrounded by pasture 4mdashfragment of savanna
1088 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
unique population Observed heterozygosity was low in all
populations and most populations show deviations from
HardyndashWeinberg equilibrium with f-values significantly
different from zero for most local populations (Table 1) A
significant amount of divergence among these local popu-
lations was also observed (FST = 0267 SD = 0036
P 00001) indicating that several local populations
should be conserved to maintain all genetic diversity
Optimization solutions revealed that a minimum of
seven local populations are necessary to represent all 52
alleles at least once Several solutions for this problem
were reached and after considering a total of 100 minimum
solutions four local populations were extremely important
for achieving this goal (ie they were found in 100 of
solutions and a fiftieth additional one appeared in 95 of
the solutions) Further a total of ten populations had fre-
quencies of selection higher than 0 indicating that the
solutions are not always the same (Fig 2)
There was no significant relationship between selection
frequency and genetic parameters within local populations
except for Ar (r = 0488 P = 0013) but this is someway
tautological because optimization works to maximize
number of alleles (unique in each local population) Even
so it is important to note that these data could be also used
as covariates if one is interested for example in conserv-
ing the populations with higher selection frequency that
have more expected heterozygosity
Given the distribution of alleles in local populations (ie
many rare alleles are found in one or two populations
only) the mean amount of proportional remaining habitat
around the seven local populations selected (equal to 022)
was not significantly different from a 1000 random sam-
ples with same size (032 plusmn 014 P = 0265) However in
none of these random samples were the total number of
alleles represented (the mean number of alleles represented
in random samples of seven populations is 385 plusmn 33)
(Fig 3) This supports the idea that although human
actions cannot be minimized because of data constraints
random solutions are much less efficient than the optimized
one as expected
For the alternative analysis for an ex situ SCP strategy
samples of only four additional local populations would be
necessary to optimally complement the genetic variability
currently represented in the germplasm bank (Fig 4) Only
these four populations have maximum frequency of
selection (ie because only they appeared in all solutions)
Minimizing distances to Goiania did not change this
solution in this particular case because of the rare variants
found in the state of Mato Grosso are unique and conse-
quently they have maximum frequencies of selection (ie
appear in all solutions)
Discussion
Here we showed that it is possible to design optimal con-
servation strategies for the conservation of genetic diver-
sity under the framework of SCP Moreover alternative
applications of SCP for in situ and ex situ conservation
strategies were done based on the same dataset although
using distinct weights revealing their distinct purposes
We understand that these ex situ and in situ strategies can
Fig 2 Frequency of solutions
from SCP maximizing the total
number of alleles represented
minimizing the number of local
populations and maximizing the
amount of natural remnants
This count if based on
combination of several solutions
with seven local populations
that we found for optimizing the
in situ conservation Local
populations with frequencies
tending to 100 tend to be
irreplaceable so that losing
them will not allow one to
achieve the conservation goal
Conserv Genet (2012) 131085ndash1093 1089
123
Authors personal copy
be implemented together so as to maximize the effective-
ness of conservation planning In our case study dealing
with the genetic variability of D alata natural populations
we showed that it is possible to represent all known alleles
at least once by strategically conserving (in situ) seven
local populations distributed in the Cerrado biome
Because of the analytical constraints imposed by the dis-
tribution of alleles in different local population and the
predetermined targets trying to define a solution that
minimizes the human impacts of these local populations
(ie by selecting local population in regions with more
natural cover remnants) did not change the selected pop-
ulations although it may help to define priorities among
the populations studied (eg planning a schedule for con-
servation interventions) Further assuming that the germ-
plasm bank is a fully protected lsquolsquopopulationrsquorsquo we also
showed that even fewer local populations need to be
sampled to represent the known genetic variability of the
species aiming at its ex situ conservation
Systematic conservation planning is usually applied to
species conservation building conservation priority
regions based on several goals with different conservation
targets (Sarkar and Illoldi-Rangel 2010) This initial
application with genetic data represents a step further to the
theoretical ideas originally presented by Diniz-Filho and
Telles (2006) who proposed how different algorithms
could be used to represent genetic diversity under distinct
spatial population structures The analysis shown here for
D alata indeed suggests that systematic conservation
planning can be a quite useful and objective tool to guide
actions for within-species conservation although of course
further improvements may be important and more work is
needed to expand the framework
A first important issue to be discussed is that our
application is focused on neutral molecular markers which
represents the overall variability of the species that have
been accumulated throughout its evolutionary history Of
course this does not necessarily reflect adaptive traits that
must be important for population persistence or the traits
(ie fruit production and quality) that may be important for
000 015 030 045 060 075
Mean proportion of natural remnants
25
35
45
55N
umbe
r of
alle
les
repr
esen
ted
Best solution
Fig 3 Relationship between number of alleles represented and
proportion of natural remnants in the conserved populations under a
null model in which the seven local populations are randomly
sampled from the pool of 25 and combined in a reserve network The
optimum solution obtained by SCP is highlighted
Fig 4 Local populations
defined by SCP necessary to
better complement the
germplasm collection in the exsitu conservation program The
four local populations are
connected by arrows to Goiania
the locality where the
germplasm of D alata is
maintained
1090 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
were then calculated and used as a surrogate for regional
level of habitat conservation (see Fig 1 for the overall
patterns of natural remnants in the region) We also used a
randomization procedure to evaluate if the amount of mean
proportion of natural remnants in the best solution differs
from random solutions with the same number of local
populations
Finally there is a large accessible germplasm collection
for D alata composed by 178 fully growth adult trees
located at the Agronomy School of the Federal University
of Goias Brazil These 178 individuals came from several
locations in the state of Goias and were also genotyped for
the eight microsatellite loci A different analysis was
conducted in which the individuals in the germplasm bank
were included as another lsquolsquolocal populationrsquorsquo We then
repeated the SCP analysis by assuming that this germplasm
bank was already protected (ie we included this
population in the initial and final portfolios when running
the algorithm) In that case the optimization problem was
to find the smallest number of local populations that better
complement the genetic variability already preserved in the
germplasm bank This is thus equivalent to running a gap
analysis in which a single reserve (the germplasm bank) is
already established We also calculated the SCP solutions
by minimizing the geographic distance to Goiania (ie
using this distance as a cost variable) so that overall costs
of sampling and transporting material to the locality where
the germplasm collection is maintained are minimum
Results
After coding the eight microsatellites a total of 52 alleles
were recorded out of which only six were found in a
Table 1 Genetic characterization for 25 populations of D alata based on eight microsatellite loci
Population N A Ar Ap Ho He f Habitata
ABMT 32 2375 2223 0 0291 0382 0238 2
AMG 32 2250 1973 0 0293 0310 0055ns 3
AMS 32 4250 3609 1 0349 0476 0267 3
AQMS 31 3375 2817 0 0442 0459 0038ns 1
ARTO 15 2250 2205 0 0381 0372 -0025ns 3
ATO 32 3000 2747 0 0382 0488 0217 1
CAMT 30 3750 3152 2 0278 0466 0405 2
CMS 13 2875 2861 0 0466 0480 0029ns 4
CMT 32 2625 2502 1 0249 0322 0229 1
ENGO 12 2500 2478 0 0408 0474 0139 1
IGO 13 2500 2447 0 0350 0453 0226 1
ISP 32 2375 2212 0 0322 0455 0291 3
JGO 32 2625 2480 0 0638 0599 -0065ns 1
LGO 32 2500 2425 0 0424 0509 0166 1
MAMG 32 2875 2582 0 0448 0514 0128 4
NTO 12 2000 2093 0 0458 0393 -0165ns 3
PCMS 13 2875 2808 0 0169 0345 0509 1
PGO 32 2500 2164 0 0259 0426 0336 3
PMG 32 2375 2103 0 0176 0257 0314 1
PMS 13 3125 3059 0 0215 0410 0476 1
RAGO 32 3250 2865 0 0473 0462 -0024ns 3
RAMT 32 3375 2976 2 0308 0462 0333 3
SMGO 32 2625 2409 0 0354 0336 -0052ns 1
SMS 32 3625 3213 0 0422 0482 0125 2
STGO 12 2875 2823 0 0356 0387 0080ns 1
Overall 644 2835 2609 6 0356 0429 0171 ndash
P [ 005
N sample size A total number of alleles Ar Allelic richness Ap private alleles Ho observed heterozygosity He expected heterozygosity
f inbreeding coefficient ns not significanta 1mdashIsolated adult individuals in pasture or crop field 2mdashisolated adult individuals in remnant of savanna at roadsides 3mdashsavanna remnant
surrounded by pasture 4mdashfragment of savanna
1088 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
unique population Observed heterozygosity was low in all
populations and most populations show deviations from
HardyndashWeinberg equilibrium with f-values significantly
different from zero for most local populations (Table 1) A
significant amount of divergence among these local popu-
lations was also observed (FST = 0267 SD = 0036
P 00001) indicating that several local populations
should be conserved to maintain all genetic diversity
Optimization solutions revealed that a minimum of
seven local populations are necessary to represent all 52
alleles at least once Several solutions for this problem
were reached and after considering a total of 100 minimum
solutions four local populations were extremely important
for achieving this goal (ie they were found in 100 of
solutions and a fiftieth additional one appeared in 95 of
the solutions) Further a total of ten populations had fre-
quencies of selection higher than 0 indicating that the
solutions are not always the same (Fig 2)
There was no significant relationship between selection
frequency and genetic parameters within local populations
except for Ar (r = 0488 P = 0013) but this is someway
tautological because optimization works to maximize
number of alleles (unique in each local population) Even
so it is important to note that these data could be also used
as covariates if one is interested for example in conserv-
ing the populations with higher selection frequency that
have more expected heterozygosity
Given the distribution of alleles in local populations (ie
many rare alleles are found in one or two populations
only) the mean amount of proportional remaining habitat
around the seven local populations selected (equal to 022)
was not significantly different from a 1000 random sam-
ples with same size (032 plusmn 014 P = 0265) However in
none of these random samples were the total number of
alleles represented (the mean number of alleles represented
in random samples of seven populations is 385 plusmn 33)
(Fig 3) This supports the idea that although human
actions cannot be minimized because of data constraints
random solutions are much less efficient than the optimized
one as expected
For the alternative analysis for an ex situ SCP strategy
samples of only four additional local populations would be
necessary to optimally complement the genetic variability
currently represented in the germplasm bank (Fig 4) Only
these four populations have maximum frequency of
selection (ie because only they appeared in all solutions)
Minimizing distances to Goiania did not change this
solution in this particular case because of the rare variants
found in the state of Mato Grosso are unique and conse-
quently they have maximum frequencies of selection (ie
appear in all solutions)
Discussion
Here we showed that it is possible to design optimal con-
servation strategies for the conservation of genetic diver-
sity under the framework of SCP Moreover alternative
applications of SCP for in situ and ex situ conservation
strategies were done based on the same dataset although
using distinct weights revealing their distinct purposes
We understand that these ex situ and in situ strategies can
Fig 2 Frequency of solutions
from SCP maximizing the total
number of alleles represented
minimizing the number of local
populations and maximizing the
amount of natural remnants
This count if based on
combination of several solutions
with seven local populations
that we found for optimizing the
in situ conservation Local
populations with frequencies
tending to 100 tend to be
irreplaceable so that losing
them will not allow one to
achieve the conservation goal
Conserv Genet (2012) 131085ndash1093 1089
123
Authors personal copy
be implemented together so as to maximize the effective-
ness of conservation planning In our case study dealing
with the genetic variability of D alata natural populations
we showed that it is possible to represent all known alleles
at least once by strategically conserving (in situ) seven
local populations distributed in the Cerrado biome
Because of the analytical constraints imposed by the dis-
tribution of alleles in different local population and the
predetermined targets trying to define a solution that
minimizes the human impacts of these local populations
(ie by selecting local population in regions with more
natural cover remnants) did not change the selected pop-
ulations although it may help to define priorities among
the populations studied (eg planning a schedule for con-
servation interventions) Further assuming that the germ-
plasm bank is a fully protected lsquolsquopopulationrsquorsquo we also
showed that even fewer local populations need to be
sampled to represent the known genetic variability of the
species aiming at its ex situ conservation
Systematic conservation planning is usually applied to
species conservation building conservation priority
regions based on several goals with different conservation
targets (Sarkar and Illoldi-Rangel 2010) This initial
application with genetic data represents a step further to the
theoretical ideas originally presented by Diniz-Filho and
Telles (2006) who proposed how different algorithms
could be used to represent genetic diversity under distinct
spatial population structures The analysis shown here for
D alata indeed suggests that systematic conservation
planning can be a quite useful and objective tool to guide
actions for within-species conservation although of course
further improvements may be important and more work is
needed to expand the framework
A first important issue to be discussed is that our
application is focused on neutral molecular markers which
represents the overall variability of the species that have
been accumulated throughout its evolutionary history Of
course this does not necessarily reflect adaptive traits that
must be important for population persistence or the traits
(ie fruit production and quality) that may be important for
000 015 030 045 060 075
Mean proportion of natural remnants
25
35
45
55N
umbe
r of
alle
les
repr
esen
ted
Best solution
Fig 3 Relationship between number of alleles represented and
proportion of natural remnants in the conserved populations under a
null model in which the seven local populations are randomly
sampled from the pool of 25 and combined in a reserve network The
optimum solution obtained by SCP is highlighted
Fig 4 Local populations
defined by SCP necessary to
better complement the
germplasm collection in the exsitu conservation program The
four local populations are
connected by arrows to Goiania
the locality where the
germplasm of D alata is
maintained
1090 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
unique population Observed heterozygosity was low in all
populations and most populations show deviations from
HardyndashWeinberg equilibrium with f-values significantly
different from zero for most local populations (Table 1) A
significant amount of divergence among these local popu-
lations was also observed (FST = 0267 SD = 0036
P 00001) indicating that several local populations
should be conserved to maintain all genetic diversity
Optimization solutions revealed that a minimum of
seven local populations are necessary to represent all 52
alleles at least once Several solutions for this problem
were reached and after considering a total of 100 minimum
solutions four local populations were extremely important
for achieving this goal (ie they were found in 100 of
solutions and a fiftieth additional one appeared in 95 of
the solutions) Further a total of ten populations had fre-
quencies of selection higher than 0 indicating that the
solutions are not always the same (Fig 2)
There was no significant relationship between selection
frequency and genetic parameters within local populations
except for Ar (r = 0488 P = 0013) but this is someway
tautological because optimization works to maximize
number of alleles (unique in each local population) Even
so it is important to note that these data could be also used
as covariates if one is interested for example in conserv-
ing the populations with higher selection frequency that
have more expected heterozygosity
Given the distribution of alleles in local populations (ie
many rare alleles are found in one or two populations
only) the mean amount of proportional remaining habitat
around the seven local populations selected (equal to 022)
was not significantly different from a 1000 random sam-
ples with same size (032 plusmn 014 P = 0265) However in
none of these random samples were the total number of
alleles represented (the mean number of alleles represented
in random samples of seven populations is 385 plusmn 33)
(Fig 3) This supports the idea that although human
actions cannot be minimized because of data constraints
random solutions are much less efficient than the optimized
one as expected
For the alternative analysis for an ex situ SCP strategy
samples of only four additional local populations would be
necessary to optimally complement the genetic variability
currently represented in the germplasm bank (Fig 4) Only
these four populations have maximum frequency of
selection (ie because only they appeared in all solutions)
Minimizing distances to Goiania did not change this
solution in this particular case because of the rare variants
found in the state of Mato Grosso are unique and conse-
quently they have maximum frequencies of selection (ie
appear in all solutions)
Discussion
Here we showed that it is possible to design optimal con-
servation strategies for the conservation of genetic diver-
sity under the framework of SCP Moreover alternative
applications of SCP for in situ and ex situ conservation
strategies were done based on the same dataset although
using distinct weights revealing their distinct purposes
We understand that these ex situ and in situ strategies can
Fig 2 Frequency of solutions
from SCP maximizing the total
number of alleles represented
minimizing the number of local
populations and maximizing the
amount of natural remnants
This count if based on
combination of several solutions
with seven local populations
that we found for optimizing the
in situ conservation Local
populations with frequencies
tending to 100 tend to be
irreplaceable so that losing
them will not allow one to
achieve the conservation goal
Conserv Genet (2012) 131085ndash1093 1089
123
Authors personal copy
be implemented together so as to maximize the effective-
ness of conservation planning In our case study dealing
with the genetic variability of D alata natural populations
we showed that it is possible to represent all known alleles
at least once by strategically conserving (in situ) seven
local populations distributed in the Cerrado biome
Because of the analytical constraints imposed by the dis-
tribution of alleles in different local population and the
predetermined targets trying to define a solution that
minimizes the human impacts of these local populations
(ie by selecting local population in regions with more
natural cover remnants) did not change the selected pop-
ulations although it may help to define priorities among
the populations studied (eg planning a schedule for con-
servation interventions) Further assuming that the germ-
plasm bank is a fully protected lsquolsquopopulationrsquorsquo we also
showed that even fewer local populations need to be
sampled to represent the known genetic variability of the
species aiming at its ex situ conservation
Systematic conservation planning is usually applied to
species conservation building conservation priority
regions based on several goals with different conservation
targets (Sarkar and Illoldi-Rangel 2010) This initial
application with genetic data represents a step further to the
theoretical ideas originally presented by Diniz-Filho and
Telles (2006) who proposed how different algorithms
could be used to represent genetic diversity under distinct
spatial population structures The analysis shown here for
D alata indeed suggests that systematic conservation
planning can be a quite useful and objective tool to guide
actions for within-species conservation although of course
further improvements may be important and more work is
needed to expand the framework
A first important issue to be discussed is that our
application is focused on neutral molecular markers which
represents the overall variability of the species that have
been accumulated throughout its evolutionary history Of
course this does not necessarily reflect adaptive traits that
must be important for population persistence or the traits
(ie fruit production and quality) that may be important for
000 015 030 045 060 075
Mean proportion of natural remnants
25
35
45
55N
umbe
r of
alle
les
repr
esen
ted
Best solution
Fig 3 Relationship between number of alleles represented and
proportion of natural remnants in the conserved populations under a
null model in which the seven local populations are randomly
sampled from the pool of 25 and combined in a reserve network The
optimum solution obtained by SCP is highlighted
Fig 4 Local populations
defined by SCP necessary to
better complement the
germplasm collection in the exsitu conservation program The
four local populations are
connected by arrows to Goiania
the locality where the
germplasm of D alata is
maintained
1090 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
be implemented together so as to maximize the effective-
ness of conservation planning In our case study dealing
with the genetic variability of D alata natural populations
we showed that it is possible to represent all known alleles
at least once by strategically conserving (in situ) seven
local populations distributed in the Cerrado biome
Because of the analytical constraints imposed by the dis-
tribution of alleles in different local population and the
predetermined targets trying to define a solution that
minimizes the human impacts of these local populations
(ie by selecting local population in regions with more
natural cover remnants) did not change the selected pop-
ulations although it may help to define priorities among
the populations studied (eg planning a schedule for con-
servation interventions) Further assuming that the germ-
plasm bank is a fully protected lsquolsquopopulationrsquorsquo we also
showed that even fewer local populations need to be
sampled to represent the known genetic variability of the
species aiming at its ex situ conservation
Systematic conservation planning is usually applied to
species conservation building conservation priority
regions based on several goals with different conservation
targets (Sarkar and Illoldi-Rangel 2010) This initial
application with genetic data represents a step further to the
theoretical ideas originally presented by Diniz-Filho and
Telles (2006) who proposed how different algorithms
could be used to represent genetic diversity under distinct
spatial population structures The analysis shown here for
D alata indeed suggests that systematic conservation
planning can be a quite useful and objective tool to guide
actions for within-species conservation although of course
further improvements may be important and more work is
needed to expand the framework
A first important issue to be discussed is that our
application is focused on neutral molecular markers which
represents the overall variability of the species that have
been accumulated throughout its evolutionary history Of
course this does not necessarily reflect adaptive traits that
must be important for population persistence or the traits
(ie fruit production and quality) that may be important for
000 015 030 045 060 075
Mean proportion of natural remnants
25
35
45
55N
umbe
r of
alle
les
repr
esen
ted
Best solution
Fig 3 Relationship between number of alleles represented and
proportion of natural remnants in the conserved populations under a
null model in which the seven local populations are randomly
sampled from the pool of 25 and combined in a reserve network The
optimum solution obtained by SCP is highlighted
Fig 4 Local populations
defined by SCP necessary to
better complement the
germplasm collection in the exsitu conservation program The
four local populations are
connected by arrows to Goiania
the locality where the
germplasm of D alata is
maintained
1090 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
economic use of these species Our application is more
focused on overall conservation of variability within spe-
cies someway equivalent in this sense to definition of
evolutionary significant units (although this is usually
based on explicitly historical data obtained by mtDNA or
cpDNAmdashbut see Fraser and Bernatchez 2001 for a more
general definition) Our main purpose here was to show the
possibility of developing a systematic conservation plan
based on genetic data of course if adaptive data is avail-
able the same procedures can be applied (perhaps with
more sophisticated targets related to the persistence of local
populations or its economic use) Also other targets can be
added to allow improving chances of population persis-
tence and this could be coupled with the analyses per-
formed here
Another limited aspect of our analyses is that genetic
data is based on a sample of local populations and this
does not ensure that all genetic variability for the species
was actually sampled There are two different issues mixed
here First because of the relatively small sample sizes
within local populations it is not possible to ensure that all
genetic diversity (ie all alleles) have been sampled and
adding more rare alleles can change the frequencies of
selection reported here This is a general problem in SCP
when applied to species data when it is assumed that all
species found in the alternative sites or localities are known
(usually because these analyses are based on maps of
extents of occurrence although it is well known that these
maps have important omission and commission errorsmdashsee
Lemes et al 2011 for a recent discussion) In our case with
genetic data this problem could be solved in the future by
using simulations to generate stochastic distributions of
alleles within populations and applying SCP to the simu-
lated data Alternatively other algorithms could be devel-
oped to deal directly with allele frequencies giving less
weight to rare alleles or targeting not representation of
alleles only but also their combinations in genotypic fre-
quencies (ie taking into account how and where they
appear in heterozygosity or homozygosity) as well which
could also be better linked with population persistence
Second and perhaps more important although we
sampled D alata along most of its geographic range and
analyzed a relatively large number of localities it is quite
probable that sampling more populations will lead to dis-
covery of new (rare) alleles that should deserve attention
Even though there was a significant and positive autocor-
relation for most allele frequencies and overall variability
(see Soares et al 2008) rare alleles are by definition ran-
domly distributed in geographical space So we are actu-
ally showing only how the known genetic variability can be
optimally represented Even so we believe that our pro-
cedure is geographical representative because of the
underlying spatial structure in data
As pointed out above the purpose of our SCP was to
represent the estimated genetic variability in microsatellite
neutral markers we trust that our samples captured most of
the genetic diversity using this surrogate When comparing
the local populations analyzed here this can be better
viewed as a model II design for statistical analyses in
which local populations are actually samples of an
unknown number of local populations widely distributed
throughout speciesrsquo range Although it is not certain that
these local samples represent all genetic diversity infor-
mation about autocorrelation structure can be used to
establish if a local population not sampled and analyzed
can be effective in conserving genetic diversity (see Diniz-
Filho and Telles 2002) Applying a Mantel correlogram to
genetic distances revealed that correlogram intercept is
about 300ndash350 km with Mantelrsquos correlation in the first
distance class equal to 0324 (P 001 with 1000 per-
mutations) (see Diniz-Filho and Telles 2002 Epperson
2003) Thus although correlation is not too high (most
likely because of the rare alleles) if a non-sampled local
population is within this autocorrelation range of about
300ndash350 km to one of the local population considered
important in our SCP it quite probably holds a similar set
of alleles Even rare alleles could be found in this unknown
population if gene flow is effective at these small geo-
graphic distances (ie many private alleles could be
actually not private if closer populations are sampled)
Consequently it is safe to assume that this new unknown
local population would be effective to achieve the con-
servation goals at least in terms of the more common
alleles (which tend to determine the spatial patterns) If
opportunities to conserve this new local population actually
arise they should be prioritized even in the absence of
genetic information about it The same reasoning is valid if
lsquolsquoBarursquorsquo trees are found in protected areas close to a pop-
ulation assigned here with high selection frequency which
will increase the conservation value of this protected area
(because this reserve will also probably represent the
genetic diversity of the target species beyond its other
potential benefits)
We believe that the most important issue raised by our
analysis is the possibility of applying the methods of sys-
tematic conservation planning to cope with within-species
genetic variation and based on distinct approaches for in situ
and ex situ strategies Although many improvements can be
made to deal with more complex aspects of genetic data (such
as dealing with allele frequencies rather than with allele
presence-absence doing independent analyses for the distinct
loci and dealing with within-population variability using
genotypes as targets adding more adaptive markers or
including more socio-economic costs of conservation action)
we believe that the analyses presented here are a good starting
point for planning for the conservation of genetic diversity in a
Conserv Genet (2012) 131085ndash1093 1091
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
more systematic and objective way The most important idea
is that different plans can be developed for dealing with in situ
and ex situ situations
In general we understand that for in situ conservation the
applications match those frequently used with other conser-
vation goals usually species in which development-conser-
vation conflicts are solved (or at least minimized) by selecting
sites (in this case local populations) that have less human
impacts Of course depending on the distribution of goals and
defined targets this minimization will not produce a lot of
changes (for example if irreplaceable sites are found in
regions with higher levels of human occupation) Even so
another possibility is to relax the targets so that some of these
targets can be lost if the cost of the total solution becomes too
high This could be done more effectively by also incorpo-
rating more complex targets based on allele frequency or
doing particular combinations of targets within populations
However this is difficult to do in practice because we are
usually not aware of the biological or ecological meaning of
the variable used to constraint the selection of sites or popu-
lations In our case here with D alata for example it is dif-
ficult to establish which is the minimum amount of natural
remnants within the buffer that will ensure the persistence of
local populations We know that individual trees can persist in
disturbed environments such as highly disturbed pastures
because the tree furnishes shadows and food for cattle but
these isolated trees have their fitness widely reduced because
of lack of pollinators and dispersers so populations will col-
lapse in short ecological times The existence of some private
alleles (see Table 1) suggests that some level of isolation
already exists among these local populations and this may be
also related to broad scale habitat fragmentation in Cerrado
(see Telles et al 2007 Diniz-Filho et al 2007b) If a next step
determining how this isolation reduces fitness at more local
scales is thus very important for establishing how the cost
variable can be a surrogate for such demographic processes
within local populations This can be done for example by
testing departures from HW equilibrium (ie see Table 1) of
local populations with high selection frequencies in the final
solution If these crucial local populations which will tend to
be characterised by rare or private alleles because of how
algorithm achieve the conservation goal are dominated by
rare allele homozygous individuals this may indicate whether
the conservation of these local populations is only going to be
effective in the short-term and should be augmented with
active management As pointed out above further develop-
ments in SCP procedures that deals with genotypes and not
only alleles as conservation targets may be effective in dealing
with this situation
On the other hand for ex situ conservation it is also
possible to derive effective conservation plans based on
different approaches Here we lsquolsquofixedrsquorsquo an additional pop-
ulation preserved in the germplasm bank that is maintained
and which ensures long-term persistence of the existing
genetic variability Doing this revealed that only four
additional samples are necessary to optimally represent all
the variability Other solutions could be used for instance
by minimizing the distance from each local population to
the germplasm bank (this would reduce transport costs for
example) In our case as discussed above the distinct
solutions did not change a lot the final solutions because of
the distribution of alleles in the populations
An overall principle in producing conservation plans based
on genetic data would also resemble reactive and pro-active
conservation strategies at broader scales (Brooks et al 2006)
When dealing with in situ conservation a pro-active strategy
is being applied minimizing human impacts in selected
regions to increase persistence in natural habitats Perhaps for
ex situ conservation the opposite strategymdasha reactive
approachmdashshould be established by selecting regions with
higher levels of human impacts (in this case by inverting the
direction of cost vector) Doing this would ensure that genetic
variability found in regions with higher impacts that may
have reduced fitness will be prioritized for sampling and
seeding in the germplasm collection
Thus despite the simplicity of the approach adopted here
and the problems and caveats pointed out above we believe
that this initial application of the systematic conservation
planning theory to genetic data can be a useful starting point
for methodological and conceptual improvements Improving
our knowledge on the ecological meaning of the cost variable
used in the prioritization process may be a first important step
towards a comprehensive and quantitative balance definition
of goals and will allow establishing threshold for acceptable
loss of conservation targets within species In general dealing
with more complex genetic data can be important for increase
the range of applications and explicitly incorporating eco-
nomic use of the species can shed more light in new possi-
bilities for in situ and ex situ designs
Acknowledgments We thank two anonymous reviewers for sug-
gestions that improved initial version of this manuscript Our research
program integrating macroecology and molecular ecology of plants
and the DTI fellowship to GO has been continuously supported by
several grants and fellowships to the research network GENPAC
(Geographical Genetics and Regional Planning for natural resources
in Brazilian Cerrado) from CNPqMCTCAPES (projects
5647172010-0 and 5636242010-8) and by the lsquolsquoNucleo de Excel-
encia em Genetica e Conservacao de Especies do CerradorsquorsquomdashGECER
(PRONEXFAPEGCNPq CP 07-2009) Field work has been sup-
ported by Systema Naturae Consultoria Ambiental LTDA Work by
JAFD-F MPCT LJC RGC and RDL have been contin-
uously supported by productivity fellowships from CNPq and work
by DBM and JSS by fellowships by CAPES
References
Abbitt RJF Scott JM Wilcove DS (2000) The geography of
vulnerability incorporating species geography and human
1092 Conserv Genet (2012) 131085ndash1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy
development patterns into conservation planning Biol Conserv
96169ndash175 doi101016S0006-3207(00)00064-1
Araujo MB (2003) The coincidence of people and biodiversity in
Europe Glob Ecol Biogeogr 125ndash12 doi101046j1466-822X
200300314x
Balmford A Moore JL Brooks T Burgess N Hansen LA Williams
P Rahbek C (2001) Conservation conflicts across Africa
Science 2912616ndash2619 doi101126science29155132616
Brooks T da Fonseca GAB Rodrigues ASL (2004) Species data and
conservation planning Conserv Biol 181682ndash1688 doi
101111j1523-1739200400457x
Brooks TM Mittermeier RA Fonseca GAB Da Gerlach J Hoffmann
M Lamoreux JF Mittermeier CG Pilgrim JD Rodrigues ASL
(2006) Global biodiversity conservation priorities Science
31358ndash61 doi101126science1127609
Cabeza M Moilanen A (2001) Design of reserve networks and the
persistence of biodiversity Trends Ecol Evol 16242ndash248 doi
101016S0169-5347(01)02125-5
Charlesworth D Charlesworth B (1987) Inbreeding depression and its
evolutionary consequences Annu Rev Ecol Syst 18237ndash268
doi101146annureves18110187001321
Collevatti RG Lima JS Soares TN Telles MPDC (2010) Spatial
genetic structure and life history traits in Cerrado tree species
inferences for conservation Nat Conservacao 854ndash59 doi
104322natcon00801008
Diniz-Filho JAF Bini LM (2011) Geographical patterns in biodiver-
sity towards an integration of concepts and methods from genes
to species diversity Nat Conservacao 9(2)179ndash187 doi
104322natcon2011023
Diniz-Filho JAF Telles MPC (2002) Spatial autocorrelation analysis
and the identification of operational units for conservation in
continuous populations Conserv Biol 16924ndash935 doi101046
j1523-1739200200295x
Diniz-Filho JAF Telles MPC (2006) Optimization procedures for
establishing reserve networks for biodiversity conservation
taking into account population genetic structure Genet Mol
Biol 29207ndash214
Diniz-Filho JAF Bini LM Pinto MP Rangel TFLVB Carvalho P
Vieira SL Bastos RP (2007a) Conservation biogeography of
Anurans in Brazilian Cerrado Biodivers Conserv 16997ndash1008
doi101007s10531-006-9010-4
Diniz-Filho JAF Nabout JC Bini LM Soares TN Telles MPC
DeMarco P Collevatti RG (2007b) Niche modeling and
landscape genetics of Caryocar brasiliense (lsquolsquoPequirsquorsquo tree
Caryocaraceae) in Brazilian Cerrado an integrative approach
for evaluating central-peripheral population patterns Tree Genet
Genomes 5617ndash627 doi101007s11295-009-0214-0
Epperson BK (2003) Geographical genetics Princeton University
Press Princeton
Felfili JM Ribeiro JF Borges Filho HC Vale AT (2004) Potencial
economico da biodiversidade do Cerrado estadio atual e
possibilidades de manejo sustentavel dos recursos da flora In
Aguiar LMS Camargo AJA (eds) Cerrado ecologia e caracter-
izacao Embrapa Informacao Tecnologica Brasılia pp 17ndash40
Frankham R (2003) Genetics and conservation biology C R Biol
32622ndash29 doi101016S1631-0691(03)00023-4
Fraser DJ Bernatchez L (2001) Adaptive evolutionary conservation
towards a unified concept for defining conservation units Mol Ecol
102741ndash2752 doi101046j1365-294X2001t01-1-01411x
Goudet J (2002) FSTAT a program to estimate and test gene
diversities and fixation indices (version 2932) Available from
httpwwwunilchizeasoftwaresfstathtml
Grelle CEV Lorini ML Pinto MP (2010) Reserve selection based on
vegetation in the Brazilian Atlantic Forest Nat Conservacao
846ndash53 doi104322natcon00801007
Kirkpatrick JB (1983) An iterative method for establishing priorities
for the selection of nature reserves an example from Tasmania
Biol Conserv 25127ndash134 doi1010160006-3207(83)90056-3
Lemes P Faleiro FAMV Tessarolo G Loyola RD (2011) Refinando
dados espaciais para conservacao da biodiversidade Nat Con-
servacao 9240ndash243 doi104322natcon2011032
Loyola RD Oliveira-Santos LGR Almeida-Neto M Nogueira DM
Kubota U Diniz-Filho JAF Lewinsohn TM (2009) Integrating
economic costs and biological traits into global conservation
priorities for carnivores Plos One 4(8)e6807 doi101371
journalpone0006807
Loyola RD Eizirik E Machado RB Aguiar LMS Brito D Grelle
CEV (2011) Toward innovative integrated approaches for the
conservation of mammals Nat Conservacao 91ndash6 doi104322
natcon2011001
Margules CR Pressey RL (2000) Systematic conservation planning
Nature 405243ndash253 doi10103835012251
Margules CR Sarkar S (2007) Systematic conservation planning
Cambridge University Press Cambridge
McCarthy MA Thompson CJ Possingham HP (2005) Theory for
designing nature reserves for single species Am Nat
165250ndash257 doi0003-0147200516502-4046
Myers N Mittermeier RA Mittermeier CG Fonseca GAB Kents J
(2000) Biodiversity hotspots for conservation priorities Nature
403853ndash858 doi10103835002501
Neel MC Cummings MP (2003) Effectiveness of conservation targets
in capturing genetic diversity Conserv Biol 17219ndash229 doi
101046j1523-1739200301352x
Possingham H Ball I Andelman S (2000) Mathematical methods for
identifying representative reserve networks In Ferson S
Burgman M (eds) Quantitative methods for conservation biol-
ogy Springer New York pp 291ndash305
Pressey RL (2004) Conservation planning and biodiversity assem-
bling the best data for the job Conserv Biol 181677ndash1681 doi
101111j1523-1739200400434x
Sarkar S Illoldi-Rangel P (2010) Systematic conservation planning an
updated protocol Nat Conservacao 819ndash26 doi104322natcon
00801003
Segelbacher G Cushman SA Epperson BK Fortin M-J Francois O
Hardy OJ Holderegger R Taberlet P Waits LP Manel S (2010)
Applications of landscape genetics in conservation biology
concepts and challenges Conserv Genet 11375ndash385 doi
101007s10592-009-0044-5
Soares TN Chaves LJ Telles MPD Diniz-Filho JAF Resende LV
(2008) Spatial distribution of intrapopulational genetic variabil-
ity in Dipteryx alata Pesqui Agropecu Bras 431151ndash1158
Soares TN Melo DB Resende LV Vianello RP Chaves LJ
Collevatti RG Telles MPC (2012) Development of microsatel-
lite markers for the Neotropical tree species Dipteryx alata(Fabaceae) Am J Bot 99e72ndashe73
Telles MPC Diniz-Filho JAF Bastos RP Soares TN Guimaraes
LDH Lima LP (2007) Landscape genetics of Physalaemuscuvieri in Brazilian Cerrado correspondence between population
structure and levels of human occupation and habitat loss Biol
Conserv 13937ndash46 doi101016jbiocon200706003
Weir BS Cockerham CC (1984) Estimating F-statistics for the
analysis of population structure Evolution 381358ndash1370 doi
1023072408641
Williams JC Revelle CS Levin SA (2004) Using mathematical
optimization models to design nature reserves Front Ecol Environ
298ndash105 doi1018901540-9295(2004)002[0098UMOMTD]2
0CO2
Conserv Genet (2012) 131085ndash1093 1093
123
Authors personal copy