Continental Monophyly and Molecular Divergence of Peninsular Malaysia’s Macaca fascicularis...

Research ArticleContinental Monophyly and Molecular Divergence ofPeninsular Malaysiarsquos Macaca fascicularis fascicularis

Muhammad Abu Bakar Abdul-Latiff1 Farhani Ruslin1 Hamdan Faiq1

Mohd Salleh Hairul2 Jeffrine Japning Rovie-Ryan2 Pazil Abdul-Patah12

Salmah Yaakop1 and Badrul Munir Md-Zain1

1 School of Environmental and Natural Resource Sciences Faculty of Science and Technology Universiti Kebangsaan Malaysia43600 Bangi Selangor Malaysia

2 Department of Wildlife and National Parks (PERHILITAN) Km 10 Jalan Cheras 50664 Kuala Lumpur Malaysia

Correspondence should be addressed to Badrul Munir Md-Zain abgbadd1966yahoocom

Received 28 February 2014 Revised 7 May 2014 Accepted 10 June 2014 Published 17 July 2014

Academic Editor Gabriele Gentile

Copyright copy 2014 Muhammad Abu Bakar Abdul-Latiff et alThis is an open access article distributed under theCreativeCommonsAttribution License which permits unrestricted use distribution and reproduction in any medium provided the original work isproperly cited

The phylogenetic relationships of long-tailed macaque (Macaca fascicularis fascicularis) populations distributed in PeninsularMalaysia in relation to other regions remain unknown The aim of this study was to reveal the phylogeography and populationgenetics of Peninsular Malaysiarsquos M f fascicularis based on the D-loop region of mitochondrial DNA Sixty-five haplotypes weredetected in all populations with only Vietnam and Cambodia sharing four haplotypesTheminimum-spanning network projecteda distant relationship between Peninsular Malaysian and insular populations Genetic differentiation (119865ST Nst) results suggestedthat the gene flow among Peninsular Malaysian and the other populations is very low Phylogenetic tree reconstructions indicateda monophyletic clade of Malaysiarsquos population with continental populations (NJ = 97 MP = 76 and Bayesian = 100 posteriorprobabilities)The results demonstrate that Peninsular MalaysiarsquosM f fascicularis belonged to Indochinese populations as opposedto the previously claimed Sundaic populationsM f fascicularis groups are estimated to have colonized Peninsular Malaysia sim047million years ago (MYA) directly from Indochina through seaways by means of natural sea rafting or through terrestrial radiationduring continental shelf emersion Here the Isthmus of Kra played a central part as biogeographical barriers that then separated itfrom the remaining continental populations

1 Introduction

Macaca fascicularis [1] commonly known as the long-tailedmacaque or crab-eating macaque is called kera in Malaysia[2]M fascicularis is probably themost successful nonhumanprimate in Southeast Asia long-tailed macaques are dis-tributed in Malaysia Brunei Bangladesh Cambodia Nico-bar Islands Indonesia Laos Myanmar the Philippines Sin-gapore Thailand Timor-Leste and Vietnam [3] In additionto its extensive geographical distribution the opportunisticnature of M fascicularis enables it to naturally inhabit awide range of habitat namely primary and secondary forestriverine swamps coastal areas and mangrove forest fromsea level up to an elevation of 2000m [4 5] Furthermore

due to human introduction this opportunistic species is ableto survive in new habitats far from its natural distributionspecifically in the Pacific Ocean (Palau) Indian Ocean (Mau-ritius) and New Guinea [3]

Long-tailed macaques have been classified into as manyas 50 subspecies and even several different species [6]but the most recognized classifications are 10 subspecies ofM fascicularis [6ndash8] The 10 subspecies of M fascicularisthat are presently recognized based on their morphologicalcharacteristics are as follows (Figure 1) M f atriceps (Kloss1919) M f aurea (Geoffroy 1831) M f condorensis (Kloss1926) M f fascicularis (Raffles 1821) M f fusca (Miller1903) M f karimondjawae (Sody 1949) M f lasiae (Lyon1916) M f philippinensis (Geoffroy 1843) M f tua (Kellog

Hindawi Publishing CorporationBioMed Research InternationalVolume 2014 Article ID 897682 18 pageshttpdxdoiorg1011552014897682

2 BioMed Research International

Figure 1The distribution of 10 subspecies ofM fascicularis A =Mf aurea B = M f fascicularis C = M f philippinensis The isolatedisland subspecies are labeled with numbers 1 =M f umbrosa 2 =Mf lasiae 3 = M f fusca 4 = M f atriceps 5 = M f condorensis 6 =M f karimondjawae and 7 =M f tua [3]

1944) and M f umbrosa (Miller 1902) [6ndash8] Only a singlesubspecies of the long-tailed macaque is distributed in Peni-nsular Malaysia namely M f fascicularis [1] and it is themost widely distributed compared to the other subspecies InPeninsular Malaysia M f fascicularis is found on the main-land peninsula and surrounding islands such as LangkawiIsland FurthermoreM fascicularis is at the center of human-wildlife conflict in this region especially in secondary forestand palm oil plantations neighboring human settlements [29]

Previous studies have extensively examined themolecularphylogeny and biogeography ofM fascicularis using variousmolecular data such as allozymes [10] mitochondrial DNA(mtDNA) [11ndash20] and nuclear data [11 12 14] Blancher et al[15] successfully defined the continental-insular populationsof M fascicularis in Southeast Asia but whether PeninsularMalaysiarsquos M fascicularis belong to continental or insulargroups remains unknown Roos et al [21] proposed thatcolobines may have invaded Eurasia diversified into sev-eral lineages and radiated from mainland Southeast Asiadownwards to Java Sunda and Sumatra therefore it maybe possible to suggest that Peninsular Malaysiarsquos long-tailedmacaque should be classified as continental However Penin-sular Malaysia has been hypothesized to be the bridge thatfacilitated the radiation of nonhuman primates from Java tomainland Southeast Asia [22]Thus PeninsularMalaysiarsquosMfascicularis cannot simply be defined as a continental groupas in [15] because it is found in mainland Southeast Asia

In mammals mtDNA is inherited as a haploid from themother [23] This gives a bigger picture of diversity in theparticular gene pool of an organism caused by the occurrenceand accumulation of mutations in mtDNA [24] MoreovermtDNA does not undergo DNA recombination [25] All ofthese factorsmakemtDNAa very valuable tool when it comesto studying the relationships between populations However

Table 1 Details on the samples used in this study

No Sample name Taxon Locality(1) ALMFA63 M f fascicularis Malay Peninsula(2) ALMFA64 M f fascicularis Malay Peninsula(3) ALMFD16 M f fascicularis Malay Peninsula(4) ALMFD17 M f fascicularis Malay Peninsula(5) ALMFD28 M f fascicularis Malay Peninsula(6) ALMFK109 M f fascicularis Malay Peninsula(7) ALMFK110 M f fascicularis Malay Peninsula(8) ALMFK111 M f fascicularis Malay Peninsula(9) ALMFK112 M f fascicularis Malay Peninsula(10) FRMFB1 M f fascicularis Malay Peninsula(11) FRMFB2 M f fascicularis Malay Peninsula(12) FRMFB3 M f fascicularis Malay Peninsula(13) ZMW135 M f fascicularis Malay Peninsula(14) ZMW136 M f fascicularis Malay Peninsula(15) ZMW137 M f fascicularis Malay Peninsula(16) ALMFT322 M f fascicularis Malay Peninsula(17) ALMFJ204 M f fascicularis Malay Peninsula(18) ALMFJ264 M f fascicularis Malay Peninsula(19) ALMFJ195 M f fascicularis Malay Peninsula(20) ALMFR370 M f fascicularis Malay Peninsula(21) ALMFR371 M f fascicularis Malay Peninsula(22) ALMFC227 M f fascicularis Malay Peninsula(23) ALMFC228 M f fascicularis Malay Peninsula

cases of mtDNA-derived nuclear pseudogenes (Numts) havebeen reported to arise in phylogenetic studies on primates[26]The amplification ofNumts rather than targetedmtDNAwill disturb the molecular study of organisms due to theinclusion of paralogous nuclear sequences in the analysisinstead of mtDNA sequences [27 28] This study will exploitthe noncoding hypervariable region of mtDNA because thisevolves more rapidly thereby reflecting more differentiationamong closely related taxa [29 30]

Despite extensive studies on the molecular phylogeny oflong-tailed macaques the molecular data and phylogeneticposition of Peninsular Malaysiarsquos M fascicularis in relationto other countries remain unknown This may hold thekey to revealing the biogeographic and radiation history ofthis species in Southeast Asia Thus the objectives of thisstudy were to analyze the phylogeography and populationgenetics of Peninsular Malaysiarsquos M f fascicularis throughcomparison with the available data onM f fascicularis fromother countries using the D-loop region of mtDNA

2 Methodology

21 DNA Extraction Polymerase Chain Reaction (PCR) andSequencing A total of 23 fecal genetic samples of M ffascicularis were used in this study (Table 1) These wereobtained with the assistance of the Department of Wildlifeand National Parks Malaysia (PERHILITAN) All 23 sampleswere collected across mainland Peninsular Malaysia (Figure2) while with the exception of Penang Island no samples

BioMed Research International 3

Mauritius

ix

ix

viiviii

i

ii iii

ivvvi

VietnamCambodiaThailand

N

Siva-Malayan routesSino-Malayan routes

sim024MYA

sim091MYA

sim047MYA

Peninsular Malaysia

IndonesiaMauritiusPhilippinesMalaysia

Figure 2Map depicting the sampling location ofM f fascicularis in PeninsulaMalaysia (i-ALMFJ204264195 ii-FRMFB1-3 iii-ALMFC227-228 iv-ALMFT322 v-ALMFD16-17 vi-ALMFA63-64 vii-ALMFK109-112 viii-Penang samples from GenBank ix-ALMFR370-371) andlocality of sequence extracted from GenBank are color coded with respect to the legends provided The gray shading represents continentalshelf emersion [35] Siva-Malayan and Sino-Malayan routes are also illustrated on the map

were used from surrounding islands as there are somecontradictions in the classifications of M f fascicularis [7 832ndash34] The samples from Penang Island (10 sequences fromGenBank) were confirmed as M f fascicularis DNA wasextracted from 05ndash10 g of fecal samples using the innuPREPStool DNA Kit (Analytik Jena) following the manufacturerrsquosprotocol

To conduct a comparative analysis of Malaysiarsquos M ffascicularis we used representatives of all M f fascicularissequences available in GenBank for the mtDNA controlregion (CR) There were 253 available sequences Two werefrom Java [16] 77 from the Philippines Indonesia andMauritius [15] 9 from Java Sumatra Kalimantan Bali thePhilippines China and Mauritius [17] 10 from Thailand[18] 45 from Penang Malaysia [19] and 95 from CambodiaVietnam Indonesia and the Philippines [20] To avoidredundancy in the data analysis 77 sequences ofM f fascicu-laris were randomly selected from these 253 sequences (eachrepresenting a unique haplotypeclade with known localityinformation) across seven countries (Indonesia MalaysiaMauritius the Philippines Cambodia Vietnam and Thai-land Table 2) In addition two sequences ofM mulatta andM sylvanuswere used as an outgroup to root the phylogenetictrees and as a calibration point for molecular clock rateestimation

A 1100 bp fragment of mtDNA D-loop was amplifiedthrough a polymerase chain reaction (PCR) using a Master-cycler Nexus (Eppendorf North America Inc) PCR reac-tions were generated using the Phusion Flash High-FidelityPCR Master Mix (Finnzymes OY) which has high accuracy(proofreading DNA polymerase with a fidelity of 25X Taqpolymerase) extreme speed (extension times of 15 skb orless) and a very high yield in a reduced length of time Wedesigned our own primer for the PCR reactions in order tomaximize the extent of the D-loop sequence and to avoidamplifyingNumtsThe primers usedwere LATIFF1638 F (51015840-ACAGTCCTAGTATTAACCTGC-31015840) and LATIFF1689 R(51015840-CAAGGGGTGTTTAGTGAAGT-31015840) The parametersfor the PCR reaction were as follows initial denaturation for10 s at 98∘C followed by 30 cycles of denaturation for 1 s at98∘C annealing for 30 s at 52∘C extension for 15 s at 72∘Cand a final extension stage for 1min at 72∘C Vivantis G-F1PCR Clean-up Kits were used to purify the PCR productand the samples were subsequently sent to 1st Base Sdn Bhd(Malaysia) for sequencing purposes

22 Sequence and Phylogenetic Analysis D-loop sequencesobtained after the sequencing process were edited usingBioedit Sequence Alignment Editor To ensure the targetedspecies locus sequences were obtained the edited sequences


Table 2 The HVSII region of M f fascicularis sequences obtainedfrom GenBank

No Sample name Taxon Locality(1) KF793835a M f fascicularis Lombok Island(2) KF793836a M f fascicularis Lombok Island(3) AB281359b M f fascicularis Jatibarang Java(4) AB281360b M f fascicularis Tabuan Sumatra(5) AB281361b M f fascicularis Pangkalanbun Kalimantan(6) AB281362b M f fascicularis Ubud Bali Indonesia

(7) AB281363b M f fascicularis Cotabato MindanaoPhilippines

(8) AB281364b M f fascicularis Ban Tapoy Laos(9) AB281365b M f fascicularis China(10) AB281366b M f fascicularis Mauritius(11) AB281367b M f fascicularis Mauritius(12) EF208868c M f fascicularis Khao Nor Thailand(13) EF208869c M f fascicularis Khao Nor Thailand(14) EF208870c M f fascicularis Khao Nor Thailand(15) EF208871c M f fascicularis Khao Nor Thailand(16) EF208872c M f fascicularis Thailand(17) JX113352d M f fascicularis Pulau Pinang Malaysia(18) JX113353d M f fascicularis Pulau Pinang Malaysia(19) JX113354d M f fascicularis Pulau Pinang Malaysia(20) JX113355d M f fascicularis Pulau Pinang Malaysia(21) JX113356d M f fascicularis Pulau Pinang Malaysia(22) JX113357d M f fascicularis Pulau Pinang Malaysia(23) JX113358d M f fascicularis Pulau Pinang Malaysia(24) JX113359d M f fascicularis Pulau Pinang Malaysia(25) JX113360d M f fascicularis Pulau Pinang Malaysia(26) JX113361d M f fascicularis Pulau Pinang Malaysia(27) AB261938e M f fascicularis Philippines(28) AB261939e M f fascicularis Philippines(29) AB261937e M f fascicularis Philippines(30) AB261936e M f fascicularis Philippines(31) AB261929e M f fascicularis Indonesia(32) AB261928e M f fascicularis Indonesia(33) AB261934e M f fascicularis Mauritius(34) AB261933e M f fascicularis Mauritius(35) AB261918e M f fascicularis Indonesia(36) AB261926e M f fascicularis Indonesia(37) AB261915e M f fascicularis Indonesia(38) AB261900e M f fascicularis Indonesia(39) AB542813f M f fascicularis Cambodian-Chinese(40) AB542814f M f fascicularis Cambodian-Chinese(41) AB542815f M f fascicularis Cambodian-Chinese(42) AB542816f M f fascicularis Cambodian-Chinese(43) AB542817f M f fascicularis Cambodian-Chinese(44) AB542818f M f fascicularis Cambodian-Chinese(45) AB542819f M f fascicularis Cambodian-Chinese

Table 2 Continued

No Sample name Taxon Locality(46) AB542820f M f fascicularis Cambodian-Chinese(47) AB542821f M f fascicularis Cambodian-Chinese(48) AB542822f M f fascicularis Cambodian-Chinese(49) AB542823f M f fascicularis Cambodian-Chinese(50) AB542824f M f fascicularis Cambodian-Chinese(51) AB542825f M f fascicularis Cambodian-Chinese(52) AB542826f M f fascicularis Cambodian-Chinese(53) AB542827f M f fascicularis Cambodian-Chinese(54) AB542860f M f fascicularis Vietnam(55) AB542861f M f fascicularis Vietnam(56) AB542862f M f fascicularis Vietnam(57) AB542863f M f fascicularis Vietnam(58) AB542864f M f fascicularis Vietnam(59) AB542865f M f fascicularis Vietnam(60) AB542866f M f fascicularis Vietnam(61) AB542867f M f fascicularis Vietnam(62) AB542868f M f fascicularis Vietnam(63) AB542869f M f fascicularis Vietnam(64) AB542870f M f fascicularis Vietnam(65) AB542871f M f fascicularis Vietnam(66) AB542872f M f fascicularis Vietnam(67) AB542873f M f fascicularis Vietnam(68) AB542874f M f fascicularis Vietnam(69) AB542883f M f fascicularis Indonesia(70) AB542884f M f fascicularis Indonesia(71) AB542885f M f fascicularis Indonesia(72) AB542886f M f fascicularis Indonesia(73) AB542887f M f fascicularis Indonesia(74) AB542902f M f fascicularis Philippines(75) AB542903f M f fascicularis Philippines(76) AB542904f M f fascicularis Philippines(77) AB542905f M f fascicularis Philippines(78) JN885886g M mulatta(79) AB261974e M sylvanusaWandia et al [16] bKawamoto et al [17] cMalaivijitnond et al [18] dRovie-Ryan et al [19] eBlancher et al [15] fShiina et al [20] gYu et al [31]

were validated using sequence similarity searches (GenBankBLASTn) The MEGA 5 ClustalW multiple alignment algo-rithm was used to align all 102 sequences [36] The alignedD-loop sequences were then analyzed at three different levelsnamely sequence analysis phylogenetic analysis and popu-lation genetics analysisMEGA5 [36]was heavily exploited inthe sequence analysis as well as PAUP 40b10 [37] andDnaSP40 [38] Sequence analyses are crucial in revealing a fewkey end results such as genetic distance single-nucleotidepolymorphisms (SNPs) net nucleotide divergence (Da) andnucleotide diversity (120587)


Population expansion events were inferred by employingmismatch distribution analysis [39 40] using Arlequin ver31 with 1000 permutations [41] The haplotype relationshipsof M fascicularis were reconstructed by assuming that atany given site two randomly drawn haplotypes were unlikelyto have arisen from more than one mutational step [42]Network 4612 was used to generate a minimum-spanningnetwork (MSN) Genetic differentiation such as nucleotidesubdivision (Nst) [43] population subdivision (119865ST) andnumber of migrants per generation (119873

119898) estimated using

[44] were calculated in DnaSP 40The demographic history ofM f fascicularis in Southeast

Asia was examined by employing Tajimarsquos test of neutrality119863 [45] Fu and Lirsquos119863lowast and 119865lowast [46] and Fursquos Fs [47] Tajimarsquos119863 test compares the average number of pairwise nucleotidedifferences (119896) between haplotypes in a sample (M) expectedfrom the number of segregating sites (119870) Fu and Lirsquos119863lowast and119865lowast and Fursquos Fs were used to test for deviation of sequence

variation from evolutionary neutrality Fursquos Fs is based on theprobability of the observed number of haplotypes occurringunder conditions of neutrality whereas Fu and Lirsquos 119863lowast and119865lowast compare estimates of theta based onmutations in internal

and external branches of a genealogyPhylogenetic trees were constructed using three dis-

tinct criteria namely distance-based (neighbor-joining (NJ)tree) character-based (maximum parsimony (MP) tree) andBayesian inference Different software programs were usedto construct the phylogenetic tree namely MEGA 5 forthe NJ tree [36] PAUP 40b10 for the MP tree [37] andMrBayes 31 for Bayesian inference [48] The Kimura 2-parameter model was used in NJ tree reconstructions testedwith a bootstrap value of 1000 and the tree bisection andreconnection (TBR) algorithms were used for the MP treeThe heuristic searching method and 1000 random stepwiseadditions were applied to find the best tree through theapplication of the 50 consensus majority rule All the treesconstructed underwent 1000 bootstrap replications to obtainthe bootstrap confidence level

The best substitution model for D-loop sequences wasselected using Modeltest version 37 software [49] by meansof the Akaike information criterion (AIC) requirements Thebest model for the sequences selected was the TrN+I+G witha gamma shape parameter of 05597 and base frequencies of02915 for adenosine 03310 for cytosine 01035 for guanineand 02741 for thymine Metropolis-coupled Markov chainMonte Carlo (MCMC) was run with 10 million generationsand the tree was sampled every 1000 generations A splitfrequencies probability (119875) of 0006136 was obtained acrosstwo different runs of MrBayes The first 10 of the treesobtained in the analysis were discarded as burn-in (1000 treesdiscarded from a total of 10000 trees) and a majority-ruleconsensus for the remaining trees was constructed the pos-terior probabilities (119875119875) were summarized for each branch

The divergence times of M fascicularis in this studywere estimated using BEAST version 175 [50] Two datasetswere defined in the analysis namely ingroup and outgroupwhere the outgroup dataset included only M sylvanus Theuncorrelated lognormal relaxed-clock model [51] was usedto reconstruct the molecular divergence phylogenetic tree to

Table 3 Summary of sequences analyzed across seven populationsofM f fascicularis

Total characters examined 395Constant characters 291Parsimony-uninformative characters 23Parsimony-informative characters 81 informative no characters 205Ratio of TITV calculated from pairwise base differences 101

estimate the substitution rate for all nodes in the tree withuniform priors on the mean (0 100) and standard deviation(0 10)The birth-death speciationmodel [52] which suggeststhat births and deaths of lineages occur at a constant rate andare independent was used to reconstruct the starting treewith the assumption that the ingroups were monophyleticwith respect to the outgroupM sylvanuswas used to root theingroups and as themost recent common ancestor (TMRCA)or calibration point estimated around 55 million years ago(MYA) based on fossil data [53 54] MCMC was run for 10million generations and the trees were sampled every 1000generations with 1 of the sample discarded as burn-inTracer version 15 was used to assess the estimated samplesize (ESS) from the log files produced by BEAST After 10million generations the ESS of all parameters (posteriorprior likelihood ucldmean etc) well exceeded 200 sug-gesting that the MCMC steps were more than adequate Themaximum-clade-credibility tree topologies were calculatedusing posterior distribution and TreeAnnotator version 175was employed to produce the final summary trees finallyFigTree version 140 was used to view the tree

3 Results

D-loop sequences as low as 1000 bp were successfullysequenced for all 23 genetic samples used in this study(Table 1) All samples matched the same GenBank sequencesJX113341 from Penang with a minimum score of 95 querycover when blasted for sequence similarity searches usingGenBank BLASTn Although we successfully sequencedmore than 1000 bp of the D-loop fragment when wecompared it with the sequence available on GenBank forcomparative analysis purposes most of the D-loop sequenceswereHVSII [15] Consequently we aligned our sequence withthe sequence available fromGenBank (Table 2) and only usedthe HVSII region (sim400 bp) for this study

A total of 395 bp D-loop sequences of the HVSII regionwere obtained for sequence phylogenetic and populationgenetic analyses It was found that 291 (736) out of395 characters in the sequences were constant leaving 104(263) variable characters Eighty one (205) characterswere parsimony informative while the 23 (58) remain-ing characters were parsimony uninformative (Table 3) Thesequence showed an average of 281 of thymine 323 ofcytosine 284 of adenosine and 112 of guanine in thesequence across all taxa

Average pairwise distances amongM f fascicularis (pop-ulation as in the country they are distributed in) based on the


Table 4 Average pairwise distances among M f fascicularispopulations based on the Kimura-2-parameter model

1 2 3 4 5 6IndonesiaPhilippines 0028Mauritius 0031 0026Cambodia 0077 0068 0086Vietnam 0081 0073 0089 0026Thailand 0074 0067 0086 0033 0036Malaysia 0086 0080 0098 0044 0050 0042

Kimura 2-parameter model were also calculated (Table 4)The pairwise genetic distance exhibits a model of the rela-tionship between the populations ofM f fascicularis namelythe continental populations (Thailand Cambodia VietnamandMalaysia) and the insular populations (Indonesia Philip-pines andMauritius)The genetic distance between these twogroups (continental-insular) was relatively high comparedto distance within the groups For instance the geneticdistance between Malaysia and Vietnam was only 0033 butwith the three insular populations (Mauritius Indonesia andPhilippines) it was as high as 0098 In contrast the distanceswithin the groups were only 0026ndash0050 (continental) and0026ndash0031 (insular) SNP analysis conducted on the D-loop sequences revealed 104 SNPs throughout the sequencesanalyzed

Nucleotide diversity (120587) and net nucleotide divergence(Da) among M fascicularis populations revealed the samemodel of continental-insular relationships and separatePeninsular Malaysian populations from insular populations(Table 5)Within the insular group only a maximum value of002860 (Indonesia-Mauritius) for 120587 and 002025 (Mauritius-Philippines) for Da was obtained similar to the continentalgroup with 003227 for 120587 (Malaysia-Vietnam) and 003163 forDa (Malaysia-Thailand) However the analysis between thecontinental and insular groups showed a relatively high valuefor both 120587 and Da a minimum value of 003212 (Malaysia-Mauritius) and 004562 (Indonesia-Vietnam) respectivelyM f fascicularis populations in Peninsular Malaysia Thai-land Cambodia and Vietnam were included in the conti-nental groupThe Philippines Mauritius and Indonesia wereincluded in the insular group for additional analysis and werefound to exhibit 005101 for 120587 values and 004549 for Da

Genetic differentiation (119865ST Nst119873119898) values were calcu-lated to further elucidate the relationships amongM f fasci-cularis populations in seven different countries (Table 5) 119865STis the probability that two random gametes drawn from twopopulations are identical by descent and relative to gametestaken from the whole populations Only 119865ST values gt025strongly indicate a genetic differentiation of populations [55]M f fascicularis from all five countries showed a significantsubdivision from one another with a minimum value of119865ST of 0307 (Indonesia-Philippines) except for Cambodia-Vietnam (0001) The lowest 119865ST value between continental-insular groups was 0605 (Indonesia-Vietnam) in contrastto Mauritius populations which showed the highest division

from Thailand with 0992 Nst analysis can be used to esti-mate a populationrsquos subdivision at the nucleotide level [56]with 0 = no population subdivision and 1 = complete popula-tion division Nst analysis outcomes were completely parallelwith 119865ST with Cambodia-Vietnam exhibiting lowest Nst of000 followed by Philippines-Indonesia populations with031 The division of Mauritius populations from Thailandrevealed the highest Nst at 099 Theoretically when the119873

119898

value is lt1 populations are expected to genetically divergeover time and when 119873

119898is gt1 they are expected to retain

gene flow Thus the 119873119898value will be inversely proportional

to both 119865ST and Nst Here 119873119898analysis validated both 119865ST

and Nst as Cambodia-Vietnam had the highest119873119898 with an

astonishing value of 49453 with the same population size (15for each population) 119873

119898describes the average number of

individuals per generation migrating between populationsthus there appear to be nearly 500 individuals migratingbetween Cambodia and Vietnam per generation retainingtheir gene flow as a result The 119873

119898value for Mauritius-

Thailand was the lowest at 000 suggesting that the gene flowbetween these two populations was cut off over time

Sixty-five haplotypes with a size of 104 bp were definedfrom the seven populations of M f fascicularis (Table 6)and obtained from 100 analyzed sequences (excluding out-groups) Populations originating from Malaysia IndonesiaCambodia and Vietnam exhibited high haplotype diversity(Hd gt 09) with Mauritius populations having considerablylower haplotype diversity (Hd = 0500 plusmn 0265) this coincideswith the 120587 of the haplotype with Mauritius having thelowest value of 000127 plusmn 000067 Cambodia and Vietnamare the only populations that share the same haplotypes(Hap 23 Hap 27 Hap 29 and Hap 33 Table 7) Thailandpopulations only contain one unique haplotype Hap 47Malaysian populations on the other hand have the highestnumber with 18 unique haplotypes (Hap 48ndashHap 65) MSNwas generated with the haplotype data obtained to illustratethe relationships of the seven populations ofM f fascicularis(Figure 3) The network analysis revealed that PeninsularMalaysiarsquosM f fascicularis ismore related to continental pop-ulations (Vietnam Cambodia andThailand) as there are farfewer mutational steps between the populations as comparedto insular populations The analysis also portrayed Cambo-diaVietnam as the connecting point for both populationsfrom PeninsularMalaysia and insular populations the fewestmutational steps to their respective haplotypes were found

Mismatch distribution of pairwise nucleotide differencesof the HVSII sequences was estimated to study the demo-graphic history of M fascicularis populations in SoutheastAsia using the seven populations in this study as a modelBy assuming that the amount of difference between allelesdepends directly on the length of time since they divergedwe could manipulate the whole distribution of sequence dif-ferences to observe the demographic expansion ofM fascic-ularis Thus mismatch distributions of continental (Malaysiaincluded) and insular (Malaysia excluded) groups (Figure 4)were carried out following the expected distribution undera sudden expansion model [40 58] and a spatial expansionmodel [41 59] to portray these eventsThe continental grouprsquosmismatch distribution exhibited a multimodal expansion


Table 5 Measures of nucleotide diversity (120587) net nucleotide divergence (Da) nucleotide subdivision (Nst) estimate of populationsubdivision (119865ST) and gene flow (number of migrants119873

119898) among populations ofM f fascicularis

Populations 120587 Da Nst 119865ST 119873119898

Malaysia-Indonesia 004757 005621 071452 070427 021Malaysia-Mauritius 003212 008012 089728 089241 006Malaysia-Philippines 003696 006079 082756 082108 011Malaysia-Cambodia 002907 002341 055392 054877 041Malaysia-Vietnam 003227 002358 049767 049315 051Malaysia-Thailand 002310 003163 078033 077801 014Indonesia-Mauritius 002860 001469 049134 049128 052Indonesia-Philippines 002589 000831 030647 030655 062Indonesia-Cambodia 004930 004713 066516 065523 026Indonesia-Vietnam 005321 004562 061571 060498 033Indonesia-Thailand 004270 005482 079529 078997 013Mauritius-Philippines 001558 002025 080855 080672 012Mauritius-Cambodia 004039 006834 086798 086293 008Mauritius-Vietnam 004752 006622 081271 080690 012Mauritius-Thailand 004416 007848 099242 099200 000Philippines-Cambodia 004002 004922 077953 077315 015Philippines-Vietnam 004597 004864 072125 071452 020Philippines-Thailand 003450 005879 093535 093304 004Cambodia-Vietnam 002545 000003 000004 000101 49453Cambodia-Thailand 002382 002151 067936 067781 024Vietnam-Thailand 003067 001989 056507 056662 038Continental-Insular 005101 004549 061388 060272 033

Table 6 Summary statistic of D-loop mtDNA sequence variations in seven populations ofM f fascicularis

Populations 119873 119867 119878 Hddagger 120587dagger

119870 119863 Fs 119863lowast

119865lowast

Malaysia 33 18 45 09191 plusmn 0032 001805 plusmn 000264 7131 minus130238 minus3422 minus105396 minus134515Indonesia 17 16 44 0993 plusmn 0023 002915 plusmn 000271 11515 minus047866 minus5846 minus062676 minus067653Mauritius 4 2 1 0500 plusmn 0265 000127 plusmn 000067 0500 minus061237 0172 minus061237 minus047871Philippines 9 4 8 0750 plusmn 001257 000844 plusmn 000143 3333 060112 1546 013479 027529Cambodian-Chinese 15 14 27 0990 plusmn 0028 002045 plusmn 000294 8076 minus011460 minus6054 minus001858 minus005199Vietnam 15 14 40 0990 plusmn 0028 003043 plusmn 000436 12019 minus009810 minus4187 027234 019491All populations 98 65 104 0985 plusmn 0005 005101 plusmn 000168 20147 minus000311 minus22794 minus054873 minus038190Nmdashnumber of sequences analyzedHmdashnumber of haplotypes Smdashnumber of segregating sites Hdmdashhaplotype diversity 120587mdashnucleotide diversity Kmdashaveragenumber of nucleotide differences DmdashTajimarsquos statistic [45] FsmdashFursquos statistic [47] 119863lowast and 119865lowastmdashFu and Lirsquos statistics [46] lowast119875 lt 010 (for 119863 119863lowast and 119865lowast)Significance was determined using coalescent simulations in DnaSP version 40 (Rozas et al 2003) [38] daggerSites with gaps were completely excluded

pattern by means of the sum of squared deviation (SSD) =00023 with significance observed of 119875 = 088 and Harpend-ingrsquos raggedness index = 00054 with significance observedat 119875 = 076 The insular groups also indicated a multi-modal expansion distribution by means of SSD = 0074 with119875 = 026 and Harpendingrsquos raggedness index = 00168 with119875 = 014 The mismatch distribution of pairwise nucleotidedifferences among HVSII sequences for both continental andinsular populations exhibited ragged multimodal distribu-tion characteristics of population expansion and revealedthat the observed distribution is parallel with the expecteddistribution under the sudden (recent) expansion model[40 58] and the spatial expansion model (range expansionwith high levels of migration between neighboring demes[41 59])Themultimodal expansion pattern usually reflects a

highly stochastic shape of gene pool or a recent demographicexpansion

The reconstructedNJ phylogenetic tree (Figure 5) showeda monophyletic formation of ingroup samples (M f fasci-cularis) supported with a 79 bootstrap value Two cladesof M fascicularis populations were further defined namelythe continental groups (Peninsular Malaysia CambodiaThailand and Vietnam) and insular groups (the PhilippinesIndonesia and Mauritius) supported by 97 and 81 boot-strap values respectivelyTheMPphylogenetic tree (Figure 6)and Bayesian inference phylogenetic tree (Figure 7) likewisesupported the hypothesis that Peninsular Malaysiarsquos popula-tions are continental populations and revealed continental-insular clade formation supported by a 92 bootstrapvalue100 posterior probabilities and a 54 bootstrap


Table7Segregatingsites

(104

bp)in395-bp

segm

ento

fD-lo

opgene

defin

ing65

haplotypes

andtheird

istrib

utionacrosssevenpo

pulations

ofMffascic

ularis

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

11111

11111111112

2222222223

3333333334

4444444445

5555555556

6666666667

7777777778

8888888889

9999999990

0000

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234

Hap1

CCCCGACATA

GTTACTTGCG

GACCTAAGTT

CAATCATCTA

AAGTATCCCA

CCACGCCTAA

ACCCATACCA

ACCTGATCGT

CACACGGGGC

GCAGTACCTT

TACC

1Hap2

GA

AG

TGG

GT

TG

C

1Hap3

GA

AG

TGG

GT

TG

C

1Hap4

TT

A

AGACC

G

GGA

A

A

TG

C

1Hap5

AGC

GC

T

A

T

TGG

CC

1Hap6

AT

T

A

C

1Hap7

T

AGC

TG

AT

TG

C

2Hap8

C

AC

TGG

GCT

C

TG

C

1Hap9

AC

TGG

GCT

C

TG

C

3Hap10

AC

TGG

GCT

C

TG

C

1Hap11

T

A

G

1Hap12

A

AC

TG

GCT

AC

TG

CT

1Hap13

AGC

TGG

G

C

C

TGG

C

1Hap14

A

GT

T

GC

AG

G

TGG

C

2Hap15

T

C

A

T

G

G

G

TG

C

1Hap16

A

G

T

G

G

G

TG

C

1Hap17

C

C

AGC

T

G

G

GG

TG

C

1Hap18

A

AG

T

G

G

G

TG

C

1Hap19

A

A

T

G

G

G

TG

C

1Hap20

AGC

T

T

T

G

C

4Hap21

AGC

TG

TT

A

TG

C

1Hap22

T

AGC

T

T

T

G

C

1Hap23

TT

C

ATGC

T

AT

TTCTTT

CG

C

TT

TGT

C

11

Hap24

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGT

C

2Hap25

TTT

ACA

ATG

TC

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap26

TTC

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap27

TT

C

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap28

TT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap29

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap30

TTT

ACA

ATG

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap31

TT

C

ATGC

T

AT

TTCTTTG

CG

C

TT

TGT

C

1Hap32

TTG

A

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap33

TT

C

ATGC

T

A

TTCTTT

CG

C

TT

TGT

C

11

Hap34

TTT

C

AGC

T

AT

TTCTTT

CG

C

TT

TGT

C

1Hap35

TTT

ACA

AT

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap36

TTT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap37

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

C

TA

ATGT

CT

2Hap38

TT

CA

TTTG

GT

ATT

CTTT

C

C

TT

ATGT

C

1Hap39

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGTC

C

1


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia

2mdashMauritius3mdash

Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52



Figure 3 The minimum-spanning network (MSN) generated by Network 4612 [57] illustrating the relationships of the long-tailedmacaquesM f fascicularis in seven countries Each circle represents a haplotype and the diameter is scaled to the haplotype frequency

value09916 posterior probabilities respectively The molec-ular divergence phylogenetic tree (Figure 7) was constructedusing the uncorrelated lognormal relaxed-clock model Thiswas done to estimate the substitution rate for all nodesin the tree to establish the divergence dates of PeninsularMalaysiarsquosM f fascicularis populations as compared to othercountriesrsquo populations By exploiting M sylvanus samples asa calibration point and TMRCA the analysis indicated thatM f fascicularis groups diverged fromMmulattasim171MYAContinental-insular populations diverged at sim091MYA fol-lowed by another divergence of continental populations atsim047MYA that separated populations ofM f fascicularis in

Peninsular Malaysia from the rest of continental SoutheastAsia

4 Discussion

The analysis in this study has shown that the M fascicularissubspecies group forms a monophyletic clade as comparedto M mulatta and despite reported cases of introgressionof M mulatta and M fascicularis based on Y-chromosomeinvestigation [11] In Peninsular Malaysia M fascicularisexists sympatrically with M nemestrina thus a case ofintrogression is a possibility but by employing mtDNA as


0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference

ObservedSpatial expansionSudden expansion

Continental-Malaysia included

(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference


Insular-Malaysia excluded

(b)

Figure 4 Mismatch distribution of expected and observed frequencies of pairwise differences among HVSII sequences of continental andinsular groups ofM f fascicularis under the sudden and spatial expansion models

molecular mtDNA we could infer the phylogenetic relation-ships of targeted groups more precisely This represents thefirst study to analyze the comparative phylogenetic positionof M f fascicularis in Peninsular Malaysia although itis the centerpiece of the connection between insular andcontinental populations of M fascicularis in Southeast AsiaThe hypervariable locus of mtDNA has proven to be effectivein resolving the phylogeny ofM f fascicularis populations inSoutheast Asia consistent with Blancher et alrsquos work [15]

Geographical (distance and barriers) and anthropological(deforestation land conversion and habitat destruction) fac-tors may play a crucial role in separation of M f fascicularispopulations in Southeast Asia The mismatch distributionanalysis revealed a multimodal expansion pattern whichheavily suggests a recent demographic expansion parallelwith the opportunistic nature of the long-tailed macaqueInstead of being threatened due to an inability to survive inthe face of habitat destructionM fascicularis group adapt toinhabit areas neighboring human settlements where they willhave access to gardens farms and even houses to crop raid[60 61]

41 The Dispersal Mechanism of M f fascicularis fascicularisin Southeast Asia Population genetic analysis of PeninsularMalaysiarsquos M fascicularis revealed a complete separation ofthe populations from six populations in other countriesWhile it showed a closer relationship to populations origi-nating from Vietnam Cambodia andThailand as comparedto other insular populations the results (119865ST Nst and 119873119898)suggest an almost cut-off gene flow concerning the rest ofthe continental populations Not a single haplotype is sharedbetween the Peninsular Malaysian population and the restof the continental populations and MSN analysis clearlyshowed the distant relationship between all the populationsparticularly continental-insular groups Furthermore the

network analysis (Figure 3) revealed a more geographic rela-tionship ofM f fascicularis populations in Southeast Asia asthe insular populations were more closely related to those inCambodia andVietnamThis is unprecedented as PeninsularMalaysia has been hypothesized to act as a connecting bridgefor the Sundaic populations allowing radiation of primatesbetweenmainland Southeast Asia and its insular area [21 22]thus it should have much more closer relationships with theinsular populations

Our hypothesis is that the radiation of M f fascicularispossibly began from the Indochinese region and underwenttwo different dispersal mechanisms that led to the forma-tion of insular lineages and the colonization of the MalayPeninsula (Figure 2) First the long-tailed macaque radiatedfrom Indochina to the Sunda shelf around sim091MYA thispopulation subsequently diverged and colonized a differentpart of the Sunda shelf Second M f fascicularis radiated toPeninsular Malaysia sim047MYA directly from Indochina viaseaways colonized the area and remained separated from therest of the continental populationsThe Isthmus of Kra playeda pivotal role as a barrier to gene flow These suggestionsare congruent with the fossil records collected in the Sundashelf as early as at least the later Early Pleistocene aroundsim1MYA from Trinil east central Java [57] During the glacialperiods of the Pleistocene the fluctuations of sea level led tothe emersion of a huge continental shelf extending to marineareas estimated at around 200m in depth (Figure 2) [35] Ifthis is the case then the radiation ofM f fascicularis by landis possible

Alternatively in the event that the emersion of thecontinental shelf did not overlap during the radiation periodofM f fascicularis sea level fluctuations before 08MYAweremoderate with a mean of 70m and the lowest sea levelsat around 100m below that of the present day which mayhave also facilitated the radiation [62] One of the primehabitats of the widely adaptive M f fascicularis is coastal


JX113356 P Pinang

JX113353 P PinangJX113361 P PinangJX113360 P Pinang JX113359 P Pinang

JX113355 P PinangJX113354 P PinangJX113352 P Pinang

ALMFT322 Malaysia16JX113358 P Pinang

ALMFA63 Malaysia1ALMFA64 Malaysia2

ALMFK110 Malaysia7

AB281360 Sumatra

AB542862 VietnamAB542817 Cambodian-Chinese

53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China

AB261928 IndonesiaAB261929 Indonesia

AB542827 Cambodian-Chinese

AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92




AB261934 MauritiusAB281367 MauritiusAB281366 MauritiusAB261933 Mauritius

AB261918 IndonesiaAB282359 Java

AB261926 Indonesia

AB261939 Philippines

81

001

9485

53

99

8886

61

8050

90

ALMFK111 Malaysia8ALMFK112 Malaysia9ALMFK109 Malaysia6

ALMFJ195 Malaysia19ALMFJ204 Malaysia17

ALMFC227 Malaysia22ALMFC228 Malaysia23

ALMFD28 Malaysia5ALMFD16Malaysia3

ALMFD17Malaysia4ALMFR370 Malaysia20ALMFR371 Malaysia21

AB281364 BanTaPoyAB542821 Cambodian-Chinese

AB542873 Vietnam


AB542874 VietnamAB542860 VietnamAB542863 Vietnam

AB542868 VietnamAB542822 Cambodian-ChineseAB542816 Cambodian-Chinese

KF793836 LombokAB281362 Bali

AB542884 Indonesia

AB542903 PhilippinesAB261938 PhilippinesAB281363 Mindanao

AB542904 PhilippinesAB542902 PhilippinesAB542905 PhilippinesAB261937 Philippines

AB261936 PhilippinesJN885886 M mulatta

AB2619741 M sylvanus

FRMFB1 Malaysia10FRMFB2 Malaysia11ZMW136 Malaysia14ZMW137 Malaysia15 FRMFB3 Malaysia12

ZMW135 Malaysia13AB542865 Vietnam

AB542870 Vietnam

AB542813 Cambodian-ChineseAB542871 Vietnam


EF208868 ThailandEF208869 ThailandEF208870 ThailandEF208871 ThailandEF208872 Thailand


KF793835 Lombok

ALMFJ264 Malaysia18

AB542824 Cambodian-ChineseAB542814 Cambodian-Chinese



AB542866 VietnamAB542872 Vietnam

AB542867 Vietnam

Figure 5 The neighbor-joining phylogenetic tree estimated using the Kimura-2-parameter algorithm and 1000 bootstrap replications Theoptimal tree with the sum of branch length = 06544 is shown and bootstrap values are indicated on the branches


3399

56

99

84

69

80

30

4473

40

98

85

41

57

ALMFT322 Malaysia16JX113355 P PinangJX113352 P PinangJX113361 P PinangJX113360 P Pinang JX113357 P PinangJX113354 P PinangJX113359 P PinangJX113356 P PinangALMFA63 Malaysia1ALMFA64 Malaysia2JX113358 P PinangALMFK111 Malaysia8ALMFK112 Malaysia9ALMFK109 Malaysia6ALMFC227 Malaysia22ALMFC228 Malaysia23ALMFJ264 Malaysia18ALMFJ204 Malaysia17ALMFJ195 Malaysia19ALMFR371 Malaysia21ALMFR370 Malaysia20ALMFD16 Malaysia3ALMFD28 Malaysia5ALMFD17 Malaysia4ZMW136 Malaysia14ZMW135 Malaysia13FRMFB3 Malaysia12ZMW137 Malaysia15ALMFK110 Malaysia7FRMFB2 Malaysia11FRMFB1 Malaysia10


AB542867 Vietnam

AB542861 Vietnam AB542869 Vietnam

AB281364 BanTaPoy

AB542871 Vietnam

AB542874 Vietnam AB542864 VietnamAB542866 Vietnam

AB281365 China

AB542902 PhilippinesAB261939 PhilippinesAB261936 PhilippinesAB261937 PhilippinesAB542905 PhilippinesAB261915 IndonesiaAB542883 IndonesiaAB542884 IndonesiaAB542886 IndonesiaAB261900 IndonesiaAB542887 IndonesiaAB542885 IndonesiaAB281363 MindanaoAB261938 PhilippinesAB542903 PhilippinesAB542904 PhilippinesAB281360 SumatraAB281361 KalimantanAB261926 IndonesiaAB282359 Java

AB261918 IndonesiaAB261933 MauritiusAB261934 MauritiusAB281366 Mauritius

76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam

AB542820 Cambodian-ChineseAB542826 Cambodian-ChineseAB542870 VietnamAB542815 Cambodian-ChineseAB542824 Cambodian-ChineseAB542814 Cambodian-ChineseAB542865 VietnamAB542863 VietnamAB542868 VietnamAB542860 VietnamAB542816 Cambodian-ChineseAB542822 Cambodian-ChineseEF208871 ThailandEF208869 ThailandEF208872 ThailandEF208868 ThailandEF208870 ThailandAB281362 BaliKF793836 LombokAB261929 IndonesiaAB261928 IndonesiaKF793835 Lombok

AB281367 Mauritius

JN885886 M mulattaAB2619741 M sylvanus

JX113353 P Pinang

Figure 6 The maximum parsimony (MP) phylogenetic tree estimated using the TBR algorithm heuristic searching method and 1000bootstrap replications Bootstrap values are shown on the branches (Tree length = 264 CI = 04009 RI = 08944 HI = 04337)


03309 MYA

09989

09169

ALMFT322 Malaysia16JX113354 P PinangJX113360 P Pinang JX113356 P PinangJX113355 P PinangJX113353 P PinangJX113357 P PinangJX113359 P PinangJX113361 P PinangJX113352 P Pinang


AB261929 IndonesiaAB261928 IndonesiaAB281361 KalimantanAB261938 PhilippinesAB542903 PhilippinesAB281363 MindanaoAB542904 PhilippinesAB261939 PhilippinesAB542902 PhilippinesAB261936 PhilippinesAB542905 PhilippinesAB261937 PhilippinesAB261926 IndonesiaAB261933 MauritiusAB261934 MauritiusAB281367 MauritiusAB281366 MauritiusAB261918 IndonesiaAB282359 JavaAB281360 SumatraAB261900 IndonesiaAB542885 IndonesiaAB542886 IndonesiaAB542884 IndonesiaAB542887 IndonesiaAB261915 IndonesiaAB542883 Indonesia

100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA

JN885886 M mulattaZMW135 Malaysia13FRMFB3 Malaysia12ALMFK110 Malaysia7FRMFB1 Malaysia10ZMW137 Malaysia15ZMW136 Malaysia14FRMFB2 Malaysia11ALMFR371 Malaysia21ALMFR370 Malaysia20ALMFJ195 Malaysia19ALMFJ264 Malaysia18ALMFC228 Malaysia23ALMFC227 Malaysia22ALMFJ204 Malaysia17

ALMFK109 Malaysia6ALMFK111 Malaysia8ALMFK112 Malaysia9JX113358 P Pinang

ALMFD17 Malaysia4ALMFD28 Malaysia5ALMFD16 Malaysia3AB542820 Cambodian-ChineseAB542826 Cambodian-ChineseAB542865 VietnamAB542870 VietnamAB542824 Cambodian-ChineseAB542814 Cambodian-ChineseAB542815 Cambodian-ChineseAB542873 VietnamAB542817 Cambodian-ChineseAB542867 VietnamAB542819 Cambodian-ChineseAB542862 VietnamAB542861 VietnamAB542874 VietnamAB542823 Cambodian-ChineseAB542869 VietnamAB542871 VietnamAB542813 Cambodian-ChineseAB281364 BanTaPoyAB542821 Cambodian-ChineseAB542827 Cambodian-ChineseAB542818 Cambodian-ChineseAB542825 Cambodian-ChineseAB542872 VietnamAB281365 ChinaAB542864 VietnamAB542866 VietnamAB542860 VietnamAB542868 VietnamAB542863 VietnamAB542822 Cambodian-ChineseEF208870 ThailandEF208868 ThailandEF208872 ThailandEF208871 ThailandEF208869 ThailandAB542816 Cambodian-ChineseAB281362 BaliKF793836 LombokKF793835 Lombok


0469MYA

171MYA

0909MYA

Figure 7 Bayesian inference of the 50majority rule consensus and the molecular divergence tree of the HVSII sequence ofM f fascicularispopulations with Bayesian posterior probability (119875119875) are accordingly indicated on the branches The numbers on the nodes representdivergence time in millions of years (MYA)


habitat long-tailed macaques are excellent swimmers evenunderwater [6] making the passive dispersal theory ofnatural sea rafting by means of the Siva-Malayan route afitting idea for the dispersal of the species

Minimum-spanning network analysis (Figure 3) geneticdistances and population genetic analysis revealed that pop-ulations from the Philippines are much more closely relatedto Indochinese populations If by any chanceM f fascicularisdispersed to the Philippines via the Siva-Malayan route thenit should have a closer relationship to Peninsular Malaysiarather than to Indochinese populations Based on Chineseaffinities of the fauna found in the Philippines but not onthe Sunda shelf the authors in [63 64] proposed an alternatemigration route of mammals during the Pleistocene in whichthey reached Java via the Philippines and BorneoThis theorymight explain the closer genetic distance of M f fascicularisin the Philippines to Indochinese populations as compared toPeninsular Malaysiarsquos However this theory has largely beendiscredited [65] as Sulawesi shared similar island faunassuggesting that they were not part of a continuous landmigration routeAlternatively the haplotypes observedmightpossibly be derived from a single ancestral haplotype withlow genetic and nucleotide diversities within the Philippinepopulations [15]

Indeed the dispersal theory in the field of biogeographyrelies heavily on fossil and geological records which comprisethe main pillar of the theory For example in the case ofthe radiation history of Pongo pygmaeus fossil remains fromthe Late Middle Pleistocene were found in South ChinaVietnam Laos Cambodia andThailand and the same fossilswere discovered in Late Pleistocene sites in Indonesia [65] Asea level fall sim70000 years ago after the glacial maximumsim135000 years ago might have initiated the migrationbetween the mainland and Indonesia and Borneo [66]However it is almost impossible to illustrate the migra-tion routes of the other Indochinese species whether theyare limited southward to Thailand or Peninsular Malaysiabecause of the near total lack of Pleistocene fossiliferoussites in Peninsular Malaysia The fossil discovery of extinctspecies of Equus namadicus with Indochinese characteristicsin Tambun Peninsular Malaysia [57] makes clear that it ispossible that Peninsular Malaysia is not a definite Sundaicregion This supports the findings of this study

42 The Role of the Isthmus of Kra in the Colonizationof Peninsular Malaysia by M f fascicularis The orien-tal biogeographical regions that comprise the IndochineseSundaic and Wallacean provinces are an important part ofthe mysterious history of faunal dispersal and radiation inSoutheast Asia [67] The boundary between the Indochineseand Sundaic regions is claimed to be located at the Isthmusof Kra in PeninsularThailand [67] as distinct assemblages ofmammals [68] have been observed between the two ends ofthis barrier However reviews based on fossil records by [65]on the Pleistocene distribution of large mammals (129 extantspecies of large mammals including primates) concludedthat the biogeographical barriers to northern PeninsularMalaysia lay much farther south of the Isthmus of Kra during

Pleistocene Therefore the southern biogeographical transi-tions on Peninsular MalaysiaThailand lie approximately 500km south of the Isthmus of Kra near the Thailand-Malaysiaborder [69]

This southern transition also involves a distinctive changebetween perhumid evergreen rainforest and wet seasonalevergreen rainforest [70ndash72] but has not necessarily affectedthe long-tailed macaquesrsquo radiation and distribution asthere is no adequate evidence that they are influenced byclimate and environmental changes [73] In the case of M ffascicularis they are classified as a northern-southern group(with respect to the Isthmus of Kra) based on morphologicaland genetic traits [6 10ndash12 74]

Tosi and Coke [14] proposed the Isthmus of Kra as abiogeographical barrier to the monophyletic clade of M ffascicularis populations that does not undergo introgressionwith M mulatta because the Y-chromosome of M mulattadetected in M fascicularis north of the Isthmus of Kra isabsent in the southern populations The differences discov-ered in fossil records the variety of vegetation and thegenetic and morphological traits ofM f fascicularis have ledto the assumption that the differences have arisen becausethey belong to distinct biogeographical regionsThe southerngroups are always assumed to be the Sundaic population andthese deviate from the characteristics of those in Indochineseregion The phylogenetic analysis (NJ MP and Bayesianinference) in this study indicated a definite separation ofPeninsular Malaysiarsquos M f fascicularis from insular popu-lations and the monophyletic state of Peninsular Malaysiarsquospopulation which is more closely related to Indochinesepopulations

The estimation of divergence time of M f fascicularispopulations in Malaysia indicates that the colonization inPeninsular Malaysia occurred roughly sim047MYA which islargely congruent with Tosi and Cokersquos [14] estimation ofsim044MYA based on Y-chromosomal DNA and Blancher etalrsquos [15] study which dated the separations of continental-insular populations at sim055MYAThe same biogeographicalbarriers may have played a vital role in facilitating thecolonization process of PeninsularMalaysiarsquosM f fascicularisafter the radiation of the species from Indochinese regionsvia terrestrial radiation during continental shelf emersion ornatural sea rafting

The biogeographical history of Southeast Asia is complexdue to active tectonic plate movement the rise and fallof sea level during the Pliocene and Pleistocene drasticclimate change and the temporary formation of land bridgesconnectingmainland Southeast Asia to Sunda Java Sumatraand Borneo [75ndash78] These elements ultimately make itdifficult to predict the dispersal patterns ofM fascicularis inSoutheast Asia

5 Conclusion

Populations of M f fascicularis in Peninsular Malaysia werefound to be monophyletic in all phylogenetic analyses withthe absence of shared haplotypes with the other populationsin Southeast Asia This demonstrates that the species shouldbe treated as a single unique lineage of long-tailed macaques


in Southeast Asia Nevertheless populations from Malaysiaare much more closely related to populations in Indochineseregions compared to insular populations thus supporting theview that Peninsular Malaysiarsquos populations are continentalpopulations belonging to the Indochinese biogeographicalregions as opposed to Sundaic populationsThe results of thisstudy are crucial in the field of biogeography as in the case ofM f fascicularis the inclusion of Peninsular Malaysia in theSundaic regions is unsuitable

Conflict of Interests

The authors declare that there is no conflict of interestsregarding the publication of this paper

Acknowledgments

The authors are deeply indebted to the Department ofWildlife andNational Parks that provided themwith the nec-essary facilities and assistance for fecal sample collection andpermission to conduct this research with permit referencenumber (JPHLampTN(IP) 80-42 The authors acknowledgeUniversiti Kebangsaan Malaysia for providing necessaryfunding facilities and assistance This research was sup-ported by Grants FRGS12012STWN10UKM023UKM-GUP-2011-168 KOMUNITI-2011-023 ERGS12013STWN10UKM021 and DLP-2013-006

References

[1] T S Raffles ldquoDescriptive catalogue of a zoological collectionmade on account of the honourable East India company in theIsland of Sumatra and its vicinity with additional notices illus-trative of the natural history of these countriesrdquo Transactions ofthe Linnean Society vol 13 pp 239ndash274 1821

[2] B M Md-Zain M R Tarmizi and M Mohd-Zaki ldquoCam-pus monkeys of Universiti Kebangsaan Malaysia Nuisanceproblems and studentrsquos perceptionrdquo in Monkeys on the EdgeEcology and Management of Long-Tailed Macaques and theirInterface with Humans A Fuentes M Gumert and L Jones-Engel Eds Cambridge Studies in Biological and EvolutionaryAnthropology Cambridge University Press Cambridge UK2011

[3] M D Gumert A Fuentes G Engel and L J Engel ldquoFuturedirection for research and conservation of long-tailed macaquepopulationsrdquo inMonkeys on the Edge Ecology andManagementof Long-Tailed Macaques and Their Interface with HumansA Fuentes M Gumert and L Jones-Engel Eds CambridgeUniversity Press Cambridge UK 2011

[4] N Rowe The Pictorial Guide to the Living Primates PagoniasPress East Hampton NY USA 1996

[5] J Supriatna A Yanuar H TMartarinza R Sinaga I Sidik andS Iskcandar ldquoA preliminary survey of long-tailed and pig-tailedmacaques (Macaca fascicularis and Macaca nemestrina) inLampung Bengkulu and Jampi provinces Southern SumateraIndonesiardquo Tropical Biodiversity vol 3 no 2 pp 131ndash140 1996

[6] J Fooden ldquoSystematic review of Southeast Asian longtail maca-quesMacaca fascicularis (Raffles 1821)rdquo Fieldiana Zoology vol81 pp 1ndash206 1995

[7] C P Groves Primate Taxonomy Smithsonian Institution PressWashington DC USA 2001

[8] D Brandon-Jones A A Eudey T Geissmann et al ldquoAsianprimate classificationrdquo International Journal of Primatology vol25 no 1 pp 97ndash164 2004

[9] B M Md-Zain N A Sharsquoari M Mohd-Zaki et al ldquoA compre-hensive population survey and daily activity budget on long-tailed macaques of Universiti Kebangsaan Malaysiardquo Journal ofBiological Sciences vol 10 no 7 pp 608ndash615 2010

[10] D J Melnick1 and K K Kidd ldquoGenetic and evolutionary rela-tionships among Asian Macaquesrdquo International Journal of Pri-matology vol 6 no 2 pp 123ndash160 1985

[11] A J Tosi J C Morales and D J Melnick ldquoY-chromosomeand mitochondrial markers in Macaca fascicularis indicateintrogressionwith IndochineseMmulatta and a biogeographicbarrier in the Isthmus of Krardquo International Journal of Primatol-ogy vol 23 no 1 pp 161ndash178 2002

[12] A J Tosi J C Morales and D J Melnick ldquoPaternal maternaland biparental molecular markers provide unique windowsonto the evolutionary history of macaque monkeysrdquo Evolutionvol 57 no 6 pp 1419ndash1435 2003

[13] D G Smith J W Mcdonough and D A George ldquoMitochon-drial DNA variation within and among regional populationsof longtail macaques (Macaca fascicularis) in relation to otherspecies of the Fascicularis group of macaquesrdquo AmericanJournal of Primatology vol 69 no 2 pp 182ndash198 2007

[14] A J Tosi and C S Coke ldquoComparative phylogenetics offer newinsights into the biogeographic history of Macaca fascicularisand the origin of the Mauritian macaquesrdquo Molecular Phyloge-netics and Evolution vol 42 no 2 pp 498ndash504 2007

[15] A Blancher M Bonhomme B Crouau-Roy K Terao TKitano and N Saitou ldquoMitochondrial DNA sequence phy-logeny of 4 populations of the widely distributed cynomolgusmacaque (Macaca fascicularis fascicularis)rdquo Journal of Heredityvol 99 no 3 pp 254ndash264 2008

[16] I N Wandia I G Putra and I G Soma ldquoGenetic variationin long-tailed macaque (Macaca fascicularis) populations inLombok and Java Islands using mtDNA non coding region (D-loop) as molecular markerrdquo submitted to Genbank

[17] Y Kawamoto S Kawamoto K Matsubayashi et al ldquoGeneticdiversity of longtail macaques (Macaca fascicularis) on theisland ofMauritius an assessment of nuclear andmitochondrialDNA polymorphismsrdquo Journal of Medical Primatology vol 37no 1 pp 45ndash54 2008

[18] S Malaivijitnond O Takenaka J Denduangboripant N Ura-sopon I Hadi and Y Hamada ldquoA semi-wild troop of rhesus-like macaques inhabiting Foodenrsquos hybrid zone in northeasternThailand morphological characters reproduction-related fea-tures and genetic propertyrdquo Primates In press

[19] J J Rovie-Ryan F T Sitam Z Z Abidin S G Tan andM T Abdullah ldquoPopulation structure of Macaca fascicularis(Cercopithecidae) inferred from mitochondrial control regionsequences from Penang Island Malaysiardquo Genbank In press

[20] T Shiina K Tanaka Y Katsuyama et al ldquoMitochondrial DNAdiversity among three subpopulations of cynomolgusmacaques(Macaca fascicularis) originating from the Indochinese RegionrdquoExperimental Animals vol 59 no 5 pp 567ndash578 2010

[21] C Roos D Zinner L S Kubatko et al ldquoNuclear versus mito-chondrial DNA evidence for hybridization in colobine mon-keysrdquo BMC Evolutionary Biology vol 11 no 1 article 77 2011

[22] C Roos T Nadler and L Walter ldquoMitochondrial phylogenytaxonomy and biogeography of the silvered langur speciesgroup (Trachypithecus cristatus)rdquo Molecular Phylogenetics andEvolution vol 47 no 2 pp 629ndash636 2008


[23] M K Rosli S S Zakaria S M Syed-Shabthar et al ldquoPhyloge-netic relationships of Malayan gaur with other species of thegenus Bos based on cytochrome b gene DNA sequencesrdquoGenetics andMolecular Research vol 10 no 1 pp 482ndash493 2011

[24] V F Vun M C Mahani M Lakim A Ampeng and B MMd-Zain ldquoPhylogenetic relationships of leaf monkeys (PresbytisColobinae) based on cytochrome b and 12S rRNA genesrdquoGenetics andMolecular Research vol 10 no 1 pp 368ndash381 2011

[25] P D Olivo M J van deWalle P J Laipis andWW HauswirthldquoNucleotide sequence evidence for rapid genotypic shifts in thebovine mitochondrial DNA D-looprdquo Nature vol 306 no 5941pp 400ndash402 1983

[26] R V Collura and C-B Stewart ldquoInsertions and duplicationsof mtDNA in the nuclear genomes of Old World monkeys andhominoidsrdquo Nature vol 378 no 6556 pp 485ndash489 1995

[27] D X Zhang andGMHewitt ldquoNuclear integrations challengesfor mitochondrial DNA markersrdquo Trends in Ecology amp Evolu-tion vol 11 no 6 pp 247ndash251 1996

[28] M D Sorenson and TW Quinn ldquoNumts a challenge for aviansystematics and population biologyrdquoAuk vol 115 no 1 pp 214ndash221 1998

[29] M K A Rosli S M F Syed-Shabthar P Abdul-Patah et al ldquoAnew subspecies identification and population study of the AsianSmall-Clawed Otter (Aonyx cinereus) in Malay Peninsula andSouthern Thailand based on fecal DNA methodrdquoThe ScientificWorld Journal vol 2014 Article ID 457350 11 pages 2014

[30] L S Lim K C Ang M C Mahani A W Shahrom and B MMd-Zain ldquoMitochondrial DNA polymorphism and phylogene-tic relationships of Proto Malays in Peninsular Malaysiardquo Jour-nal of Biological Sciences vol 10 no 2 pp 71ndash83 2010

[31] W Yu F Huang and Z HeDirect Submission to Genbank 2011[32] L MedwayTheWild Mammals of Malaya and Offshore Islands

Including Singapore OxfordUniversity Press Oxford UK 1969[33] H C RavenWallacersquos Line and the Distribution of Indo-Austra-

lian Mammals New York Press New York NY USA 1935[34] V Weitzel C M Yang and C P Groves ldquoA catalogue of pri-

mates in the Singapore Zoological Reference Collectionrdquo TheRaffles Bulletin of Zoology vol 36 no 1 pp 1ndash166 1988

[35] C S Hutchinson Geological Evolution of South-East AsiaClarendon Press Oxford UK 1989

[36] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011

[37] D L Swofford PAUPlowast Pylogenetic Analysis Using Parsimony(lowast and Other Methods) V40b10 Sinaeur Associates Sunder-land Mass USA 2001

[38] J Rozas J C Sanchez-DelBarrio X Messeguer and R RozasldquoDNAsp DNA polymorphism analyses by the coalescent andother methodsrdquo Bioinformatics vol 19 no 18 pp 2496ndash24972003

[39] A R Rogers ldquoGenetic evidence for a Pleistocene populationexplosionrdquo Evolution vol 49 pp 608ndash615 1995

[40] A R Rogers and H Harpending ldquoPopulation growth makeswaves in the distribution of pairwise genetic differencesrdquoMolecular Biology and Evolution vol 9 no 3 pp 552ndash569 1992

[41] L Excoffier G Laval and S Schneider ldquoArlequin vers 30an integrated software package for population genetics dataanalysisrdquo Evolutionary Bioinform vol 1 pp 47ndash50 2005

[42] J Alexandrino J W Arntzen and N Ferrand ldquoNested cladeanalysis and the genetic evidence for population expansionin the phylogeography of the golden-striped salamanderChioglossa lusitanica (Amphibia Urodela)rdquo Heredity vol 88no 1 pp 66ndash74 2002

[43] M Lynch and T J Crease ldquoThe analysis of population surveydata on DNA sequence variationrdquoMolecular Biology and Evolu-tion vol 7 no 4 pp 377ndash394 1990

[44] R R Hudson M Slatkin and W P Maddison ldquoEstimation oflevels of gene flow from DNA sequence datardquo Genetics vol 132no 2 pp 583ndash589 1992

[45] F Tajima ldquoStatistical method for testing the neutral mutationhypothesis by DNApolymorphismrdquoGenetics vol 123 no 3 pp585ndash595 1989

[46] Y X Fu and W H Li ldquoStatistical tests of neutrality of muta-tionsrdquo Genetics vol 133 no 3 pp 693ndash709 1993

[47] Y X Fu ldquoStatistical tests of neutrality of mutations against pop-ulation growth hitchhiking and background selectionrdquo Genet-ics vol 147 no 2 pp 915ndash925 1997

[48] J P Huelsenbeck and F Ronquist ldquoMrBayes Bayesian inferenceof phylogenetic treesrdquo Bioinformatics vol 17 no 8 pp 754ndash7552001

[49] D Posada andK A Crandall ldquoMODELTEST testing themodelof DNA substitutionrdquo Bioinformatics vol 14 no 9 pp 817ndash8181998

[50] A J Drummond andA Rambaut ldquoBEAST bayesian evolution-ary analysis by sampling treesrdquo BMC Evolutionary Biology vol7 no 1 article 214 2007

[51] A J Drummond S Y W Ho M J Phillips and A RambautldquoRelaxed phylogenetics and dating with confidencerdquo PLoSBiology vol 4 no 5 article e88 2006

[52] T Gernhard ldquoThe conditioned reconstructed processrdquo Journalof Theoretical Biology vol 253 no 4 pp 769ndash778 2008

[53] E Delson ldquoThe oldest monkeys in Asiardquo in Proceedings ofthe International Symposium Evolution of Asian Primates p40 Freude amp Kyoto University Primate Research InstituteInuyama Aichi Japan 1996

[54] L Rook A Mottura and S Gentili ldquoFossil Macaca remainsfrom RDB quarry (villafranca drsquoasti Italy) new data and over-viewrdquo Journal of Human Evolution vol 40 no 3 pp 187ndash2022001

[55] A Lowe S Harris and P Ashton Ecological Genetics DesignAnalysis and Application Blackwell Oxford UK 2004

[56] M Bouga P C Harizanis G Kilias and S Aldiotis ldquoGeneticdivergence and phylogenetic relationships of honey bee Apismellifora (Hymenoptera Apidae) populations from Greeceand Cypnes using PCR-RFLP analysis of mtDNA segmentsrdquoBiochemical Genetics vol 36 pp 335ndash344 2005

[57] D A Hooijer ldquoQuaternary langurs and macaques from theMalay Archipelagordquo Zoologische Verhandelingen vol 55 pp 1ndash64 1962

[58] M Slatkin and R R Hudson ldquoPairwise comparisons of mito-chondrial DNA sequences in stable amp exponentially growingpopulationsrdquo Genetics vol 129 no 2 pp 555ndash562 1991

[59] N Ray M Currat and L Excoffier ldquoIntra-deme moleculardiversity in spatially expanding populationsrdquoMolecular Biologyand Evolution vol 20 no 1 pp 76ndash86 2003

[60] C M Crockett and W L Wilson The Ecological Separationof Macaca Nemestrina and M fascicularis in Sumatra TheMacaques Studies in Ecology Behavior and Evolution VanNostrand Reinhold New York NY USA 1980


[61] R W Sussman and I Tattersall ldquoDistribution abundance andputative ecological strategy ofMacaca fascicularis on the islandof Mauritius southwestern Indian Oceanrdquo Folia Primatologicavol 46 pp 28ndash43 1986

[62] M L Prentice and G H Denton ldquoThe deep-sea oxygen isotoperecord the global ice sheet system and hominid evolutionrdquoin Evolutionary History of the Robust Australopithecines F EGrine Ed pp 383ndash403Aldine deGruyterNewYorkNYUSA1988

[63] G H R von Koenigswald ldquoDie fossilen Saugetierfaunen JavasrdquoKoninklijke Nederlandse Akademie van Wetenschappen vol 38pp 188ndash198 1935

[64] G H R von Koenigswald ldquoThe relationship between the fossilmammalian faunae of Java and China with special reference toearly manrdquo Peking Natural History Bulletin vol 13 no 4 pp293ndash298 1939

[65] C Tougard ldquoBiogeography andmigration routes of large mam-mal faunas in South-East Asia during the late middle Pleis-tocene focus on the fossil and extant faunas from ThailandrdquoPalaeogeography Palaeoclimatology Palaeoecology vol 168 no3-4 pp 337ndash358 2001

[66] G G van den J Bergh P Y Sondaar and F Aziz ldquoPleistocenezoogeographical evolutions of Java (Indonesia) and glacio-eustatic sea level fluctuations a background for the presence ofHomordquo Bulletin of the Indo-Pacific Prehistory vol 14 pp 7ndash211996

[67] B Lekagul and J A McNeelyMammals of Thailand Saha KarnBhaet Bangkok Thailand 2nd edition 1988

[68] G B Corbett and J E Hill The Mammals of the IndomalayanRegion A Systematic Review Oxford University Press OxfordUK 1992

[69] D S Woodruff ldquoLocation of the Indochinese-Sundaic biogeo-graphic transition in plants and birdsrdquo Natural History Bulletinof the Siam Society vol 51 pp 97ndash108 2003

[70] P A Ashton ldquoPlant conservation in the Malaysian regionrdquo inHarmony with Nature Y S Kheong and L S Win Eds pp 86ndash93 Malay Nature Society Kuala Lumpur Malaysia 1992

[71] P W Richards The Tropical Rain Forest An Ecological StudyCambridgeUniversity Press Cambridge UK 2nd edition 1996

[72] R J Morley Origin and Evolution of Tropical Rain Forests JohnWiley amp Sons England UK 2000

[73] Y Hamada B Suryobroto S Goto and S MalaivijitnondldquoMorphological and body color variation in Thai Macacafascicularis fascicularis north and south of the Isthmus of KrardquoInternational Journal of Primatology vol 29 no 5 pp 1271ndash1294 2008

[74] L L Darga M Goodman M L Weiss et al ldquoMolecular syste-matics and clinal variation in macaquesrdquo in Isozymes IV Genet-ics and Evolution G L Markert Ed pp 797ndash812 AcademicPress New York NY USA 1975

[75] J D Holloway and R Hall SE Asian Geology and BiogeographyAn Introduction Biogeography and Geological Evolution of SEAsia Backhuys Leiden The Netherlands 1998

[76] H K Voris ldquoMaps of Pleistocene sea levels in Southeast Asiashorelines river systems and time durationsrdquo Journal of Biogeo-graphy vol 27 no 5 pp 1153ndash1167 2000

[77] E Meijaard Solving mammalian riddles a reconstruction ofthe Tertiary and Quaternary distribution of mammals and theirpalaeoenvironments in island South-East Asia [PhD thesis]Department of Anthropology and Archaeology AustralianNational University Canberra Australia 2003

[78] E Meijaard ldquoMammals of South-East Asian islands and theirlate Pleistocene environmentsrdquo Journal of Biogeography vol 30no 8 pp 1245ndash1257 2003

Submit your manuscripts athttpwwwhindawicom

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Anatomy Research International

PeptidesInternational Journal of


Hindawi Publishing Corporation httpwwwhindawicom

International Journal of

Volume 2014

Zoology


Molecular Biology International

Hindawi Publishing Corporationhttpwwwhindawicom

GenomicsInternational Journal of

Volume 2014

The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014


BioinformaticsAdvances in

Marine BiologyJournal of



Signal TransductionJournal of


BioMed Research International

Evolutionary BiologyInternational Journal of



Biochemistry Research International

ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014


Genetics Research International


Advances in

Virolog y


Nucleic AcidsJournal of

Volume 2014

Stem CellsInternational



Enzyme Research



Microbiology


Figure 1The distribution of 10 subspecies ofM fascicularis A =Mf aurea B = M f fascicularis C = M f philippinensis The isolatedisland subspecies are labeled with numbers 1 =M f umbrosa 2 =Mf lasiae 3 = M f fusca 4 = M f atriceps 5 = M f condorensis 6 =M f karimondjawae and 7 =M f tua [3]

1944) and M f umbrosa (Miller 1902) [6ndash8] Only a singlesubspecies of the long-tailed macaque is distributed in Peni-nsular Malaysia namely M f fascicularis [1] and it is themost widely distributed compared to the other subspecies InPeninsular Malaysia M f fascicularis is found on the main-land peninsula and surrounding islands such as LangkawiIsland FurthermoreM fascicularis is at the center of human-wildlife conflict in this region especially in secondary forestand palm oil plantations neighboring human settlements [29]

Previous studies have extensively examined themolecularphylogeny and biogeography ofM fascicularis using variousmolecular data such as allozymes [10] mitochondrial DNA(mtDNA) [11ndash20] and nuclear data [11 12 14] Blancher et al[15] successfully defined the continental-insular populationsof M fascicularis in Southeast Asia but whether PeninsularMalaysiarsquos M fascicularis belong to continental or insulargroups remains unknown Roos et al [21] proposed thatcolobines may have invaded Eurasia diversified into sev-eral lineages and radiated from mainland Southeast Asiadownwards to Java Sunda and Sumatra therefore it maybe possible to suggest that Peninsular Malaysiarsquos long-tailedmacaque should be classified as continental However Penin-sular Malaysia has been hypothesized to be the bridge thatfacilitated the radiation of nonhuman primates from Java tomainland Southeast Asia [22]Thus PeninsularMalaysiarsquosMfascicularis cannot simply be defined as a continental groupas in [15] because it is found in mainland Southeast Asia

In mammals mtDNA is inherited as a haploid from themother [23] This gives a bigger picture of diversity in theparticular gene pool of an organism caused by the occurrenceand accumulation of mutations in mtDNA [24] MoreovermtDNA does not undergo DNA recombination [25] All ofthese factorsmakemtDNAa very valuable tool when it comesto studying the relationships between populations However

Table 1 Details on the samples used in this study

No Sample name Taxon Locality(1) ALMFA63 M f fascicularis Malay Peninsula(2) ALMFA64 M f fascicularis Malay Peninsula(3) ALMFD16 M f fascicularis Malay Peninsula(4) ALMFD17 M f fascicularis Malay Peninsula(5) ALMFD28 M f fascicularis Malay Peninsula(6) ALMFK109 M f fascicularis Malay Peninsula(7) ALMFK110 M f fascicularis Malay Peninsula(8) ALMFK111 M f fascicularis Malay Peninsula(9) ALMFK112 M f fascicularis Malay Peninsula(10) FRMFB1 M f fascicularis Malay Peninsula(11) FRMFB2 M f fascicularis Malay Peninsula(12) FRMFB3 M f fascicularis Malay Peninsula(13) ZMW135 M f fascicularis Malay Peninsula(14) ZMW136 M f fascicularis Malay Peninsula(15) ZMW137 M f fascicularis Malay Peninsula(16) ALMFT322 M f fascicularis Malay Peninsula(17) ALMFJ204 M f fascicularis Malay Peninsula(18) ALMFJ264 M f fascicularis Malay Peninsula(19) ALMFJ195 M f fascicularis Malay Peninsula(20) ALMFR370 M f fascicularis Malay Peninsula(21) ALMFR371 M f fascicularis Malay Peninsula(22) ALMFC227 M f fascicularis Malay Peninsula(23) ALMFC228 M f fascicularis Malay Peninsula

cases of mtDNA-derived nuclear pseudogenes (Numts) havebeen reported to arise in phylogenetic studies on primates[26]The amplification ofNumts rather than targetedmtDNAwill disturb the molecular study of organisms due to theinclusion of paralogous nuclear sequences in the analysisinstead of mtDNA sequences [27 28] This study will exploitthe noncoding hypervariable region of mtDNA because thisevolves more rapidly thereby reflecting more differentiationamong closely related taxa [29 30]

Despite extensive studies on the molecular phylogeny oflong-tailed macaques the molecular data and phylogeneticposition of Peninsular Malaysiarsquos M fascicularis in relationto other countries remain unknown This may hold thekey to revealing the biogeographic and radiation history ofthis species in Southeast Asia Thus the objectives of thisstudy were to analyze the phylogeography and populationgenetics of Peninsular Malaysiarsquos M f fascicularis throughcomparison with the available data onM f fascicularis fromother countries using the D-loop region of mtDNA

2 Methodology

21 DNA Extraction Polymerase Chain Reaction (PCR) andSequencing A total of 23 fecal genetic samples of M ffascicularis were used in this study (Table 1) These wereobtained with the assistance of the Department of Wildlifeand National Parks Malaysia (PERHILITAN) All 23 sampleswere collected across mainland Peninsular Malaysia (Figure2) while with the exception of Penang Island no samples


Mauritius

ix

ix

viiviii

i

ii iii

ivvvi


N


sim024MYA

sim091MYA

sim047MYA

Peninsular Malaysia












Table 2 Continued
















3 Results











119898




















119870 119863 Fs 119863lowast

119865lowast







(104

bp)in395-bp

segm

ento

fD-lo

opgene

defin

ing65

haplotypes

andtheird

istrib

utionacrosssevenpo

pulations

ofMffascic

ularis

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

11111

11111111112

2222222223

3333333334

4444444445

5555555556

6666666667

7777777778

8888888889

9999999990

0000

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234

Hap1

CCCCGACATA

GTTACTTGCG

GACCTAAGTT

CAATCATCTA

AAGTATCCCA

CCACGCCTAA

ACCCATACCA

ACCTGATCGT

CACACGGGGC

GCAGTACCTT

TACC

1Hap2

GA

AG

TGG

GT

TG

C

1Hap3

GA

AG

TGG

GT

TG

C

1Hap4

TT

A

AGACC

G

GGA

A

A

TG

C

1Hap5

AGC

GC

T

A

T

TGG

CC

1Hap6

AT

T

A

C

1Hap7

T

AGC

TG

AT

TG

C

2Hap8

C

AC

TGG

GCT

C

TG

C

1Hap9

AC

TGG

GCT

C

TG

C

3Hap10

AC

TGG

GCT

C

TG

C

1Hap11

T

A

G

1Hap12

A

AC

TG

GCT

AC

TG

CT

1Hap13

AGC

TGG

G

C

C

TGG

C

1Hap14

A

GT

T

GC

AG

G

TGG

C

2Hap15

T

C

A

T

G

G

G

TG

C

1Hap16

A

G

T

G

G

G

TG

C

1Hap17

C

C

AGC

T

G

G

GG

TG

C

1Hap18

A

AG

T

G

G

G

TG

C

1Hap19

A

A

T

G

G

G

TG

C

1Hap20

AGC

T

T

T

G

C

4Hap21

AGC

TG

TT

A

TG

C

1Hap22

T

AGC

T

T

T

G

C

1Hap23

TT

C

ATGC

T

AT

TTCTTT

CG

C

TT

TGT

C

11

Hap24

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGT

C

2Hap25

TTT

ACA

ATG

TC

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap26

TTC

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap27

TT

C

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap28

TT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap29

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap30

TTT

ACA

ATG

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap31

TT

C

ATGC

T

AT

TTCTTTG

CG

C

TT

TGT

C

1Hap32

TTG

A

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap33

TT

C

ATGC

T

A

TTCTTT

CG

C

TT

TGT

C

11

Hap34

TTT

C

AGC

T

AT

TTCTTT

CG

C

TT

TGT

C

1Hap35

TTT

ACA

AT

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap36

TTT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap37

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

C

TA

ATGT

CT

2Hap38

TT

CA

TTTG

GT

ATT

CTTT

C

C

TT

ATGT

C

1Hap39

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGTC

C

1


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia


Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


Mauritius

ix

ix

viiviii

i

ii iii

ivvvi


N


sim024MYA

sim091MYA

sim047MYA

Peninsular Malaysia












Table 2 Continued
















3 Results











119898




















119870 119863 Fs 119863lowast

119865lowast







(104

bp)in395-bp

segm

ento

fD-lo

opgene

defin

ing65

haplotypes

andtheird

istrib

utionacrosssevenpo

pulations

ofMffascic

ularis

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

11111

11111111112

2222222223

3333333334

4444444445

5555555556

6666666667

7777777778

8888888889

9999999990

0000

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234

Hap1

CCCCGACATA

GTTACTTGCG

GACCTAAGTT

CAATCATCTA

AAGTATCCCA

CCACGCCTAA

ACCCATACCA

ACCTGATCGT

CACACGGGGC

GCAGTACCTT

TACC

1Hap2

GA

AG

TGG

GT

TG

C

1Hap3

GA

AG

TGG

GT

TG

C

1Hap4

TT

A

AGACC

G

GGA

A

A

TG

C

1Hap5

AGC

GC

T

A

T

TGG

CC

1Hap6

AT

T

A

C

1Hap7

T

AGC

TG

AT

TG

C

2Hap8

C

AC

TGG

GCT

C

TG

C

1Hap9

AC

TGG

GCT

C

TG

C

3Hap10

AC

TGG

GCT

C

TG

C

1Hap11

T

A

G

1Hap12

A

AC

TG

GCT

AC

TG

CT

1Hap13

AGC

TGG

G

C

C

TGG

C

1Hap14

A

GT

T

GC

AG

G

TGG

C

2Hap15

T

C

A

T

G

G

G

TG

C

1Hap16

A

G

T

G

G

G

TG

C

1Hap17

C

C

AGC

T

G

G

GG

TG

C

1Hap18

A

AG

T

G

G

G

TG

C

1Hap19

A

A

T

G

G

G

TG

C

1Hap20

AGC

T

T

T

G

C

4Hap21

AGC

TG

TT

A

TG

C

1Hap22

T

AGC

T

T

T

G

C

1Hap23

TT

C

ATGC

T

AT

TTCTTT

CG

C

TT

TGT

C

11

Hap24

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGT

C

2Hap25

TTT

ACA

ATG

TC

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap26

TTC

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap27

TT

C

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap28

TT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap29

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap30

TTT

ACA

ATG

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap31

TT

C

ATGC

T

AT

TTCTTTG

CG

C

TT

TGT

C

1Hap32

TTG

A

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap33

TT

C

ATGC

T

A

TTCTTT

CG

C

TT

TGT

C

11

Hap34

TTT

C

AGC

T

AT

TTCTTT

CG

C

TT

TGT

C

1Hap35

TTT

ACA

AT

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap36

TTT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap37

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

C

TA

ATGT

CT

2Hap38

TT

CA

TTTG

GT

ATT

CTTT

C

C

TT

ATGT

C

1Hap39

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGTC

C

1


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia


Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology






Table 2 Continued
















3 Results











119898




















119870 119863 Fs 119863lowast

119865lowast







(104

bp)in395-bp

segm

ento

fD-lo

opgene

defin

ing65

haplotypes

andtheird

istrib

utionacrosssevenpo

pulations

ofMffascic

ularis

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

11111

11111111112

2222222223

3333333334

4444444445

5555555556

6666666667

7777777778

8888888889

9999999990

0000

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234

Hap1

CCCCGACATA

GTTACTTGCG

GACCTAAGTT

CAATCATCTA

AAGTATCCCA

CCACGCCTAA

ACCCATACCA

ACCTGATCGT

CACACGGGGC

GCAGTACCTT

TACC

1Hap2

GA

AG

TGG

GT

TG

C

1Hap3

GA

AG

TGG

GT

TG

C

1Hap4

TT

A

AGACC

G

GGA

A

A

TG

C

1Hap5

AGC

GC

T

A

T

TGG

CC

1Hap6

AT

T

A

C

1Hap7

T

AGC

TG

AT

TG

C

2Hap8

C

AC

TGG

GCT

C

TG

C

1Hap9

AC

TGG

GCT

C

TG

C

3Hap10

AC

TGG

GCT

C

TG

C

1Hap11

T

A

G

1Hap12

A

AC

TG

GCT

AC

TG

CT

1Hap13

AGC

TGG

G

C

C

TGG

C

1Hap14

A

GT

T

GC

AG

G

TGG

C

2Hap15

T

C

A

T

G

G

G

TG

C

1Hap16

A

G

T

G

G

G

TG

C

1Hap17

C

C

AGC

T

G

G

GG

TG

C

1Hap18

A

AG

T

G

G

G

TG

C

1Hap19

A

A

T

G

G

G

TG

C

1Hap20

AGC

T

T

T

G

C

4Hap21

AGC

TG

TT

A

TG

C

1Hap22

T

AGC

T

T

T

G

C

1Hap23

TT

C

ATGC

T

AT

TTCTTT

CG

C

TT

TGT

C

11

Hap24

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGT

C

2Hap25

TTT

ACA

ATG

TC

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap26

TTC

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap27

TT

C

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap28

TT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap29

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap30

TTT

ACA

ATG

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap31

TT

C

ATGC

T

AT

TTCTTTG

CG

C

TT

TGT

C

1Hap32

TTG

A

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap33

TT

C

ATGC

T

A

TTCTTT

CG

C

TT

TGT

C

11

Hap34

TTT

C

AGC

T

AT

TTCTTT

CG

C

TT

TGT

C

1Hap35

TTT

ACA

AT

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap36

TTT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap37

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

C

TA

ATGT

CT

2Hap38

TT

CA

TTTG

GT

ATT

CTTT

C

C

TT

ATGT

C

1Hap39

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGTC

C

1


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia


Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology














3 Results











119898




















119870 119863 Fs 119863lowast

119865lowast







(104

bp)in395-bp

segm

ento

fD-lo

opgene

defin

ing65

haplotypes

andtheird

istrib

utionacrosssevenpo

pulations

ofMffascic

ularis

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

11111

11111111112

2222222223

3333333334

4444444445

5555555556

6666666667

7777777778

8888888889

9999999990

0000

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234

Hap1

CCCCGACATA

GTTACTTGCG

GACCTAAGTT

CAATCATCTA

AAGTATCCCA

CCACGCCTAA

ACCCATACCA

ACCTGATCGT

CACACGGGGC

GCAGTACCTT

TACC

1Hap2

GA

AG

TGG

GT

TG

C

1Hap3

GA

AG

TGG

GT

TG

C

1Hap4

TT

A

AGACC

G

GGA

A

A

TG

C

1Hap5

AGC

GC

T

A

T

TGG

CC

1Hap6

AT

T

A

C

1Hap7

T

AGC

TG

AT

TG

C

2Hap8

C

AC

TGG

GCT

C

TG

C

1Hap9

AC

TGG

GCT

C

TG

C

3Hap10

AC

TGG

GCT

C

TG

C

1Hap11

T

A

G

1Hap12

A

AC

TG

GCT

AC

TG

CT

1Hap13

AGC

TGG

G

C

C

TGG

C

1Hap14

A

GT

T

GC

AG

G

TGG

C

2Hap15

T

C

A

T

G

G

G

TG

C

1Hap16

A

G

T

G

G

G

TG

C

1Hap17

C

C

AGC

T

G

G

GG

TG

C

1Hap18

A

AG

T

G

G

G

TG

C

1Hap19

A

A

T

G

G

G

TG

C

1Hap20

AGC

T

T

T

G

C

4Hap21

AGC

TG

TT

A

TG

C

1Hap22

T

AGC

T

T

T

G

C

1Hap23

TT

C

ATGC

T

AT

TTCTTT

CG

C

TT

TGT

C

11

Hap24

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGT

C

2Hap25

TTT

ACA

ATG

TC

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap26

TTC

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap27

TT

C

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap28

TT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap29

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap30

TTT

ACA

ATG

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap31

TT

C

ATGC

T

AT

TTCTTTG

CG

C

TT

TGT

C

1Hap32

TTG

A

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap33

TT

C

ATGC

T

A

TTCTTT

CG

C

TT

TGT

C

11

Hap34

TTT

C

AGC

T

AT

TTCTTT

CG

C

TT

TGT

C

1Hap35

TTT

ACA

AT

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap36

TTT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap37

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

C

TA

ATGT

CT

2Hap38

TT

CA

TTTG

GT

ATT

CTTT

C

C

TT

ATGT

C

1Hap39

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGTC

C

1


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia


Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology








119898




















119870 119863 Fs 119863lowast

119865lowast







(104

bp)in395-bp

segm

ento

fD-lo

opgene

defin

ing65

haplotypes

andtheird

istrib

utionacrosssevenpo

pulations

ofMffascic

ularis

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

11111

11111111112

2222222223

3333333334

4444444445

5555555556

6666666667

7777777778

8888888889

9999999990

0000

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234

Hap1

CCCCGACATA

GTTACTTGCG

GACCTAAGTT

CAATCATCTA

AAGTATCCCA

CCACGCCTAA

ACCCATACCA

ACCTGATCGT

CACACGGGGC

GCAGTACCTT

TACC

1Hap2

GA

AG

TGG

GT

TG

C

1Hap3

GA

AG

TGG

GT

TG

C

1Hap4

TT

A

AGACC

G

GGA

A

A

TG

C

1Hap5

AGC

GC

T

A

T

TGG

CC

1Hap6

AT

T

A

C

1Hap7

T

AGC

TG

AT

TG

C

2Hap8

C

AC

TGG

GCT

C

TG

C

1Hap9

AC

TGG

GCT

C

TG

C

3Hap10

AC

TGG

GCT

C

TG

C

1Hap11

T

A

G

1Hap12

A

AC

TG

GCT

AC

TG

CT

1Hap13

AGC

TGG

G

C

C

TGG

C

1Hap14

A

GT

T

GC

AG

G

TGG

C

2Hap15

T

C

A

T

G

G

G

TG

C

1Hap16

A

G

T

G

G

G

TG

C

1Hap17

C

C

AGC

T

G

G

GG

TG

C

1Hap18

A

AG

T

G

G

G

TG

C

1Hap19

A

A

T

G

G

G

TG

C

1Hap20

AGC

T

T

T

G

C

4Hap21

AGC

TG

TT

A

TG

C

1Hap22

T

AGC

T

T

T

G

C

1Hap23

TT

C

ATGC

T

AT

TTCTTT

CG

C

TT

TGT

C

11

Hap24

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGT

C

2Hap25

TTT

ACA

ATG

TC

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap26

TTC

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap27

TT

C

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap28

TT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap29

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap30

TTT

ACA

ATG

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap31

TT

C

ATGC

T

AT

TTCTTTG

CG

C

TT

TGT

C

1Hap32

TTG

A

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap33

TT

C

ATGC

T

A

TTCTTT

CG

C

TT

TGT

C

11

Hap34

TTT

C

AGC

T

AT

TTCTTT

CG

C

TT

TGT

C

1Hap35

TTT

ACA

AT

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap36

TTT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap37

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

C

TA

ATGT

CT

2Hap38

TT

CA

TTTG

GT

ATT

CTTT

C

C

TT

ATGT

C

1Hap39

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGTC

C

1


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia


Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology








119870 119863 Fs 119863lowast

119865lowast







(104

bp)in395-bp

segm

ento

fD-lo

opgene

defin

ing65

haplotypes

andtheird

istrib

utionacrosssevenpo

pulations

ofMffascic

ularis

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

11111

11111111112

2222222223

3333333334

4444444445

5555555556

6666666667

7777777778

8888888889

9999999990

0000

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234

Hap1

CCCCGACATA

GTTACTTGCG

GACCTAAGTT

CAATCATCTA

AAGTATCCCA

CCACGCCTAA

ACCCATACCA

ACCTGATCGT

CACACGGGGC

GCAGTACCTT

TACC

1Hap2

GA

AG

TGG

GT

TG

C

1Hap3

GA

AG

TGG

GT

TG

C

1Hap4

TT

A

AGACC

G

GGA

A

A

TG

C

1Hap5

AGC

GC

T

A

T

TGG

CC

1Hap6

AT

T

A

C

1Hap7

T

AGC

TG

AT

TG

C

2Hap8

C

AC

TGG

GCT

C

TG

C

1Hap9

AC

TGG

GCT

C

TG

C

3Hap10

AC

TGG

GCT

C

TG

C

1Hap11

T

A

G

1Hap12

A

AC

TG

GCT

AC

TG

CT

1Hap13

AGC

TGG

G

C

C

TGG

C

1Hap14

A

GT

T

GC

AG

G

TGG

C

2Hap15

T

C

A

T

G

G

G

TG

C

1Hap16

A

G

T

G

G

G

TG

C

1Hap17

C

C

AGC

T

G

G

GG

TG

C

1Hap18

A

AG

T

G

G

G

TG

C

1Hap19

A

A

T

G

G

G

TG

C

1Hap20

AGC

T

T

T

G

C

4Hap21

AGC

TG

TT

A

TG

C

1Hap22

T

AGC

T

T

T

G

C

1Hap23

TT

C

ATGC

T

AT

TTCTTT

CG

C

TT

TGT

C

11

Hap24

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGT

C

2Hap25

TTT

ACA

ATG

TC

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap26

TTC

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap27

TT

C

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap28

TT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap29

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap30

TTT

ACA

ATG

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap31

TT

C

ATGC

T

AT

TTCTTTG

CG

C

TT

TGT

C

1Hap32

TTG

A

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap33

TT

C

ATGC

T

A

TTCTTT

CG

C

TT

TGT

C

11

Hap34

TTT

C

AGC

T

AT

TTCTTT

CG

C

TT

TGT

C

1Hap35

TTT

ACA

AT

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap36

TTT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap37

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

C

TA

ATGT

CT

2Hap38

TT

CA

TTTG

GT

ATT

CTTT

C

C

TT

ATGT

C

1Hap39

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGTC

C

1


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia


Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology



(104

bp)in395-bp

segm

ento

fD-lo

opgene

defin

ing65

haplotypes

andtheird

istrib

utionacrosssevenpo

pulations

ofMffascic

ularis

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

11111

11111111112

2222222223

3333333334

4444444445

5555555556

6666666667

7777777778

8888888889

9999999990

0000

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234567890

1234

Hap1

CCCCGACATA

GTTACTTGCG

GACCTAAGTT

CAATCATCTA

AAGTATCCCA

CCACGCCTAA

ACCCATACCA

ACCTGATCGT

CACACGGGGC

GCAGTACCTT

TACC

1Hap2

GA

AG

TGG

GT

TG

C

1Hap3

GA

AG

TGG

GT

TG

C

1Hap4

TT

A

AGACC

G

GGA

A

A

TG

C

1Hap5

AGC

GC

T

A

T

TGG

CC

1Hap6

AT

T

A

C

1Hap7

T

AGC

TG

AT

TG

C

2Hap8

C

AC

TGG

GCT

C

TG

C

1Hap9

AC

TGG

GCT

C

TG

C

3Hap10

AC

TGG

GCT

C

TG

C

1Hap11

T

A

G

1Hap12

A

AC

TG

GCT

AC

TG

CT

1Hap13

AGC

TGG

G

C

C

TGG

C

1Hap14

A

GT

T

GC

AG

G

TGG

C

2Hap15

T

C

A

T

G

G

G

TG

C

1Hap16

A

G

T

G

G

G

TG

C

1Hap17

C

C

AGC

T

G

G

GG

TG

C

1Hap18

A

AG

T

G

G

G

TG

C

1Hap19

A

A

T

G

G

G

TG

C

1Hap20

AGC

T

T

T

G

C

4Hap21

AGC

TG

TT

A

TG

C

1Hap22

T

AGC

T

T

T

G

C

1Hap23

TT

C

ATGC

T

AT

TTCTTT

CG

C

TT

TGT

C

11

Hap24

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGT

C

2Hap25

TTT

ACA

ATG

TC

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap26

TTC

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap27

TT

C

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap28

TT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap29

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TT

TGT

C

11

Hap30

TTT

ACA

ATG

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap31

TT

C

ATGC

T

AT

TTCTTTG

CG

C

TT

TGT

C

1Hap32

TTG

A

AG

TTC

GATG

TTT

CG

C

T

TGT

C

1Hap33

TT

C

ATGC

T

A

TTCTTT

CG

C

TT

TGT

C

11

Hap34

TTT

C

AGC

T

AT

TTCTTT

CG

C

TT

TGT

C

1Hap35

TTT

ACA

AT

T

ATT

TCTTT

C

GCC

TT

TGT

C

1Hap36

TTT

C

ATGC

T

AT

TTCTT

CG

C

TT

TGT

C

1Hap37

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

C

TA

ATGT

CT

2Hap38

TT

CA

TTTG

GT

ATT

CTTT

C

C

TT

ATGT

C

1Hap39

TTT

ACA

ATG

T

ATT

TCTTT

CG

GCC

TT

TGTC

C

1


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia


Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


Table7Con

tinued

Haplotype

Locality

Nucleotide

Positions

12

34

56

7

Hap40

TT

CA

TTG

GT

ATT

CTTT

C

C

TT

TGT

C

1Hap41

TTTC

A

ATGAC

TTC

GATG

TTTC

CG

GC

TA

ATGT

CT

1Hap42

TT

C

ATGC

T

ACT

TTCTTT

CG

C

TT

TGT

C

1Hap43

TTT

ACA

ATCG

TG

ATT

TCTTT

CG

GCC

TT

TGT

C

1Hap44

TT

C

ATTGC

GT

ATT

TCTT

TC

C

TT

TGT

C

1Hap45

TT

CC

ATGC

T

GAT

TTCTTT

CG

C

TTA

TGT

C

1Hap46

TT

C

ATGC

T

A

TTCTTT

CG

CA

TT

TGT

C

1Hap47

TTC

A

AG

TTC

GATG

TGTT

CG

C

T

TGT

C

5Hap48

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

8Hap49

TTT

ACTCA

ATG

TC

ATT

TCTATG

CTTG

C

T

TT

C

1Hap50

TTT

ATCA

ATG

TC

ATT

TCTATG

CTG

C

T

TT

C

1Hap51

TTT

ATCA

ATG

TCG

ATT

TCTATG

CTG

C

T

TT

C

2Hap52

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

TGAG

TTG

CA

1Hap53

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TGTG

CA

1Hap54

TTT

ATCA

ATG

TC

AC

TCTATC

CT

C

T

TTG

CA

1Hap55

TTTC

ATCA

ATG

TC

ATT

TCTTG

CTG

C

T

TT

C

3Hap56

TTT

A

ATG

TCC

ATT

TCTATG

CTG

C

T

TT

C

5Hap57

TTT

A

ATG

TCC

ATT

TCTATT

CTG

CAAC

TTTAA

TT

C

1Hap58

TTT

A

ATG

TCC

ATT

TCTAT

CTG

TTCACTAC

TTA

TTTT

C

1Hap59

TTT

ACTCA

ATG

CTC

ACTT

TCA

TCTG

C

T

TT

CT

1Hap60

TTC

ATC

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap61

TTC

ATCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap62

TT

AGTCA

AG

TCC

ATT

TCTATG

CTG

C

T

TT

C

1Hap63

TTT

ATA

ATG

CTC

ATT

CTATG

CTT

C

T

TT

C

2Hap64

TTC

ATC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1Hap65

TTC

AC

ATG

TCC

ATT

CTATG

CTG

C

T

TT

C

1lowastLo

calityinform

ation

1mdashIndo

nesia


Philipp

ines4mdashCa

mbo

dia5mdash

Vietnam6mdashTh

ailand

7mdashMalaysia


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


H 65

H 64

H 60

H 61

H 49

H 48H 59

H 58

H 57

H 62H 50

H 32

H 26

H 47 H 43H 35

H 30H 39

H 24H 25

H 38

H 44

H 40

H 42H 36

H 28H 23

H 31H 33H 27H 46 H 45

H 12

H 3

H 8

H 9

H 21

H 7

H 22

H 20

H 11

H 10

H 1 H 13

H 5

H 6

H 15 H 2

H 18

H 16

H 17 H 19

H 14

H 41

H 37

H 29

H 4

H 51

H 63

H 56

H 54

H 53

H 52






4 Discussion



0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


0

100

200

300

400

500

600

1 3 5 7 9 11 13 15 17 19 21 23 25 27 29

Freq

uenc

y

Pairwise difference



(a)

0

20

40

60

80

100

120

140

160

1 3 5 7 9 11 13 15 17 19 21 23

Freq

uenc

y

Pairwise difference



(b)









JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


JX113356 P Pinang





ALMFK110 Malaysia7

AB281360 Sumatra


53

6786

63

75

62

7780

99

82

99

99

AB281361 Kalimantan

AB281365 China



AB542869 Vietnam


55

8863

9975

77

6267

96

66

76 69

60

58

97

78

60

9970

65

92






AB261926 Indonesia


81

001

9485

53

99

8886

61

8050

90







AB542873 Vietnam





AB542884 Indonesia







AB542870 Vietnam





KF793835 Lombok

ALMFJ264 Malaysia18





AB542867 Vietnam



3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


3399

56

99

84

69

80

30

4473

40

98

85

41

57



AB542867 Vietnam


AB281364 BanTaPoy

AB542871 Vietnam


AB281365 China



76

32

30

9936

34

93

34

70

97

67

77

9834

74

75

73

75

7148

91

54

80

92

30

4383

45

4377 33

63

42 99

91

85 83







AB542872 Vietnam


AB281367 Mauritius


JX113353 P Pinang



03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


03309 MYA

09989

09169




100

100

01945 02681MYA

05587MYA 03103

MYA

100 100 02411MYA

002

09916 04581 MYA

03108 MYA

03695MYA





0469MYA

171MYA

0909MYA












5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology











5 Conclusion






Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology





Acknowledgments


References
























































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology


































































Volume 2014

Zoology





Volume 2014


















Advances in

Virolog y



Volume 2014




Enzyme Research



Microbiology

Continental Monophyly and Molecular Divergence of Peninsular Malaysia’s Macaca fascicularis...

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Transcript of Continental Monophyly and Molecular Divergence of Peninsular Malaysia’s Macaca fascicularis...