Post on 01-Mar-2023
Maglio: Dynastic Haplotypes
Identifying Y-Chromosome Dynastic Haplotypes: The High Kings of Ireland Revisited Michael R. Maglio
Abstract
The use of median-joining network analysis to illustrate patrilineal clusters and the
selection of low mutation rate microsatellites to create a tribal haplotype provide a novel
approach for identifying dynastic relationships. Sixty-seven marker short tandem repeat
(STR) genetic analysis of Y-chromosomes reveals multiple unnoted modal haplotypes
showing a significant association with surnames claimed to have descended from the High
Kings of Ireland. This suggests that such phylogenetic prevalence is a biological record
and supports the reliability of early genealogies. This approach demonstrates genetic
genealogy building blocks and repeatable processes for practitioners.
Introduction
The septs of Ireland provide us an
opportunity to develop genetic genealogy
techniques and processes. Irish surnames are
typically patronymic. The surnames
generally take the form of Mac Cárthaigh
(McCarthy), meaning son of Cárthaigh or Ui
Néill (O’Neill), meaning grandson /
descendant of Néill. Irish septs, while not as
formal as Scottish clans, serve as a collective
of related families with shared ancestry and
patronymic surnames. Multiple septs then
belong to larger dynasties such as the
Eóganachta and the Dál gCais.
If septs are patrilineal, then yDNA
haplotypes should be consistent across sept
surnames. Research on the Uí Néill
haplotype started with a geographical
selection and then a subsequent reduction by
sept surnames (Moore et al 2006). Consistent
seventeen-marker STR haplotypes were found
across the sept. Considering that seventeen-
markers have a high probability of haplotype
convergence, this paper will revisit the Uí
Néill data at a higher STR marker level of 67
microsatellites.
Contrary to the Uí Néill paper, a subsequent
paper on Irish patrilineal kinship (McEvoy et
al 2008), found no genetic affinity among
septs. In addition to the Uí Néill dynasty, this
paper will also examine the Eóganachta, Dál
gCais and Connachta dynasties.
Two genetic genealogy techniques will be
demonstrated and their results compared to
determine the validity of the Irish dynastic
haplotypes. The first method will use
median-joining network analysis. This is not
new to genetics. Its use with 67 STR markers
will identify patrilineal clusters to within a
TMRCA of 390 years. Median-joining
network analysis with 17 or fewer markers
has been standard in the field, achieving a
TMRCA of only 2,200 years. It is not
surprising that there has been conflicting
results from previous papers.
The second method takes advantage of
“slow” mutating STR markers (Zhivotovsky
2004). Each microsatellite has its own
mutation rate (Chandler 2006) and they may
have different mutation rates per haplotype.
By selecting the 15 “slowest” markers with an
average mutation rate of 0.00024, a virtual
tribal haplotype is created that would be
stable within the last 2,000 years (90%
probability of 80 generations). This is an
order of magnitude lower than the average
Maglio: Dynastic Haplotypes
rate of 0.0029 used as a constant in typical
TMRCA calculations.
The “tribal” markers isolated are DYS426,
DYS388, DYS392, DYS455, DYS454, DYS578,
DYS590, DYS641, DYS472, DYS594, DYS436,
DYS490, DYS450 and DYS640.
Each technique will illustrate the
identification of a dynastic haplotype and the
combined results reinforce the conclusions.
Methods
For each target sept, affiliated surnames are
identified. In the case of Uí Néill, the
following surnames and associated yDNA
STR records were accessed from Family Tree
DNA projects: O’Neill, Gallagher, Doherty
and O’Donnell. The selection includes 600
records and 5 common European haplogroups
(Y Chromosome Consortium 2002).
Each group of records is anonymized to
protect the privacy of the individuals.
Duplicate haplotypes within a surname are
removed to prevent skewing the results. Any
duplicates that remain will be across
surnames and add value to the results.
The dataset is processes through Dean
McGee’s Y-Utility: Y-DNA Comparison
tool at mymcgee.com/tools/yutility.html to
produce a ych format file for the Fluxus
Software Network application. A median-
joining network analysis is calculated for the
dataset (Bandelt et al 1999).
The resulting median-joining diagram has
clusters of tightly related individuals. The
more coherent the cluster, the closer the
relationship. For the purpose of this
technique, the optimum cluster will be highly
coherent and contain an example of every
surname in the dataset. Other clusters will
typically only contain a single surname.
Figure 1a shows the complete median-
joining network analysis for the Uí Néill
surnames including outliers. The outliers are
from haplogroups G, I, J and R1a. The main
cluster is haplogroup R1b. To identify the
core clusters, the application has the ability to
display only the torso of the network. Figure
1b shows four distinct clusters.
Figure 1 Median-joining network of yDNA
from dataset with Uí Néill dynasty surnames (n = 303).
a) The outlier nodes are haplogroup J and R1a. b) Torso
only view, showing the central clusters.
Each cluster is examined for surname
content, number of nodes and potential SNP
identification. Figure 2 is an enhanced view
of the four distinct clusters. The three clusters
on the right have only O’Neill surnames. The
cluster at the far right is predominantly R-
L159 and the cluster at the lower right has R-
P311/R-L151 nodes.
Figure 2 View of the Uí Néill network torso
showing four distinct clusters. The three groups on the
right are O’Neill only clusters.
The cluster at the left contains all of the Uí
Néill surnames, has the majority of nodes and
is SNP R-M222, which is consistent with
Maglio: Dynastic Haplotypes
earlier studies. Figure 3 gives a detailed view
of the Uí Néill surname cluster.
Figure 3 Main Uí Néill cluster showing all
surnames. The O’Neill records are marked green.
Figure 4 demonstrates that a random
sampling of surnames will not resolve into a
coherent cluster of affiliated surnames.
Figure 4 Median-joining network of yDNA
sampled from three random Irish surnames (n = 340)
Duffy, Kelly and McCormick. The network resolves
into 10 distinct clusters with essentially no
commonality among the surnames.
The second technique involves examining
only the “slow” mutating markers for the Uí
Néill dataset (n=303). To manipulate the
“tribal” haplotype of 15 microsatellites faster
the resulting values are concatenated into a
string – ex. 12121411119168108101212811.
The “tribal” haplotypes are summarized per
surname and plotted to illustrate majority and
affinity.
Figure 5 Uí Néill dynastic haplotype. The
haplotypes from the Uí Néill dataset (n=303) converted
into 15 marker “tribal” haplotypes and summarized.
The Uí Néill dataset resolved into 37 unique
“tribal” haplotypes. Figure 5 shows that
haplotype 12121411119168108101212811 is
the most dominant across the Uí Néill
surnames. As with the median-joining
network analysis, this “tribal” haplotype is
consistent with SNP R-M222. As a triple
check, Figure 6 shows a traditional
phylogenetic tree. The same genetic cohorts
cluster together.
Figure 6 Uí Néill dataset phylogenetic tree.
Red bounding box designates the R-M222 cluster.
Maglio: Dynastic Haplotypes
The full 67 marker Uí Néill haplotype can be
found in the appendix.
Haplotype data from this analysis is
available in Table 1, Table 2, Table 3 and
Table 4.
Discussion
The work on the Uí Néill dataset confirms
the work by Moore et al and takes it to a
higher level of accuracy. The challenge is to
repeat the process with other Irish septs. For
this exercise the following surnames are used:
Uí Briúin (O’Brien) of the Dál gCais, Mac
Cárthaigh (McCarthy) of the Eóganachta and
Ua Conchobhair (O’Connor) of the
Connachta.
For the Uí Briúin dataset, the following
surnames and associated yDNA STR records
were accessed from Family Tree DNA
projects: O’Brien, Hogan, Kennedy and
McMahon. The selection includes 615
records and 5 common European
haplogroups.
Figure 7 shows the complete median-
joining network analysis for the Uí Briúin
surnames including outliers. The outliers are
from haplogroups E, G, I, J and R1a. The
main cluster is haplogroup R1b.
Figure 7 Median-joining network of yDNA
from dataset with Uí Briúin dynasty surnames (n =
330).
Figure 8 is an enhanced view of two distinct
clusters and multiple indistinct clusters. The
cluster on the middle left has only McMahon
surnames and is R-DF21.
Figure 8 View of the Uí Briúin network torso
showing two distinct clusters and multiple indistinct
clusters.
The lower cluster has all of the Uí Briúin
surnames, has the majority of nodes and is
SNP R-L226. This is consistent with
previous work (Wright 2009). Figure 9 gives
a detailed view of the Uí Briúin surname
cluster.
Figure 9 Main Uí Briúin cluster showing all
tested surnames.
Maglio: Dynastic Haplotypes
The “tribal” haplotypes are summarized per
surname and plotted to illustrate majority and
affinity.
Figure 10 Uí Briúin dynastic haplotype. The
haplotypes from the Uí Briúin dataset (n=330)
converted into 15 marker “tribal” haplotypes and
summarized.
The Uí Briúin dataset resolved into 46
unique “tribal” haplotypes. Figure 10 shows
that haplotype 12121311119168108101212811
is the most dominant across the Uí Briúin
surnames. As with the median-joining
network analysis, this “tribal” haplotype is
consistent with SNP R-L226. The full 67
marker Uí Briúin haplotype can be found in
the appendix.
The Mac Cárthaigh dataset has the
following surnames and associated yDNA
STR records as accessed from Family Tree
DNA projects: McCarthy, Callaghan,
Donovan and Sullivan. The selection
includes 319 records and 4 common European
haplogroups.
Figure 11 shows the complete median-
joining network analysis for the Mac
Cárthaigh surnames including outliers. The
outliers are from haplogroups E, I and J. The
main cluster is haplogroup R1b.
Figure 11 Median-joining network of yDNA
from dataset with Mac Cárthaigh dynasty surnames (n
= 207).
Figure 12 is an enhanced view of five
distinct clusters.
Figure 12 View of the Mac Cárthaigh network
torso showing five distinct clusters.
The center cluster has all of the Mac
Cárthaigh surnames, the majority of nodes
and is SNP R-CTS4466. This is consistent
with previous work (McCarthy 2013). Figure
13 gives a detailed view of the Mac Cárthaigh
surname cluster.
Maglio: Dynastic Haplotypes
Figure 13 Main Mac Cárthaigh cluster showing
all tested surnames.
The “tribal” haplotypes are summarized per
surname and plotted to illustrate majority and
affinity.
Figure 14 Mac Cárthaigh dynastic haplotype.
The haplotypes from the Mac Cárthaigh dataset
(n=207) converted into 15 marker “tribal” haplotypes
and summarized.
The Mac Cárthaigh dataset resolved into 38
unique “tribal” haplotypes. Figure 14 shows
that haplotype 12121311119168108101212811
is the most dominant across the Mac
Cárthaigh surnames. As with the median-
joining network analysis, this “tribal”
haplotype is consistent with SNP R-CTS4466.
The full 67 marker Mac Cárthaigh haplotype
can be found in the appendix.
The final dataset, Ua Conchobhair, has the
following surnames and associated yDNA
STR records as accessed from Family Tree
DNA projects: O’Connor, McManus, Reilly
and Rourke. The selection includes 352
records and 5 common European
haplogroups.
Figure 15 shows the complete median-
joining network analysis for the Ua
Conchobhair surnames including outliers.
The outliers are from haplogroups E, I and
R1a. The main cluster is haplogroup R1b.
Figure 15 Median-joining network of yDNA
from dataset with Ua Conchobhair dynasty surnames (n
= 145).
In Figure 16, the cluster on the right is a
McManus only group with a SNP of R-L513.
Figure 16 View of the Ua Conchobhair network
torso showing two distinct clusters.
The left cluster has all of the Ua Conchobhair
surnames, the majority of nodes and is SNP
Maglio: Dynastic Haplotypes
R-M222. This is consistent with previous
work relating O’Connor individuals to
O’Neill (Moore 2006). Figure 17 gives a
detailed view of the Ua Conchobhair surname
cluster.
Figure 17 Main Ua Conchobhair cluster
showing all tested surnames.
The “tribal” haplotypes are summarized per
surname and plotted to illustrate majority and
affinity.
Figure 18 Ua Conchobhair dynastic haplotype.
The haplotypes from the Ua Conchobhair dataset
(n=145) converted into 15 marker “tribal” haplotypes
and summarized.
The Ua Conchobhair dataset resolved into
22 unique “tribal” haplotypes. Figure 18
shows that haplotypes
12121311119168108101212811 and
12121411119168108101212811 are equally
dominant across the Ua Conchobhair
surnames. Tribal haplotype
12121411119168108101212811 is associated
with the central cluster from the network
analysis (consistent with SNP R-M222) and
haplotype 12121311119168108101212811 is
loosely clustered (not closely related). The
full 67 marker Ua Conchobhair haplotype can
be found in the appendix.
Conclusions
While median-joining network analysis is
not new, there are advantages to using the
technique with 67 STR markers. The same
four Uí Néill clusters found in Figure 2 are
absent when the network is analyzed at 25
markers (Fig. 19). At 67 markers the network
clusters coalesce into discernable SNP
families.
Figure 19 Using only 25 STR markers, the Uí
Néill network collapses to a single cluster.
The quantity of “tribal” markers (15) was
selected to obtain stable haplotypes with an
age of 2,000 years. Three out of the four
cases presented obvious results. In the Ua
Conchobhair case, the network analysis was
needed to differentiate the haplotypes. The
Uí Briúin and Mac Cárthaigh data presented
the same “tribal” haplotype, yet they have two
different SNPs. The 15 markers selected
Maglio: Dynastic Haplotypes
were not unique to the SNP level. The
“tribal” haplotypes did act as a first pass filter
to identify the primary families within the
larger population.
The genealogies of the Kings of Ireland are
semi-mythological. These techniques validate
the most likely descendants of these kings.
Short of opening a crypt and exhuming
remains, genetic analysis to reconstruct the
DNA of historic individuals is necessary. By
identifying the 67 marker modal haplotypes
and SNPs of the Kings, other genealogical
comparisons can be established.
Niall Noígíallach was High King of Ireland
around 378 CE and founder of the Uí Néill
dynasty. Historically, his half-brother Brión,
was one of the founders on the Connachta
dynasty and an ancestor of the last High King
of Ireland, Ruaidrí Ua Conchobair. If their
genealogies are correct, the evidence is in
their DNA. The data shows that Uí Néill and
Ua Conchobair share the same SNP, R-M222.
While the modal haplotype for each is
derived, it serves as an approximation. The
Uí Néill and Ua Conchobair modals are a 6-
step match at 67 markers. There is a 99%
probability of a relationship not further than
1,260 years ago. That time period is more
recent than Niall and Brión. TMRCA
calculations are notoriously difficult. A more
recent relationship is preferred over a more
distant relationship. A more distant
relationship does not provide evidence for
Niall and Brión’s relation. A more recent
relationship allows for fewer mutations per
generation and/or back mutations. The results
make a strong case for the validity of the
historic genealogy.
Brian Boru, High King of Ireland in 1002
CE, belonged to the Dál gCais dynasty and
Tadhg Mac Cárthaigh, the first King of
Desmond, belonged to the Eóganachta
dynasty. Ancient genealogies have the
Eóganachta and Dál gCais dynasties
descended from Ailill Aulom, the son-in-law
of legendary king Conn of the Hundred
Battles. The Mac Cárthaighs and Uí Briúins
do not share the same SNP (R-L226 vs. R-
CTS4466), but by descent they would share a
common R-DF13 ancestor. The Mac
Cárthaigh and Uí Briúin modals are an 11-
step match at 67 markers. There is a 99%
probability of a relationship not further than
1,920 years ago. This puts a Mac Cárthaigh-
Uí Briúin common ancestor as a
contemporary of the legendary Conn.
While the data can prove that a definite
genetic ancestor exists for the Mac Cárthaigh-
Uí Briúin septs and the Uí Néill-Ua
Conchobair septs, it is impossible to prove the
identity of that common ancestor. Genetic
genealogy techniques are invaluable for the
reconstruction of distant family trees at the
macro level.
Conflict of Interest
The author declares no conflict of interest.
Acknowledgements
I thank all of the DNA donors who have
made their results publically accessible for
review. Special thanks to Dean McGee for
making his DNA analysis website available.
Web Resources
Fluxus Engineering, http://www.fluxus-
engineering.com/sharenet.htm (for
NETWORK)
Y-Utility: Y-DNA Comparison Utility,
http://www.mymcgee.com/tools/yutility.ht
ml?mode=ftdna_mode
Maglio: Dynastic Haplotypes
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