Mitochondrial DNA history of Sri Lankan ethnic people: Their relations within the island and with the Indian subcontinental populations

Abstract

Located only a short distance off the southernmost shore of the Greater Indian subcontinent, the island of Sri Lanka has long been inhabited by various ethnic populations. Mainly comprising the Vedda, Sinhalese (Up- and Low-country) and Tamil (Sri Lankan and Indian); their history of settlements on the island and the biological relationships among them have remained obscure. It has been hypothesized that the Vedda was probably the earliest inhabitants of the area, followed by Sinhalese and Tamil from the Indian mainland. This study, in which 271 individuals, representing the Sri Lankan ethnic populations mentioned, were typed for their mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS-1) and part of hypervariable segment 2 (HVS-2), provides implications for their settlement history on the island. From the phylogenetic, principal coordinate and analysis of molecular variance results, the Vedda occupied a position separated from all other ethnic people of the island, who formed relatively close affiliations among themselves, suggesting a separate origin of the former. The haplotypes and analysis of molecular variance revealed that Vedda people's mitochondrial sequences are more related to the Sinhalese and Sri Lankan Tamils' than the Indian Tamils' sequences. MtDNA haplogroup analysis revealed that several West Eurasian haplogroups as well as Indian-specific mtDNA clades were found amongst the Sri Lankan populations. Through a comparison with the mtDNA HVS-1 and part of HVS-2 of Indian database, both Tamils and Sinhalese clusters were affiliated with Indian subcontinent populations than Vedda people who are believed to be the native population of the island of Sri Lanka.Journal of Human Genetics advance online publication, 7 November 2013; doi:10.1038/jhg.2013.112.

Full text

ORIGINAL ARTICLE
Mitochondrial DNA history of Sri Lankan ethnic
people: their relations within the island and with
the Indian subcontinental populations
Lanka Ranaweera1,3, Supannee Kaewsutthi1,3, Aung Win Tun1, Hathaichanoke Boonyarit1,
Samerchai Poolsuwan2and Patcharee Lertrit1
Located only a short distance off the southernmost shore of the Greater Indian subcontinent, the island of Sri Lanka has long
been inhabited by various ethnic populations. Mainly comprising the Vedda, Sinhalese (Up- and Low-country) and Tamil
(Sri Lankan and Indian); their history of settlements on the island and the biological relationships among them have remained
obscure. It has been hypothesized that the Vedda was probably the earliest inhabitants of the area, followed by Sinhalese and
Tamil from the Indian mainland. This study, in which 271 individuals, representing the Sri Lankan ethnic populations
mentioned, were typed for their mitochondrial DNA (mtDNA) hypervariable segment 1 (HVS-1) and part of hypervariable
segment 2 (HVS-2), provides implications for their settlement history on the island. From the phylogenetic, principal coordinate
and analysis of molecular variance results, the Vedda occupied a position separated from all other ethnic people of the island,
who formed relatively close affiliations among themselves, suggesting a separate origin of the former. The haplotypes and
analysis of molecular variance revealed that Vedda people’s mitochondrial sequences are more related to the Sinhalese and Sri
Lankan Tamils’ than the Indian Tamils’ sequences. MtDNA haplogroup analysis revealed that several West Eurasian haplogroups
as well as Indian-specific mtDNA clades were found amongst the Sri Lankan populations. Through a comparison with the
mtDNA HVS-1 and part of HVS-2 of Indian database, both Tamils and Sinhalese clusters were affiliated with Indian
subcontinent populations than Vedda people who are believed to be the native population of the island of Sri Lanka.
Journal of Human Genetics advance online publication, 7 November 2013; doi:10.1038/jhg.2013.112
Keywords: ethnic groups; genetic relationship; mtDNA; Sri Lanka
INTRODUCTION
With its close proximity to the Greater Indian subcontinent, separated
from the southern tip of the mainland only by the Palk Strait and the
Gulf of Mannar (with the width varying between 24 and 140 km), the
island of Sri Lanka, made accessible by sea from all parts of coastal
India, has long been inhabited by various ethnic people. The
mainland origins for the majority of these people have been
hypothesized, but without their specific migration and settlement
history on the island, they are yet to be fully elucidated. Of
approximately the total size of 20 million, the population of Sri
Lanka is heterogeneous on the bases of ethnicity, languages and
religious faiths.1,2
The Buddhist Sinhalese who speak Sinhala, affiliated with the
North Indian Prakit,3a branch of the Indo-European language family,
contribute to the majority on the island, accounting for 73.8% of the
total population. Their division into Up- and Low-country ethnic
counterparts was a recent phenomenon after the European
colonization, with people in the coastal provinces, formerly the
subjects under Western domination, recognized as the Low-country
Sinhalese, and those living in the inland mountainous area, ruled by
the Sinhalese kings, later known as the Up-country Sinhalese. With
their history on the island stretching back into the remote past, the Sri
Lankan Tamils who speak Tamil, a language of the Dravidian family,
and profess Hinduism, comprise 13.9% of the total population. Their
ethnic counterpart of the same religious faith, the Indian Tamils, of
probably more recent origin from the mainland, contributes 4.6% of
the island population. Muslims who mainly speak Tamil account for
7.2% of the total population. Other minorities on the island, with
each contributing less than 0.5% of the total population, comprise the
Muslim Malays whose language belonging to the Austronesian
linguistic family, the Christian who speak English, and the Vedda,
believed to be the most indigenous people on the island,4,5 whose
present dialects identified as a hybrid between older Vedda language
and Sinhala.6
1Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand and 2Faculty of Sociology and Anthropology, Thammasat University,
PraChan, Bangkok, Thailand
Correspondence: Professor Dr P Lertrit, Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
E-mail: patcharee.ler@mahidol.ac.th or lertrito@yahoo.com or patlertrit@gmail.com
3These authors contributed equally to this work.
Received 7 February 2013; revised 4 October 2013; accepted 9 October 2013
Journal of Human Genetics (2013), 1–9
&
2013 The Japan Society of Human Genetics All rights reserved 1434-5161/13
www.nature.com/jhg

Paleoclimates of Sri Lanka were made relatively stable under the
influences of Southwestern monsoons that have strengthened
since the terminal Pleistocene and early Holocene, the tropical
cyclones and the two intermonsoons.7Its climatic stability would
have favored human migrations for settlements in the area since the
distant past. Archeological records of human settlements on the island
were conventionally attributed to four consecutive periods: the
Paleolithic (125000–37 000 YBP), the Mesolithic (37 000–2900
YBP), the protohistorical (2900–2500 YBP) and the historical
(after 2500 YBP).8,9 Interestingly, the oldest skeletal remains of
anatomically modern man (Homo sapiens) reported from the South
Asian region, and dated tentatively to 37 000 YBP, were discovered
from the cave site, Fahien-lena,8on the island, with their association
with the present-day Vedda people proposed on a comparative
anatomical ground.10 With the molecular analyses provided on
genetic structure of the island populations, achievement for more
insights into the history of human settlements in the area is truly
promising.
The molecular genetic studies on Sri Lankan ethnic people have
been relatively scant so far, with only a few autosomal and Y
chromosome results accumulated in the forensic databases.11–13
This present study provides the first opportunity under which the
higher resolution mitochondrial DNA (mtDNA) genetic structure is
elucidated, based on sequencing of the hypervariable segment 1
(HVS-1) and part of hypervariable segment 2 (HVS-2), of the
majority of the Sri Lankan ethnic populations, the Vedda, Sinhalese
(Up- and Low-country) and Tamil (Sri Lankan and Indian),
providing an insight into the understanding of the history of
human settlements on the island.
MATERIALS AND METHODS
Samples collection
A total of 271 unrelated individuals belonging to five ethnic groups—Vedda
people, Up-country Sinhalese and Low-country Sinhalese, Sri Lankan Tamils
and Indian Tamils, were recruited in the study (Supplementary Table S1). The
sample collection sites are shown in Figure 1. With informed consent, 3–5 hair
follicles from each individual were collected. The study was carried out with
the approval of the Ethics Committee of the Faculty of Medicine, University of
Kelaniya, Sri Lanka. DNA was extracted using standard protocol.14
MtDNA sequence data
MtDNA HVS-1 (nt16024–nt16383) and part of HVS-2 (nt57–nt309) were
amplified using primers L15904: 50-CTAATACACCAGTCTTGTAAACCG
GAG-30and H 16417: 50-TTTCACGGAGGATGGTGGTC-30,andL16453:
50-CCGGGCCCATAACACTTGGG-30and H 545: 50-CGGGGTATGGGG
TTAGCAGC-30, respectively. The PCR products were purified and sequenced
using DNA Analyzer (model 3730XL, Applied Biosystems, Foster, CA, USA) by
Macrogen (Seoul, Republic of Korea). The sequencing data have been checked
by a 4-eye principle and the low quality data were resequenced, otherwise
excluded from the analysis. The samples to which definite haplogroup status
could not be assigned were additionally checked for positions C5178A,
T14783C and 9bp deletion (8281–8289) for haplogroup D, M and B,
respectively using PCR–RFLP method. MtDNA was amplified at positions
4476–5482 (L4476: 50-CCC CTG GCC CAA CCC GTC ATC TAC-30and
H5482:50-GGT AGG AGT AGC GTG GTA AGG GCG-30) and positions
14444–15360 (L14444: 50-TCC TCA ATA GCC ATC GCT G-30and H15360: 50-
GAT CCC GTT TCG TGC AAG-30), the PCR product was digested by
restriction enzyme AluI for the presence of C5178A (haplogroup D), and by
AseI for the presence of T14783C (haplogroup M), respectively. For 9bp
deletion, mtDNA were amplified from position 8211–8311 (L8211: 50-TCG
TCC TAG AAT TAA TTC CCC-30and H8311: 50-AAG TTC GCT TTA CAG-
30), and the size of PCR product was electrophoresed and visualized under
ultraviolet light.
Data analysis
The sequences of HVS-1 and part of HVS-2 were aligned and compared with
rCRS using ClustalW software in the BioEdit version 7.0.9 and ChromasLite
program, respectively. The haplogroup assignment was done using Haplogrep
(http://www.haplogrep.uibk.ac.at/)15 based on HVS-1 and part of HVS-2
sequences and manually checked according to the criteria of Phylotree
Build 15.16 To further justify the haplogroup classification, the mitochondrial
haplogroup was also assigned using MitoTool (http://www.mitotool.org).17 The
software package DnaSP version 5 (Universitat de Barcelona, Barcelona, Spain)
was used to calculate the number of polymorphic sites, haplotype diversity,
nucleotide diversity and average number of nucleotide differences.18 The
number of unique haplotypes for each population was evaluated based on
the calculation of the total number of haplotypes and the number of shared
haplotypes by ARLEQUIN version 3.5.1.219 (Swiss Institute of Bioinformatics,
Bern, Switzerland) using the same strategy as presented in Yao et al.20
The software program MEGA 4.0.221 was used to draw the unrooted
neighbor-joining trees of the Sri Lankan populations using net genetic
distances (dA), which are defined as dA ¼dXY – (dX þdY)/2, where dXY is
the mean pairwise difference between individuals from population X and Y,
and dX (dY) is the mean pairwise difference between individuals within
population X (or Y).22 As a tree presentation of the distance matrix might be
misread as a succession of population splits, principal component analysis
(PCA) was employed on the distance matrix. Two principal component
analyses were performed on 21 Sri Lankan groups using their respective net
genetic distances from HVS-1 and part of HVS-2 sequences and from
haplogroup distribution frequencies by means of GenAlEx6.23 In order to
compare with the Indian mainland, PCA was also performed on the Sri Lankan
groups and 34 groups (both tribes and castes) from India (Supplementary
Table S2) using their respective net genetic distances from HVS-1 sequences.
Genetic structure was investigated using analyses of molecular variance by
ARLEQUIN version 3.5.1.2 with a significance of variance components tested
with 1000 permutations.19 The Mantel test was performed to assess the
significance of the correlation between genetic and geographic distances of the
Sri Lankan populations with 1000 random permutations using GenAlEx6.23
Two Phylogenetic networks of Haplogroups R and U from five Sri Lanka
ethnic populations, and from Sri Lankan and Indian populations24,25 were
constructed using Network 4.6.1.1 (Fluxus Technology, Suffolk, UK).26
14
17
11
19 6
7
21
20
9
818
310 5
1
4
2
16
15
13
12
Vedda people
5. Pollebadda (6)
4. Henanigala (13)
3. Dambana (19)
2. Dalukana (19)
1. Rathugala (18)
Up-country sinhalese
6. Meemoure (18)
9. Thuppitiya (10)
10. Kukulapola (12)
8. Mulgama (6)
7. Bambarabadda (14)
Low-country sinhalese
13. Bandaraduwa (9)
Sri Lankan Tamils
12. Lankagama (13)
11. Thulawelliya (18)
17. Vauniya (3)
16. Trincomalee (5)
15. Batticaloa (11)
14. Jaffna (20)
Indian Tamils
21. Nanuoya (11)
20. Bandarawela (10)
19. Matale (18)
18. Balangoda (18)
Figure 1 The sample collection sites in Sri Lanka (within bracket indicates
the sample size from each location). A full color version of this figure is
available at the Journal of Human Genetics journal online.
mtDNA variation in Sri Lanka
L Ranaweera et al
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Journal of Human Genetics

RESULTS
MtDNA polymorphisms and shared haplotypes of Sri Lanka
The mtDNA HVS-1 (np. 16 024 to np. 16 383 of the rCRS) and part
of HVS-2 (np. 57 to np. 309 of the rCRS) sequences were obtained
from 271 individuals belonging to five Sri Lankan ethnic populations:
75 Vedda people, 60 Up-country Sinhalese and 40 Low-country
Sinhalese, 39 Sri Lankan Tamils and 57 Indian Tamils. The poly-
morphisms observed in the study are provided in Supplementary
Table S3. Deletions were observed at nucleotide positions 16166,
16 258, and 249 whereas insertions were encountered at 16188, 16 380
and 284.
There were a total of 147 haplotypes observed in the five Sri
Lankan populations of this study. Thirty of them were shared between
at least two populations. The Vedda population has the lowest
proportion of shared haplotypes among their subgroups (63%)
indicating their greater genetic diversity among subgroups. Sri Lankan
Tamils and Indian Tamils possessed similar shared proportion (85%)
whereas Up-country Sinhalese has a little higher number of popu-
lation specific haplotypes (73%) than Low-country Sinhalese (70%)
(Table 1). Interestingly, highest number of haplotype sharing was
found between Vedda with Up-country Sinhalese and with Low-
country Sinhalese. On the other hand, there was no haplotype sharing
between the Vedda people with any of the Tamils (Table 1).
Diversity indices
Genetic diversity within the subgroups of Sri Lankan ethnic popu-
lations was assessed by haplotype diversity (H) and nucleotide
diversity (p). The results are summarized in Supplementary Table
S4. Hranged from 0.503–1.000 and pfrom 0.006–0.019. In general,
Sinhalese (Up-country and Low-country) and Tamil (Sri Lankan and
Indian) subgroups exhibited relatively higher haplotype diversity
(0.861–1.000) than did those of the Vedda (0.503–0.965). The trend
of nucleotide diversity follows the haplotype diversity. Higher
nucleotide diversities (0.009–0.019) were observed among Sinhalese
and Tamils. Notably, lower nucleotide diversity (0.006–0.009) was
observed in two Vedda subgroups (VA-Rat and VA-Dal) than in the
rest of the Vedda subgroups (0.012–0.014).
Pattern of genetic variation as revealed by genetic distance and
phylogenetic analyses
Genetic distances among 21 subgroups of five ethnic populations of
Sri Lanka were calculated from HVS-1 and part of HVS-2 sequences
employing the Tajima-Nei method.27 The result is shown in
Supplementary Table S5. The Mantel test for correspondence between
genetic and geographic minimal distances was also performed, from
which the significant correlation between the two distance matrices
(r¼0.15; P¼0.02) was obtained; the result suggested the pattern of
genetic differentiation observed among studied populations to be at
least partly explicable in the light of the isolation-by-distance model.
An unrooted neighbor-joining tree was constructed for phylo-
genetic relationships among 21 subgroups of five ethnic populations
of Sri Lanka as illustrated in Figure 2. Another phylogenetic
construction was also performed for the five ethnic populations when
all subgroups within a population were collapsed; the result is shown
in Supplementary Figure S1.
It is quite clear from Supplementary Figure S1 that the Vedda
population was genetically separated from other Sri Lankan ethnic
populations, with genetic distance being less between them. Indian
Tamils established the closest genetic relationship with their Sri
Lankan ethnic counterparts. Up-country Sinhalese formed close
genetic affiliations with Sri Lankan Tamils and Low-country
Sinhalese.
Figure 2 illustrates more insights into the genetic relationships
among the studied populations, with the description of genetic
variation among subgroups within each ethnic population. From this
unrooted neighbor-joining tree, it was confirmed that there was a
greater genetic distance between the Vedda people and the rest of the
populations. Two Vedda subgroups (VA-Dam and VA-Hen) were
intermingled with the Sinhalese, both Up-country and Low-country,
but not with any of Tamils. The Tamils, both Sri Lankan and Indian,
clustered together. The genetic matrix in which the Tamil and
Sinhalese subgroups, that cannot be clearly separated from each
other, were observed towards one major branch of the tree, with the
majority of the Vedda people towards the other. Interestingly, some
Sinhalese groups (SU-Mul, SU-Mee and SL-Lan) were relatively closer
to Tamils than to the rest of Sinhalese subgroups.
Principal component analysis
The net genetic distances from HVS-1 and part of HVS-2 sequences
(Supplementary Table S5), and from haplogroup distribution fre-
quencies (Supplementary Table S6), among 21 subgroups of five
ethnic populations of Sri Lanka were treated as input vectors for PCA.
Figure 3 displays the PCA map constructed from haplogroup
distribution frequencies, for the first two principal components,
which together account for 82.44% of the total variance. The majority
of Vedda subgroups (except VA-Dam) were well separated from other
ethnic populations of Sri Lanka on the first PC axis. Their separation
from other ethnic populations is further extended on the second PC
axis. The majority of Sinhalese and Tamil subgroups form close
genetic proximities among themselves on both PC axes. Major
exception to this clustering is found in SU-Thu. It was evident that
Up-country Sinhalese are genetically closer to Sri Lankan Tamils. On
the other hand, Sri Lankan Tamil subgroups were closer to each other
when compared with Indian Tamils. Generally speaking, Vedda
Table 1 Haplotype sharing and matching probabilities between Sri Lankan populations
Number of shared haplotype Haplotype matching probabilitiesa
Population Sample size
Number of
haplotype
Unique
haplotype 1 (VA) 2 (SU) 3 (SL) 4 (TS) 1 (VA) 2 (SU) 3 (SL) 4 (TS)
1 Vedda (VA) 75 24 15 (63%)
2 Up-country Sinhalese (SU) 60 41 30 (73%) 6 0.890078
3 Low-country Sinhalese (SL) 40 23 16 (70%) 5 3 0.433 0.4165
4 Sri Lankan Tamils (TS) 39 33 28 (85%) 0 1 1 0 0.042752 0.064
5 Indian Tamils (TI) 57 47 40 (85%) 0 3 1 4 0 0.204225 0.08775 0.269312
aValues multiplied by 100.
mtDNA variation in Sri Lanka
L Ranaweera et al
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Journal of Human Genetics

subgroups were more dispersed on the PCA map than within any
other ethnic population, reflecting greater diversity among them. PCA
map constructed from the net genetic distances from HVS-1 and part
of HVS-2 sequences, which is in agreement with the PCA map
constructed from haplogroup distribution frequencies, is also shown
in Supplementary Figure S2.
The PCA is extended further to include various other ethnic
populations from the Indian subcontinent (Supplementary Table S2)
Figure 4. The result shown in Figure 5 accounted for 52.59% of the
total variation. All the Sinhalese and Tamil subgroups intermingle well
with the majority of the Indian subcontinental populations, forming a
large genetic matrix. However, Indian Tamils were separated from the
rest of the Sri Lankan subgroups, except SU-Bam and SL-Ban, on the
first PC axis. This is further strengthening of the hypothesis that
Indian Tamils are genetically distinct from the rest of the Sri Lankan
ethnic groups. Some Vedda groups (VA-Dal, VA-Hen and VA-Dam)
are located at the periphery of this genetic matrix, whereas others
(VA-Pol and VA-Rat) established only a remote relationship with the
matrix.
MtDNA haplogroup in Sri Lanka
Although the mitochondrial coding region contains several
phylogenetically relevant sites that are useful in assigning
haplotypes to a haplogroup, the control region is also promising
in putative haplogroup affiliation.28,29 According to the haplogroup
assignment based on HVS-1 and part of HVS-2 sequences of Sri
Lankan population using Mitotool (http://www.mitotool.org)17
and Haplogrep 1515 and then manually rechecked it
again with phylotree build 15 (http://www.phylotree.org)16
(Supplementary Table S3), the overall haplogroup analysis
indicated that almost 50% of the individuals from all the studied
populations belonged to haplogroup M lineages (including
haplogroup M, D and G) followed by about 25% of R lineages
(including haplogroup R, P and T) and 20% of U lineages.
Figure 2 Unrooted neighbor-joining (NJ) tree of the 21 Sri Lankan populations based on the net genetic distances. (Abbreviations are given in
Supplementary Table S1).
mtDNA variation in Sri Lanka
L Ranaweera et al
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Journal of Human Genetics

Other less frequent lineages were almost 4% of R0 (including
haplogroup HV and H) and almost 2% of N lineages (including N,
and W) (Table 2).
Haplogroup M was the most common haplogroup in Indian
Tamils (70.18%), which was contributed mainly by sub-haplogroups
M5a (14.03%) and M2a (12.28%). These sub-haplogroups were rarely
found in other populations. Up-country Sinhalese, Low-country
Sinhalese and Sri Lankan Tamils exhibited similar frequencies of
haplogroup M (41.67–43.59%), though they possessed different sub-
haplogroups frequencies. This might indicate that the later men-
tioned, especially Up-country Sinhalese and Low-country Sinhalese
are more closely related to each other than to Indian Tamils who have
a known migration history from India. Meanwhile, Vedda people had
the lowest frequency of haplogroup M (17.33%). It is quite asto-
nishing to see such a lower frequency of M haplogroup in the Vedda
population when compared with southern Indian tribal groups
(70–80%) as well as southern Indian caste populations (65%).30
This is probably due to the effect of genetic drift in the smaller
population of Vedda. This is supported by other observation of
reduced intrapopulation diversity among the subgroups of Vedda
people.
On the other hand, Vedda people and Low-country Sinhalese
showed relatively high frequencies of haplogroup R (45.33 and 25%,
respectively) which was contributed mainly by sub-haplogroup R30b
(38.67 and 20%). The haplogroup was less frequent in Up-country
Sinhalese, Sri Lankan Tamils and Indian Tamils. Haplogroup U was
mostly found in Vedda (29.33%) and Up-country Sinhalese (23.33%),
with highest contribution from sub-haplogroups U1a’c (12 and 5%,
respectively) and U7a (13.33 and 11.67%, respectively).
The haplogroup frequency of Vedda people from each site is shown
in Supplementary Table S7. Low frequency of M haplogroup and high
frequencies of R and U haplogroups were found to be the unique
characteristics of Vedda. However, the frequencies of these haplo-
groups varied among Vedda from different sites. Two Vedda groups
(VA-Dam and VA-Hen) posses the frequency of M haplogroup close
to that of Up-country Sinhalese, Low-country Sinhalese and Sri
Lankan Tamils, indicating the genetic admixture between these two
Vedda groups and the other three populations. The Vedda subgroups
Principal coordinates
Coord.2 (21.22%)
Coord.1 (61.22%)
VA-Dal
VA-Rat
TS-Vau
SU-Thu
VA- Pol
SL-Lan
VA- Hen
VA- Dam
SL-Thu
SU-Kuk
TS-Tri SL-Ban
TI-Nan
TI-Mat
TI-Ban
TI-Bal
SU-Mul
SU-Bam
SU-Mee
TS-Jaf
TS-Bat
Figure 3 Principal component analysis (PCA) map of the 21 Sri Lankan
subpopulations based on net genetic distances derived from haplogroup
distribution frequencies. (Abbreviations are given in Supplementary Table S1). A
full color version of this figure is available at the Journal of Human Genetics
journal online.
Figure 4 Populations of India that were used in this study. (Abbreviations are given in Supplementary Table S1 and Supplementary Table S2). A full color
version of this figure is available at the Journal of Human Genetics journal online.
mtDNA variation in Sri Lanka
L Ranaweera et al
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Journal of Human Genetics

shared haplogroup R30b/R8a1a3 at relatively high frequencies, the
characteristic not found among subgroups of other ethnic popu-
lations on the island, suggested a common shared origin of the Vedda
population. Median Joining network of HVS-1 and part of HVS-2
sequence of haplogroups R (62 individuals, 21 haplotypes) and U (52
individuals, 25 haplotypes) from five Sri Lankan populations were
constructed (Supplementary Figure S3). In general, the network was
in agreement with the mtDNA haplogroup analysis. Although posses
less frequency of both haplogroups, the haplotypes, belonging to these
haplogroups, of the other four Sri Lankan populations were more
diverse than Vedda haplotypes, which were also highly derived within
the tree. The Median Joining network incorporating data of HVS-1
and part of HVS-2 sequences of haplogroups R and U24,25 from
Indian populations was also performed (Supplementary Figure S4).
The Median Joining network map does not reveal a basal status of the
Vedda’s sequences for the genetic differentiation of haplogroups R
and U. It is more likely that these two haplogroups, found to be
particularly prevalent in the Vedda, were derived from ancestors on
the Indian subcontinent.
Three haplogroups, M2, U2i (U2a, U2b and U2c) and R5,
recognized as a package of Indian-specific mtDNA clades harboring
an equally deep coalescent age of about 50 000–70 000 years,30 were
present in the ethnic populations of Sri Lanka. All the ethnic
populations studied possess R5 with its highest frequency (10%)
observed in Up-country Sinhalese. Haplogroup U2 was found in all
the studied populations with its marked high frequency (10.25%)
observed in Sri Lankan Tamils. Interestingly, all the types of
haplogroups in Vedda people, except sub-haplogroups M36d and
M73’79, are presented in other ethnic groups as well.
There are several West Eurasian haplogroups, belonging to the
HV,W,T,U1,U5andU7lineages,foundinSriLankanethnic
populations (Table 2). The western Eurasian contribution to the Sri
Lankan maternal gene pool was about 19.94%, which is consistent
with the previous report.30 Interestingly, West Eurasian
contributions of 28.19, 25.33, 25 and 20% were detected in the
Sri Lankan Tamils, Vedda people, Up-country Sinhalese and Low-
country Sinhalese respectively, whereas only a 1.75% contribution
was evident in the Indian Tamils. This again reflected the close
genetic relationship among the two Sinhalese groups and Sri
Lankan Tamils when compared with Indian Tamils. Haplogroup
U1a and U7a were the only West Eurasian lineage observed in the
Vedda people. Haplogroup T was present in two populations; Low-
country Sinhalese (5%) and Sri Lankan Tamils (2.56%), whereas
Haplogroup W was present only in Up-country Sinhalese (3.33%).
Lower frequencies than the West Eurasean haplogroups were
observed for the East Asian haplogroups (M12 and G), which
accounted for 5.91% of the total variation.
The genetic structure of the Sri Lankan populations
Grouping of the Sri Lankan populations according to different
criterion was performed and statistically tested, using an analysis of
molecular variance, to reveal the best model representing natural
population differentiation. Beside the ethnic criteria adopted all
through this study, populations were classified into groups according
to linguistic, geographic and putative racial criterion. Results are
shown in Table 3. When populations were classified into two groups,
Vedda people probably representing earliest inhabitants of the island
and others for newcomers, this grouping gave the minimum variance
among subgroups within a population (87.85, Po0.001) and maxi-
mum variance among populations (8.15, Po0.001), representing the
best model for population differentiation. This model of population
differentiation is compatible with a deeper root of genetic divergence
between the Vedda and non-Vedda populations than between
subgroups within each population.
DISCUSSION
This study demonstrates the mtDNA genetic relationships among five
main recognized ethnic groups on the island of Sri Lanka, as well as
Principal coordinates
Coord. 2 (18.95%)
Coord. 1 (33.64%)
Figure 5 Principal component analysis (PCA) map of the 21 Sri Lankan subpopulations with Indian populations based on net genetic distances.
(Abbreviations are given in Supplementary Table S1 and Supplementary Table S2). A full color version of this figure is available at the Journal of Human
Genetics journal online.
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Table 2 Haplogroup frequency in Sri Lankan population
No. of samples (%)
Haplogroup Vedda Sinhalese Up-country Sinhalese Low-country Sri Lankan Tamils Indian Tamils Total
Haplogroup M 13 (17.33) 25 (41.67) 17 (42.5) 17 (43.59) 40 (70.18) 112 (41.33)
Ma2 (2.67) 3 (5) 2 (5) 1 (2.56) 0 (0) 8 (2.95)
M/N 0 (0) 1 (1.67) 1 (2.5) 1 (2.56) 2 (3.51) 5 (1.85)
M2 0(0) 0(0) 0(0) 0(0) 2(3.51) 2(0.74)
M2a1 0 (0) 2 (3.33) 0 (0) 1 (2.56) 6 (10.53) 9 (3.32)
M2a3a 0 (0) 0 (0) 0 (0) 0 (0) 1 (1.75) 1 (0.37)
M3 0(0) 0(0) 2(5) 1(2.56) 0(0) 3(1.11)
M3c1 2 (2.67) 0 (0) 0 (0) 0 (0) 1 (1.75) 3 (1.11)
M5a1 0(0) 0(0) 0(0) 1(2.56) 3(5.26) 4(1.48)
M5a2a2 0(0) 0(0) 0(0) 0(0) 4(7.02) 4(1.48)
M5a4 0(0) 0(0) 0(0) 0(0) 1(1.75) 1(0.37)
M6a 3 (4) 0 (0) 2 (5) 2 (5.13) 3 (5.26) 10 (3.69)
M6b 0 (0) 0 (0) 0 (0) 2 (5.13) 0 (0) 2 (0.74)
M12a1b 0 (0) 2 (3.33) 0 (0) 0 (0) 0 (0) 2 (0.74)
M18038 0(0) 0(0) 0(0) 1(2.56) 1(1.75) 2(0.74)
M18 0 (0) 0 (0) 0 (0) 0 (0) 1 (1.75) 1 (0.37)
M18a 0 (0) 0 (0) 1 (2.5) 1 (2.56) 2 (3.51) 4 (1.48)
M30 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
M30c1 0 (0) 0 (0) 0 (0) 0 (0) 4 (7.02) 4 (1.48)
M30f 0(0) 0(0) 3(7.5) 0(0) 0(0) 3(1.11)
M33a1b/M35þ199 2 (2.67) 6 (10) 3 (7.5) 0 (0) 1 (1.75) 12 (4.43)
M33a2 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
M34a 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
M35a 0 (0) 3 (5) 0 (0) 1 (2.56) 0 (0) 4 (1.48)
M35b þ16304 0 (0) 0 (0) 0 (0) 0 (0) 2 (3.51) 2 (0.74)
M36a 1 (1.33) 1 (1.67) 0 (0) 0 (0) 0 (0) 2 (0.74)
M36d 2 (2.67) 0 (0) 0 (0) 0 (0) 0 (0) 2 (0.74)
M38a 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
M41 0 (0) 0 (0) 3 (7.5) 0 (0) 0 (0) 3 (1.11)
M45 0 (0) 2 (3.33) 0 (0) 0 (0) 0 (0) 2 (0.7 4)
M52 0 (0) 1 (1.67) 0 (0) 0 (0) 0 (0) 1 (0.3 7)
M53 0 (0) 0 (0) 0 (0) 0 (0) 2 (3.51) 2 (0.74)
M65a 0(0) 3(5) 0(0) 0(0) 0(0) 3(1.11)
M65b 0(0) 0(0) 0(0) 0(0) 1(1.75) 1(0.37)
M66 0 (0) 1 (1.67) 0 (0) 1 (2.56) 3 (5.26) 5 (1.85)
M73079 1 (1.33) 0 (0) 0 (0) 0 (0) 0 (0) 1 (0.37)
Haplogroup D 2 (2.67) 1 (1.67) 0 (0) 2 (5.13) 0 (0) 5 (1.85)
D4a 2 (2.67) 1 (1.67) 0 (0) 0 (0) 0 (0) 3 (1.11)
D4j3 0 (0) 0 (0) 0 (0) 2 (5.13) 0 (0) 2 (0.74)
Haplogroup G 4 (5.33) 2 (3.33) 4 (10) 1 (2.56) 3 (5.26) 14 (5.17)
G3a102 0 (0) 2 (3.33) 3 (7.5) 1 (2.56) 3 (5.26) 9 (3.32)
G3b1 4 (5.33) 0 (0) 1 (2.5) 0 (0) 0 (0) 5 (1.85)
Haplogroup HV 0 (0) 1 (1.67) 1 (2.5) 7 (17.95) 0 (0) 9 (3.32)
H 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
H1ag1a 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
H2a2a1c 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
H5 0 (0) 1 (1.67) 0 (0) 3 (7.69) 0 (0) 4 (1.48)
HV2 0 (0) 0 (0) 1 (2.5) 0 (0) 0 (0) 1 (0.37)
HV4b 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
Haplogroup N 0 (0) 2 (3.33) 0 (0) 0 (0) 1 (1.75) 3 (1.11)
Nb0 (0) 1 (1.67) 0 (0) 0 (0) 0 (0) 1 (0.37)
N1a102 0 (0) 1 (1.67) 0 (0) 0 (0) 0 (0) 1 (0.37)
N5 0(0) 0(0) 0(0) 0(0) 1(1.75) 1(0.37)
Haplogroup R/U 0 (0) 1 (1.67) 0 (0) 0 (0) 3 (5.26) 4 (1.48)
R/U 0 (0) 0 (0) 0 (0) 0 (0) 3 (5.26) 3 (1.11)
R8/U409 0 (0) 1 (1.67) 0 (0) 0 (0) 0 (0) 1 (0.37)
Haplogroup R 34 (45.33) 10 (16.67) 10 (25) 3 (7.69) 5 (8.77) 62 (22.88)
R5a2a 0 (0) 3 (5) 0 (0) 0 (0) 1 (1.75) 4 (1.48)
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their affiliations with several ethnic people of the Greater Indian
subcontinent. All the island populations, except some subgroups of
the Vedda, form close genetic affiliations among themselves and with
majority of the groups from the mainland suggesting the origin of the
majority of the island population on the Indian mainland. No definite
association of the Sinhalese with any specific ethnic or linguistic
groups of India was, however, detected in this study; thus, their exact
immediate origin on the mainland remains yet to be confirmed.
There is no clear genetic separation based on the PCA map between
Sinhalese and Tamils, and between Up- and Low-country Sinhalese of
Sri Lanka. The latter phenomenon suggests a recent division of
the Sinhalese into Up- and Low-country, the fact confirmed on a
historical ground.31 For the groups represented in this study, majority
of the Up-country Sinhalese formed closer association among
themselves than did their Low-country ethnic counterparts. This is
to a certain degree explicable in a light of the isolation-by-distance;
the Up-country Sinhalese groups are more geographically proximal
with each other than do their Low-country counterparts. However,
the closer association of the Up-country Sinhalese with the Sri Lankan
Tamils than with the Indian Tamils is not in agreement with the
geographic distances among them. Despite recent habitation of the
Indian Tamils in proximity of the Up-country Sinhalese, the Indian
Tamils might have admixed, during the long distant past, more with
Sri Lankan Tamils, who have lived on the island longer than their
Indian ethnic counterparts.32,33
The genetic distinctiveness of the Vedda people on the island of Sri
Lanka, as reported in this study, confirm previous results based on the
analyses of nuclear markers.11–13 The markedly higher frequencies of
Table 2 (Continued )
No. of samples (%)
Haplogroup Vedda Sinhalese Up-country Sinhalese Low-country Sri Lankan Tamils Indian Tamils Total
R5a2b 5 (6.67) 3 (5) 1 (2.5) 1 (2.56) 1 (1.75) 11 (4.06)
R6a 0 (0) 3 (5) 0 (0) 0 (0) 0 (0) 3 (1.11)
R7 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
R7a’b 0 (0) 0 (0) 1 (2.5) 1 (2.56) 1 (1.75) 3 (1.11)
R8a1a3 0 (0) 0 (0) 0 (0) 0 (0) 1 (1.75) 1 (0.37)
R30b/R8a1a3 29 (38.67) 1 (1.67) 2 (5) 0 (0) 1 (1.75) 33 (12.18)
R30b 0 (0) 0 (0) 6 (15) 0 (0) 0 (0) 6 (2.21)
Haplogroup U 22 (29.33) 14 (23.33) 6 (15) 6 (15.38) 4 (7.02) 52 (19.19)
U1a’c 9 (12) 3 (5) 0 (0) 1 (2.56) 1 (1.75) 14 (5.17)
U2 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
U2a 3 (4) 0 (0) 0 (0) 2 (5.13) 3 (5.26) 8 (2.95)
U2b 0 (0) 1 (1.67) 0 (0) 0 (0) 0 (0) 1 (0.37)
U5a 0 (0) 0 (0) 2 (5) 1 (2.56) 0 (0) 3 (1.11)
U6 0 (0) 1 (1.67) 1 (2.5) 0 (0) 0 (0) 2 (0.74)
U7 0 (0) 2 (3.33) 0 (0) 0 (0) 0 (0) 2 (0.74)
U7a 10 (13.33) 7 (11.67) 3 (7.5) 1 (2.56) 0 (0) 21 (7.75)
Haplogroup T 0 (0) 0 (0) 2 (5) 1 (2.56) 0 (0) 3 (1.11)
T 0 (0) 0 (0) 0 (0) 1 (2.56) 0 (0) 1 (0.37)
T1a103 0 (0) 0 (0) 2 (5) 0 (0) 0 (0) 2 (0.74)
Haplogroup P 0 (0) 2 (3.33) 0 (0) 2 (5.13) 1 (1.75) 5 (1.85)
P4a 0 (0) 2 (3.33) 0 (0) 0 (0) 0 (0) 2 (0.74)
P5 0 (0) 0 (0) 0 (0) 2 (5.13) 1 (1.75) 3 (1.11)
Haplogroup W 0 (0) 2 (3.33) 0 (0) 0 (0) 0 (0) 2 (0.74)
W 0(0) 2(3.33) 0(0) 0(0) 0(0) 2(0.74)
aunidentified haplogroup M.
bunidentified haplogroup N.
Table 3 Analysis of molecular variance (AMOVA) of Sri Lankan populations
Among groups Among populations within groups Within populations
Model VaraP-value VaraP-value VaraP-value
Ethnic criteriab1.72 0.039 8.61 o0. 001 89.66 o0.001
Linguistic criteriac2.57 0.002 8. 20 o0.001 89.23 o0.001
Geographic criteriad0.55 0.677 10.56 o0.001 89.99 o0.001
Vedda vs others 4.00 0.002 8.15 o0.001 87.8 5 o0.001
Up-country Sinhalese vs Low-country Sinhalese 1.19 0.814 9.82 o0.001 91. 37 o0.001
Sri Lankan Tamils vs Indian Tamils 0.73 0.027 2.19 0.028 97.08 0.003
aVariance (%).
bFive groups (Vedda people, Up-country Sinhalese, Low-country Sinhalese, Sri Lankan Tamils and Indian Tamils).
cThree groups (Vedda dialect, Indo-European language and Dravidian language).
dSeven provinces (North, North-Central, Central, Eastern, Uva, Sabaragamuwa and South).
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the haplogroup R30b/R8a1a3 in all Vedda subgroups than in other Sri
Lankan populations is compatible with a hypothesis that all the Vedda
subgroups would have shared a common origin. The greatest inter-
population genetic diversity observed among the Vedda subgroups
coupled with their relatively low haplotype and nucleotide diversity
would reflect greater effect of the genetic drift in the Vedda than in
other ethnic groups of Sri Lanka. The pattern of genetic
differentiation observed in the Vedda is a characteristic also
observed in various other aboriginal populations of the world with
their relatively small subgroups experiencing a long history of
separation.34–39 Such population history was also proposed for the
Vedda based on the anatomical analysis.10 Much greater genetic
similarities with Sinhalese, and to a lesser degree with Sri Lankan
Tamils, observed in some Vedda subgroups (VA-Dam, VA-Hen and
VA-Pol) in comparison with other subgroups of the same ethnic
category (VA-Rat and VA-Dal) suggests that the pattern of genetic
admixture between older inhabitants (Vedda) and more recent
newcomers (Sinhalese and Tamils) on the island was truly
heterogeneous. Advance admixture of VA-Dam, VA-Hen and VA-
Pol with other ethnic populations on the island is confirmed by the
presence of several shared sub-haplogroups (M33a1, D, R5a and U7a)
among them that are not found in VA-Rat and Va-Dal. The reduced
intrapopulation genetic diversity observed among subgroups of the
Vedda is most likely a result of severe genetic drift associated with the
practice of endogamy among small-sized villages during the long
distant past, a phenomenon with firm historical evidence.4,5
ACKNOWLEDGEMENTS
We are grateful to all the people who have donated their hair samples
for making this study possible. We would like to thank Dr Upeksha
Samaraweerachchi, Deepal Edirisinghe, Nirmala Ranaweera, Dayarathna
Ranaweera, Sanjeewa Jayakody, G.G. Sirisena, U.S. Yapa, K. Sanath,
Achala Chandradasa, T. Kumarasiri, M. Pushpawathi, Nimesha Palliyaguruge
and H. Ranaweera for their excellent help in the field trips. Our special thanks
extended to Professor Dr Senake Bandaranayake, Associate Professor Dr
Suraphan Na Bangchang and Dr Bhoom Suktitipat and the three anonymous
reviewers for their critical comments of the manuscript and their constructive
discussions, to Dr Russell Thomson for the proof-reading of this manuscript
and to Professor Drs Hans Jurgen Bandelt and Walther Parson for their valuable
comments on the dataset validation. We also thank scholars who kindly
provided their published mtDNA HVS-1 sequences. This work was partly
supported by Siriraj Graduate Thesis Scholarship, Faculty of Medicine
Siriraj Hospital Mahidol University, Thailand to LR. PL is supported by
‘Chalermphrakiat’ Grant, Faculty of Medicine Siriraj Hospital, Mahidol
University, Thailand.
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