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

Authors:
  • Faculty of Medicine, university of Kelaniya
  • Faculty of Graduate Studies, Mahidol University, Bangkok, Thailand

Abstract and Figures

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.
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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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Supplementary Information accompanies the paper on Journal of Human Genetics website (http://www.nature.com/jhg)
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... Two studies have been carried out on Vedda and Sinhalese populations of Sri Lanka based on mitochondrial HVS1 and HVS2 (Ranaweera et al. 2013;Ranasinghe et al. 2015). However, additional markers from the HVS3 could increase the discrimination capacity of similar mito-genomic sequences. ...
... Although the Vedda population is believed to be indigenous to Sri Lanka, diversity measures indicated possible genetic admixtures with other populations which migrated to Sri Lanka at different periods. However, two previous studies on HVS1 and HVS2 reported that genetic indices of the Vedda population were different from those of the Sinhalese population and other contemporary ethnic groups of Sri Lanka, and that the Vedda forms a distinct cluster, supporting the historical view of them being early inhabitants of this region (Ranaweera et al. 2013;Ranasinghe et al. 2015). Therefore, the absence of diversity between Vedda and Sinhalese populations in relation to the (CA) n repeat variation reported in this study should be taken with caution. ...
Article
Sinhalese and Vedda people are respectively the major ethnic group and the descendants of the probably earliest inhabitants of Sri Lanka, both believed to have a long history of settlement on the island. However, very little information is available on the origin and possible migration patterns of the two populations. Some studies have focused on (CA) dinucleotide repeat variations located in the mitochondrial hypervariable region 3 (HVS3) (base pairs 514-524) as a useful biomarker to understand migration patterns of different populations. Hence, here we analyze these repeat variations in these two ethnic groups to understand their historical roots and possible patterns of gene flow. Blood samples were collected from healthy, maternally unrelated individuals (N = 109) and mitochondrial D-loop was amplified and sequenced. The (CA) 4 dinucleotide repeat in hypervariable region 3 was detected in the majority of Vedda samples while the remaining samples were defined by a (CA) 5 cluster. In contrast, the (CA) 5 repeat was the most frequent among Sinhalese followed by (CA) 4 and (CA) 7 repeats. Haplogroup diversity of (CA) 4 variation indicated that the majority of Sinhalese individuals grouped into the M30 haplogroup while Vedda clustered into the R5a2b and U7a2 haplogroups. No significant differences in diversity measures were observed among the two populations. However, Multidimensional Scaling indicated a separate clustering for aboriginal Vedda and contemporary Sinhalese populations. Results from this study can be used together with mitochondrial DNA information from hypervariable regions 1 and 2 to perform anthropological and forensic investigations in the two populations studied.
... This view has persisted in the popular literature and collective imagination. However, anthropomorphic, dental, and genetic studies show only minor differences between the 'Vedda,' Tamil, and Sinhala people (Stoudt, 1961;Hawkey, 2002;Peiris et al., 2011;Ranaweera et al., 2014). These groups shared a common gene pool throughout prehistoric and historic times, and today no clearly discerned boundaries exist, morphologically (Kennedy, 1971;Bowles, 1977;Kulatilake, 2000;Kulatilake and Hotz, 2017), genetically (Ranasinghe et al., 2015), or linguistically (Dharmadasa, 1974;Brow, 1978;Dharmadasa and Samarasinghe, 1990). ...
... Classical and molecular genetic studies show that the Sinhala and Tamil people of Sri Lanka share strong biological links with each other; and are less connected to their ances- tral groups in mainland South Asia, the Ancestral North Indians and Ancestral South Indians, respectively (Kshatriya, 1995;Moorjani et al., 2013;Ranaweera et al., 2014;Liu et al., 2017). For instance, Sri Lankan Tamils are more closely genetically related to the Sinhalese than they are to Indian Tamils (Kshatriya, 1995;Ranasinghe et al., 2015). ...
Article
Swiss naturalists Paul and Fritz Sarasin visited Sri Lanka on five occasions. Their later visits were focused on anthropological research on the Indigenous Wannila Atto (‘Vedda’) people and exploration of prehistoric settlements in Sri Lanka. Among the Sarasins’ anthropological and archaeological collections are skeletal material of several ethnic groups of Sri Lanka belonging to the 19th and early 20th centuries. This collection is curated at the Natural History Museum of Basel, Switzerland. The ethnolinguistic groups represented in the Sarasins’ collection include the ‘Vedda,’ Tamil, and Sinhala people of Sri Lanka, and it constitutes the largest ‘Vedda’ cranial collection housed at a single institution. The objective of this paper is to compare cranial variation of the Indigenous ‘Vedda’ and other Sri Lankan ethnic groups using this important dataset, while publishing the raw craniometric data for further studies. Observations on the dentition show that the Tamil and Sinhala individuals had high incidences of caries and dental abscesses that are typically associated with agriculturalists and that cribra orbitalia associated with iron deficiency was relatively common among all three ethnic groups. Betel quid chewing for recreational and cultural purposes, a practice that is widespread even today, had left dark stains on the teeth of many individuals of all groups in the sample. Multivariate statistical analyses on the craniometric data show that there is significant overlap among the three ethnic groups in terms of cranial shape. These findings underscore the importance of considering the ‘Vedda,’ Tamil, and Sinhala groups from Sri Lanka as closely related, due to gene flow over millennia.
... Germline mutations such as T16189C, T16519C and G10398A have been reported as risk factors in breast cancer, whereas variations such as T3197C and G13708A are reported to serve as protective factors in certain populations (25,26). mtDNA is primarily inherited maternally and the mutational profile varies in different populations and ethnicities (27,28). Previous studies have investigated the variations in the mitochondrial genome of patients in different populations (26,29,30); however, to the best of our knowledge, there are no studies on Sri Lankan patients. ...
... Furthermore, the absence of a link between previously reported mutations and haplogroups with breast cancer risk in the present study highlights the need for exercising caution when using non-localised biomarker panels to assess disease risk in populations. However, the association of previously reported mitochondrial D loop mutations and haplogroups with breast cancer risk in other Sri Lankan ethnic groups cannot be excluded, in view of the ethnic differences in the mtDNA and haplogroups among other ethnicities (27,28). The mutations that showed a weak effect in the present study, and those reported in other studies, need to be further evaluated in larger cohorts and in other ethnic groups before their use as predictive biomarkers can be recommended. ...
Article
Mitochondrial DNA (mtDNA) mutations have been reported to be associated with various diseases, including cancer. The present study investigated the mtDNA non-coding region mutations and mitochondrial haplogroups as potential biomarkers of sporadic breast cancer in Sri Lankan Sinhalese women. Mitochondrial macro-haplogroups were determined using PCR-restriction fragment length polymorphism, whereas non-coding region sequences were determined using Sanger sequencing. The sequence of the non-coding region was also used to confirm haplogroup status. Neither the mutations in the non-coding region nor the mitochondrial haplogroups that were reported as risk factors in other populations, were determined to be potential risk factors for sporadic breast cancer in the present study. Furthermore, several novel mutations were identified in the present matched pairs case-controlled study. The M65a haplogroup with an additional mutation at position 16311 (P=0.0771) and mutations at the ori-b site (P=0.05) were considered a weak risk factor and protective factor, respectively, for sporadic breast cancer in Sinhalese women. Previous studies have indicated the use of mtDNA mutations as a biomarker; however, the present study showed that such biomarkers need to be validated for individual ethnic groups before they can be recommended for use in the prediction of disease.
... These include the earliest skeletal evidence for AMH in South Asia known as "Balangoda Man" (37 kya) [4], microfossils of several botanical taxa (47.8 kya) [5] and oldest microlithic technology in the region [6,7]. However, to date there are no data for ancient DNA from Sri Lanka, although a few studies have reported on contemporary populations, i.e.: Sinhalese, Sri Lankan Tamils, Sri Lankan Indian Tamils (with a very recent history in the island), Muslims (Moors), Malays, and the Adivasi (Vedda) [8,9]. ...
Article
Sri Lanka is an island in the Indian Ocean connected by the sea routes of the Western and Eastern worlds. Although settlements of anatomically modern humans date back to 48,000 years, to date there is no genetic information on pre-historic individuals in Sri Lanka. We report here the first complete mitochondrial sequences for Mesolithic hunter-gatherers from two cave sites. The mitochondrial haplogroups of pre-historic individuals were M18a and M35a. Pre-historic mitochondrial lineage M18a was found at a low prevalence among Sinhalese, Sri Lankan Tamils, and Sri Lankan Indian Tamil in the Sri Lankan population, whereas M35a lineage was observed across all Sri Lankan populations with a comparatively higher frequency among the Sinhalese. Both haplogroups are Indian derived and observed in the South Asian region and rarely outside the region.
... 37 Mitochondrial DNA haplogroup analysis also has revealed that several West Eurasian haplogroups as well as Indian-specific mtDNA clades were found among the Sri Lankan populations. 38 The study of genetic admixture revealed that the Sinhalese of Sri Lanka have a higher contribution from the Tamils of southern India (69.86%) compared with the Bengalis of northeast India (25.41%). 39 USA NMDP South Asian Indians clustered with the South Indian population. ...
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South Indians are a heterogeneous population who speak different languages and differ in their life style and physical appearance. Major population movements, social structure and caste endogamy have influenced the genetic structure of Indian populations. The HLA system of populations is highly informative because of the high level of polymorphisms. Knowledge of allele and haplotype frequencies of the HLA system is important in the search for unrelated bone marrow donors. We investigated the distribution of HLA A, B, C, DRB1 and DQB1 loci in five linguistic groups from South India. HLA –A*01:01:01~B*57:01:01:01~C*06:02:01~DRB1*07:01:01~DQB1*03:03:02 was the common haplotype with highest frequency in all the five populations studied. A few relevant haplotypes were identified as most common haplotypes in each linguistic group. Comparison of HLA‐ A, ‐B and ‐DRB1 allele distribution in these five linguistic groups with the other Asian population showed that the South Indian populations were closely related to Sri Lankan populations. A large South Indian donor registry might serve as good source of donors for patients from Sri Lanka and vice versa. This article is protected by copyright. All rights reserved.
... While the discourse of the 'original inhabitants' of the island includes many theories, the 'Veddas' are known to be the most indigenous/native to the island of Sri Lanka. Later settlements (although the timing of these settlements is a matter lacking scholarly consensus) led to the presence of the Sinhalese (with the arrival of Prince Vijaya in 5th century BCE from Indian mainland), and the Sri Lankan Tamils (with the creation of the Tamil/Jaffna Kingdom in 7th century BCE) (Lanka et al., 2014). Both ethnic groups, as per anthropological and archaeological evidence, are known to have a very long history in Sri Lanka, while the timing of this history varies in different accounts. ...
Article
Although postcolonial analyses examining the sexualized imagery of women in tourism have been conducted, previous studies have predominantly focused on gender and (post)colonialism from a patriarchal perspective. By doing so, other (neo)colonial power asymmetries, such as race, class and ethnicity, have often been neglected. This paper mobilises postcolonial feminist theory to expand the existing analyses and discourses concerning gendered representations in tourism. Through a narrative analysis of the images published in the official Instagram page of Sri Lanka's Ministry of Tourism, we contend that the images produced and circulated to promote Sri Lanka in many instances echo essentialist gendered binaries (e.g. men/women; coloniser/colonised; hegemonic/subordinated). However, as the images tend to produce and reiterate Sri Lankan national identity through a hegemonic Sinhalese Buddhist discourse, they also show the intersections between gender and other asymmetries of power (e.g. race, ethnicity, religion, and social class)-in reproducing (post)colonial gendered identities.
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A new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.
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Spirometry and Peak Expiratory Flow Rate (PEFR) are important measurements in diagnosing and monitoring of COPD and asthma. Ethnic specific reference equations are necessary in interpretation of these parameters. However, equations for Sri Lankan Tamil adults are not available. This study aims to establish reference equations for lung function parameters of Sri Lankan Tamils. A descriptive cross sectional study was carried out in all 5 districts of Northern Sri Lanka. Participants were selected by cluster sampling. Base line data were obtained by a questionnaire. Height, sitting height, weight, arm span, mid arm circumference, and chest expansion were measured. Respiratory functions were assessed by a calibrated spirometer (Cosmed Micro Quark, Italy) and Wright compatible peak expiratory flow meter. Means, and standard deviations for Vital Capacity (VC), Forced Vital Capacity (FVC), Forced Expiratory Volume in the first second (FEV 1 ), FEV 1 %, Peak Expiratory Flow Rate (PEFR) and for other forced expiratory parameters of 775 males and 687 females were determined. Lung function parameters have significant p<0.05 positive correlations with most of the anthropometric measures. Age had a significant p<0.05 negative correlation with lung function parameters in adults >20 years and positive correlation p<0.05 in 14–20 years group. Step wise multiple regression analysis was used to determine the prediction equations. Also equations based on age, height and age, arm span were derived. Age, height based equations were retested in the same population. Predicted values by the developed equations had better agreement than that of GLI 2012 equations. This can be useful in assessing the respiratory function in Sri Lankan Tamil population as there are no already existing equations.
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Preprint
A new 16 X- short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.
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Indigenous and traditional foods of Sri Lanka inherit a long history and unique traditions continued from several thousands of years. Sri Lankan food tradition is strongly inter-wound with the nutritional, health-related, and therapeutic reasoning of the food ingredients and the methods of preparation. The diverse culinary traditions and preparations reflect multipurpose objectives combining in-depth knowledge of flora and fauna in relation to human well-being and therapeutic health benefits. Trans-generational knowledge dissemination related to indigenous and traditional food is now limited due to changing lifestyles, dwindling number of knowledge holders, and shrinking floral and faunal resources. Awareness on the relationship between non-communicable diseases and the diet has garnered the focus on traditional ingredients and foods by the consumers and major food producers in Sri Lanka. This review presents concise details on the indigenous and traditional foods of Sri Lanka, with scientific analysis when possible.
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An ongoing source of controversy in mitochondrial DNA (mtDNA) research is based on the detection of numerous errors in mtDNA profiles that led to erroneous conclusions and false disease associations. Most of these controversies could be avoided if the samples' haplogroup status would be taken into consideration. Knowing the mtDNA haplogroup affiliation is a critical prerequisite for studying mechanisms of human evolution and discovering genes involved in complex diseases, and validating phylogenetic consistency using haplogroup classification is an important step in quality control. However, despite the availability of Phylotree, a regularly updated classification tree of global mtDNA variation, the process of haplogroup classification is still time-consuming and error-prone, as researchers have to manually compare the polymorphisms found in a population sample to those summarized in Phylotree, polymorphism by polymorphism, sample by sample. We present HaploGrep, a fast, reliable and straight-forward algorithm implemented in a Web application to determine the haplogroup affiliation of thousands of mtDNA profiles genotyped for the entire mtDNA or any part of it. HaploGrep uses the latest version of Phylotree and offers an all-in-one solution for quality assessment of mtDNA profiles in clinical genetics, population genetics and forensics. HaploGrep can be accessed freely at http://haplogrep.uibk.ac.at. Hum Mutat 31:–8, 2010. © 2010 Wiley-Liss, Inc.
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BACKGROUND: Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be contextualized within the phylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzed mtDNA control and coding region variation in 796 Indian (including both tribal and caste populations from different parts of India) and 436 Iranian mtDNAs. The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia. RESULTS: Four new Indian-specific haplogroup M sub-clades were defined. These, in combination with two previously described haplogroups, encompass approximately one third of the haplogroup M mtDNAs in India. Their phylogeography and spread among different linguistic phyla and social strata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealed patterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed the identification of different assemblies of shared mtDNA sub-clades. CONCLUSIONS: Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.
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The central Indian state Madhya Pradesh is often called as 'heart of India' and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic). There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe) with the Austroasiatic (Munda) group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints.
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The paper raises, at random, a few issues of history and ethnicity which have some bearing on the national question, and on the contradictions, conflicts and debates that have arisen. -from Author
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The environment of the late Quaternary 24,000 yrs BP (Before Present) (i.e. late Pleistocene and Holocene) in Sri Lanka as experienced by the Mesolithic, Neolithic and Early Iron Age communities were different from today. Man's effect upon his environment was considerable during the late Pleistocene. However, more technologically advanced groups of people were stimulated to exploit new opportunities as they moved into new ecozones during the late Holocene. An attempt was made to reconstruct t h e palaeoclimatic sequence with radiocarbon dated multi-proxy data at a mire in the Horton Plains, central Sri Lanka. Since the end of the Last Glacial Maximum (LGM),approximately 18,000 years ago, the Indian ocean Southwest monsoon strengthen in stages during the late Pleistocene and early Holocene. Late Pleistocene hunting, gathering and farming activities (24,000-10,000 yrs BP) Between 24,000 and 18,000 years BP, the landscape of the Horton Plains was probably open with a prevailing semi-arid climate as indicated by pollen, stable carbon isotopes (613C) and Total Organic Carbon (TOC) records. The vegetation composition deduced from the pollen data and soil forming processes detected from mineral magnetic properties suggest that the population of the area consisted of nomadic groups of hunter-foragers. It is possible that this life style could have dominated due to the low carrying capacity (i.e. lack of rain forest) in the Horton Plains as well as in most parts of the island during the LGM. It is thought that they settled in small camps i n different environments ranging from the damp and cold high plains (e.g. Horton Plains) to the lowlands (e.g. Mannar). Multi-proxy records (e.g. pollen, phytolith and TOC) from Horton Plains indicate that herding (Bos indicus?) and the incipient management of cereals (i.e. oat and barley) occured to some extent from 17,500 yrs BP onwards. Frequent burning and forest clearances (i.e. slash-and-burn) by prehistoric people may have contributed to the expansion of patanas in the Horton Plains. This also coincides with a semi-humid event (17.6 -16 ka BP) suggesting favourable climatic conditions (i.e. warmerhumid) influencing the plant management system. Multi-proxy records also indicate that the incipient management of oat and barley continued for a period of 4.5 ka BP (17.5-13 ka BP). During this period, prehistoric humans developed advanced techniques and practices for plant domestication. In the Horton Plains, environmental factors such as climate and soil forming processes coincided with incipient and succeeding land use. It is also suggested that the time lag (i.e. 4.5 ka BP) is reasonably long to consider that the origins of agriculture indicated a macro-evolutionary experiment.
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The determination of human mitochondrial DNA (mtDNA) haplogroups is not only crucial in anthropological and forensic studies, but is also helpful in the medical field to prevent the making of wrong disease associations. In recent years, high-throughput technologies and the huge amounts of data they create, as well as the regular updates to the mtDNA phylogenetic tree, mean there is a need for an automated approach which can make a speedier determination of haplogroups than can be made by using the traditional manual method. Here, we update the MitoTool (www.mitotool.org) by incorporating a novel scoring system for the determination of mtDNA into haplogroups, which has advantages on speed, accuracy and ease of implementation. In order to make the access to MitoTool easier, we also provide a stand-alone version of the program that will run on a local computer and this version is freely available at the MitoTool website.
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GENALEX is a user-friendly cross-platform package that runs within Microsoft Excel, enabling population genetic analyses of codominant, haploid and binary data. Allele frequency-based analyses include heterozygosity, F statistics, Nei&apos;s genetic distance, population assignment, probabilities of identity and pairwise relatedness. Distance-based calculations include AMOVA, principal coordinates analysis (PCA), Mantel tests, multivariate and 2D spatial autocorrelation and TWOGENER. More than 20 different graphs summarize data and aid exploration. Sequence and genotype data can be imported from automated sequencers, and exported to other software. Initially designed as tool for teaching, GENALEX 6 now offers features for researchers as well. Documentation and the program are available at http://www.anu.edu.au/BoZo/GenAlEx/
Book
Spectacular progress has been made recently in the study of evolution at the molecular level, primarily due to new biochemical techniques such as gene cloning and DNA sequencing. In this book, the author summarizes new developments and seeks to unify studies of evolutionary histories of organisms and the mechanisms of evolution into a single science - molecular evolutionary genetics.