Journal of Human Genetics (2013), 1–3
& 2013 The Japan Society of Human Genetics All rights reserved 1434-5161/13
COMMENTARY
Language isolates and their genetic identity:
a commentary on mitochondrial DNA history of
Sri Lankan ethnic people: their relations within the
island and with the Indian subcontinental populations
Gyaneshwer Chaubey
Journal of Human Genetics advance online publication, 21 November 2013; doi:10.1038/jhg.2013.122
S outh Asia is the home to more than a
fifth of the world’s population, and is
thought, on genetic grounds, to have been
the first main reservoir in the dispersal
of modern humans Out of Africa.1,2
Additionally, high level of endogamy within
and between various castes, along with the
influence of several evolutionary forces and
long-term effective population size, facilitate
the formation of complex demographic
history of the subcontinent.3 Therefore, the
ancestry of peopling of the South Asia is a
question of fundamental importance in
archaeogenetics, linguistics and historical
disciplines, and it is not surprising that the
number and timing of migrations in and out
of South Asia is still vigorously debated.2–4
Researches from various disciplines focused
on testing the hypothesis that several separate
migrations entered to the subcontinent with
each migration being associated with
different tool technology, linguistic and
genetic characteristics.2,3,5,6 The mtDNA
(mitochondrial DNA) data suggest deep
autochthonous diversity with minor sharing
with East and West Eurasians,3 whereas, in
contrast with this, the recent autosomal data
showed substantial similarities of their
genome with Caucasus and West Asians.4,6
However, at the current resolution, it is
unclear that this sharing is extremely
ancient or arisen with the arrival of new
languages and farming.7
Among South Asian countries, India
and Pakistan have somewhat better
Dr G Chaubey is at Evolutionary Biology Department,
Estonian Biocentre, Tartu, Estonia
E-mail: gyanc@ebc.ee
www.nature.com/jhg
understanding of their genetic structuring,
whereas genetic information from Nepal,
Bangladesh, Bhutan, Sri Lanka and the
Maldives are either published at the level of
forensic data or restricted to few populations.
Being at the offshoot of southernmost tip of
South Asia and along the proposed southern
migration route, the island of Sri Lanka has
long been settled by various ethnic groups
and may offer a unique insight into initial
peopling of the subcontinent. Most impor-
tantly, it is one and only precursor of modern
humans fossil in South Asia dated back to
37 000 years ago.8,9 Therefore, it is important
to study prehistoric human settlement of Sri
Lanka, and their relation to other adjoining
populations.
Though each and every population of
South Asia is unique in terms of their genetic
structuring, dialect and specific rituals, there
are few language isolates who have hypothe-
sized to be the remnants of the ancient
settlers and may provide an insight to the
initial peopling of the subcontinent.10 Hence,
it is important to study the genome structure
of these groups. However, it is also important
to note that the language isolates may not be
always the genetic isolates. Except from the
Andaman islanders, none of the studied
South Asian language isolates hitherto were
found to be true genetic isolate.1,11,12 The
linguistic isolate of Sri Lanka is known as
Vedda (aka Vadda).8,10 Vedda is small
hunter-gatherer tribe existing in Northwest
province of Sri Lanka. They are called as
aboriginal people of Sri Lanka and were
suggested to represent the indigenous
population of the entire subcontinent.8,10
The first genetic study of Vedda along
with other Asian populations suggested
their long period of isolation.13 However,
the analysis of alpha-2-HS-glycoprotein
allele frequencies supports the view that
the Veddas are biologically most closely
related to the Sinhalese.14 Till date, a high-
resolution genetic data was not available
from this population and their affinity with
other populations of Eurasia remained
obscure.
In previous issue, Ranaweera and collea-
gues9 rectified this issue by generating the
novel informations from the HVS-I and
HVS-II region of mtDNA to date for the
Vedda, including other major ethnic groups
of Sri Lanka. Through a well-covered
sampling strategy, they filled a major
geographic ‘white spot’ inhabited by B20
million people. Their analysis led to the more
precise identification of South Asian-specific
indigenous mtDNA haplogroups and a better
understanding of the extent of East and West
Eurasian admixture among Sri Lankan
populations. In addition, for the first time
by generating mtDNA data on relic Vedda
populations, this study was able to confirm
that they exhibit low genetic variability,
which is consistent with their small
population size and strong effect of genetic
drift.
The haplogroup distribution and sharing
among different ethnic groups is intriguing.9
Majority of mtDNA haplogroups were
belonging to South Asian-specific clades
(Figure 1). However, the Sri Lankan popula-
tions (except Indian Tamils sampled in Sri
Lanka) have significantly higher West
 Commentary
2
  R Root
 
8584
  R30

2331A 152
  4025
5074
 8508 2056 373
15924 3316 R30b
16291 4232
16311 5442 1598 152
6764s 16189 6290s
R30c 9156s 7280s
9242s R30b1 7843s
11047A 13539s
12714s 16292
15055s 16+8.4 kya R30b2

R30a 6599s 15148s

7702s R30b2a
8027
              14766 150 14000A
      16242 11016 16497
11863s

India
Rani 2010 16286 Behar 2008

Sri Lanka GC#CoB23

Figure 1 (a) The sharing of maternal ancestry of Sri Lankan populations in comparison with different states of Southern India. ( b) The most parsimonious
tree of haplogroup R30 complete mtDNA sequences showing the most recent common clad of Vedda (R30b2). Coalescent times were calculated by a
calibration method described elsewhere. 16 16182C, 16183C and 16519 polymorphisms were omitted. Suffixes A, C, G and T indicate transversions,
recurrent mutations are underlined. Synonymous (s) mutations are distinguished. Sequences were taken from the published and our unpublished sourc es. 17–19
A full color version of this figure is available at the Journal of Human Genetics journal online.

Eurasian ancestry than any other Southern find out the population sharing the closest In the era of Genomics and cutting edge
Indian states (Figure 1). The most common common ancestry with Vedda. technology, it can be expected that in
West Eurasian haplogroup observed were From this study it is apparent that the; near future the complete understanding of
haplogroup U1 and U7. Majority of haplo- (1) considerable number of maternal lineages the Sri Lankan genepool will help to con-
types among studied populations have a of Sri Lanka is shared with India, more tribute significantly to the knowledge of
complete or nearly complete match with precisely with southern part of India; genetic variation of modern humans in
South Indian variants, whereas only three (2) the maternal genetic structuring is shaped South Asia.15
haplogroups (M2, M6, M33 and R5) are by both ethnicity and geography; and (3) the
common and share haplotypes across all the language isolate Vedda is not likely a genetic ACKNOWLEDGEMENTS
studied groups. isolate and shares their lineages with their This study was supported by the EU through the
Another important element of this study neighbors. As this study is lacking the highest European Regional Development Fund through the
was generating the maternal haplogroup level level of resolution of mtDNA, therefore it is Centre of Excellence in Genomics to Estonian
data from one of the so far genetically hard to establish any timeline for the pre- Biocentre and University of Tartu.
virtually unstudied language isolate of South sence of these haplogroups (most impor-
Asia known as Vedda.9 This study reports tantly west Eurasian-specific haplogroups),
that the Vedda is most distinct among all the into this region, although the archeological
ethnic groups, which is likely due to elevated record suggest the presence of modern 1 Thangaraj, K., Chaubey, G., Kivisild, T., Reddy, A. G.,
Singh, V. K., Rasalkar, A. A. et al. Reconstructing the
frequency of haplogroups R30, U1 and U7, human since Upper Paleolithic time.8 origin of Andaman Islanders. Science 308, 996
altogether represent 64% of maternal lineages Moreover, mtDNA is highly prone to (2005).
of Vedda. The haplotype distribution of these genetic drift, especially in small tribal 2 Mellars, P., Gori, K. C., Carr, M., Soares, P. A. &
Richards, M. B. Genetic and archaeological perspec-
haplogroups clearly indicates this scenario as populations like Vedda, thus one or more tives on the initial modern human colonization of
a result off ounder effect(s) due to random mtDNA founding haplogroups can easily be southern Asia. Proc. Natl Acad. Sci. USA 110,
10699–10704 (2013).
genetic drift. Owing to this unique lost among them. Therefore, one cannot 3 Chaubey, G., Metspalu, M., Kivisild, T. & Villems, R.
haplogroup structuring, Vedda single out as dismiss the possibility, for instance, that the Peopling of South Asia: investigating the caste-tribe
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