Advances in Anthropology
2012. Vol.2, No.4, 181-197
Published Online November 2012 in SciRes (http://www.SciRP.org/journal/aa) http://dx.doi.org/10.4236/aa.2012.24021
Copyright © 2012 SciRes. 181
Molecular Genetic Perspectives on the Origin of the Lyngngam
Tribe of Meghalaya, India*
Banrida T. Langstieh1,2#, Vikrant Kumar1,3#, Meka Aruna1#, Alla Govardhan Reddy4,
Shilpi Dasgupta1, Alla Nirmala1, Kumarasamy Thangaraj4, Lalji Singh4,
Battini Mohan Reddy1†
1Molecular Anthropology Group, Indian Statistical Institute, Hyderabad, India
2Department of Anthropology, North-Eastern Hill University, Shillong, India
3Human Genetics Group, Genome Institute of Singapore, Singapore City, Singapore
4Centre for Cellular and Molecular Biology, Hyderabad, India
Email: langstieh.banrida@gmail.com, kumarv@gis.a-star.edu.sg, aruna.m79@gmail.com,
agreddy@ccmb.res.in, shilpidasgupta1@gmail.com, allanirmala@gmail.com,
thangs@ccmb.res.in, lalji@ccmb.res.in, bmrisi@gmail.com
Received July 10th, 2012; revised August 22nd, 2012; accepted September 10th, 2012
Meghalaya, one of the Northeast Indian states, is inhabited by two major tribal clusters, Khasi and Garo.
The disputed origin of the Lyngngam tribe of Meghalaya is a result of their geographic distribution, which
is sandwiched between that of the above two major tribal clusters. Our earlier analysis of ethnohistoric,
linguistic and demographic data suggested the neighbouring Khasi and Garo as the putative parental
population(s) of Lyngngam. In this paper, we have investigated the Lyngngam, Garo and all the 7 sub-
tribes of Khasi of Meghalaya using molecular genetic markers-autosomal, Y-chromosome and mtDNA-to
explore the possible origin of the Lyngngam tribe. We obtained admixture estimates for Lyngngam versus
the putative parental populations. While autosomal STRs and mtDNA results clearly suggest Khasi origin
of the Lyngngam, Y-STR distances show greater proximity of Lyngngam to the Garo. Further, the com-
parative analysis of the Y-Chromosome and mtDNA haplogroup data on relevant Austro-Asiatic and Ti-
beto-Burman populations from South and Southeast Asia, published by us earlier, clearly exclude the
possibility of Lyngngam origin from outside Meghalaya. The molecular genetic evidence in conjunction
with the linguistic, demographic and ethno-historic information clearly suggests Khasi origin of the
Lyngngam tribe.
Keywords: Austro-Asiatics; Admixture; Autosomal STRs; Y-Chromosome Markers;
MtDNA HVS-I and II Sequences
Introduction
One of the most fundamental and unique features of Indian
population structure is the division of its population into strictly
defined hierarchical endogamous castes, tribes and religious
groups (Figure 1) within any particular geographic region
and/or linguistic category (Reddy et al., 2010; Malhotra, 1984;
Malhotra & Vasulu, 1993). However, it is the subdivision of
each of these castes, tribes and religious groups into a number
of endogamous subunits like subcastes or subtribes and the
processes involved in this sub-structuring of the Indian popula-
tion that makes it quite fascinating for population geneticists.
Basically, two different models-fission and fusion-can explain
this continuous process of subdivision and/or amalgamation/
admixture, although a totally contrasting model especially to
negate the process of fission behind formation of subcastes has
also been proposed and demonstrated with empirical evidence
(Karve, 1961; Karve & Dandekar, 1951; Karve & Malhotra,
1968). On the other hand, subsequently, number of investi-
gators have documented situations where in a number of en-
dogamous subcastes, subtribes and/or breeding isolates have
arisen within a single caste or tribe which had a relatively
greater genetic affinity among them as compared to other such
groups (Malhotra, 1978, 1979; Reddy, 1983, 1984, 2010;
Reddy et al., 1995, 1999, 2001a, 2001b, 2001c, 2007; Crawford
et al., 2001; Mitchell et al., 2006; Kumar et al., 2004, 2007). A
number of different factors and/or processes have been impli-
cated to be responsible for such subdivisions and subsequent
maintenance of their endogamy with distinct group identity
(Malhotra, 1978, 1979; Reddy, 2010).
Admixture is also a continual process, which occurs over
many generations. The correct identification of ancestral popu-
lations and the degree of asymmetry in gene flow (sex biased
admixture) are important issues in the admixture studies
(Chakraborty, 1986). Recent studies indicate the trend of
studying ethnic admixture by identifying the patterns of pater-
nal and maternal gene flow and their contribution to the gene
pool of the admixed group, which is made possible with the
analysis of Y-chromosome (paternal) and mtDNA (maternal)
specific markers (Dipierri et al., 1998; Kittles et al., 1999;
Kivisild et al., 1999; Kivisild et al., 2002; Kivisild et al., 2003).
India offers immense variety of such situations, which continue
o fascinate evolutionary anthropologists. The interest in dis-
*Declaration of Interest: The authors report no declarations of interest.
#Banrida, Vikrant and Aruna were with us at ISI as Ph.D. students when
they participated in this project.
Corresponding author. t
B. T. LANGSTIEH ET AL.
Figure 1.
Schematic diagram depicting essential features of Indian population structure. The exogamous “clans” in
tribes are equivalent to “lineages” in the caste and religious groups.
Figure 2.
Location map of Meghalaya showing the core areas of distribution of different sub-tribes of the Khasi,
Lyngngam and Garo. Filled circles denote Khasi subtribes, whereas dotted circle denotes the capital of
Meghalaya (Shillong).
Copyright © 2012 SciRes.
182
B. T. LANGSTIEH ET AL.
secting Indian population structure has therefore been redou-
bled in recent years, especially with the proliferation of DNA
(2
s considered as an Austro-Asiatic group, particu-
la
identify the Lyngngam as “Megam”, one of the sub-
tr
rally intermediate between the Khasis and
th
hur, 1979).
T
n of the Lyngngam and given
th
convincingly. However, based on the linguistic affiliation, it
appears that the Lyngngam might have been relatively more
akin to the Khasi than to the Garo. The Lexico-Statistical
it with a population of about 7000 individuals organ-
iz
ed
from 515 subjects, after obtaining written informed consent.
These subjects r Garo, all the 7
a. The sampled popula-
s that could be successfully
sc
examine if Lyngngam has any specific and close relationship
technology and development of rapid screening techniques.
Meghalaya is one of the states of Northeastern India (Figure 2)
inhabited mostly by the tribes whose population is ~2,306,069
001 census). Amidst the ethnic majority of populations with
East Asian physical features and speaking Tibeto-Burman lan-
guages in the northeastern region, while the Khasi represents
Khasi-Khmuic (earlier categorized as Mon-Khmer) speakers of
the Austro-Asiatic linguistic family (Diffloth, 2005), occupying
the central and eastern regions of Meghalaya, the Garo repre-
sents Tibeto-Burman speakers of the state, inhabiting the re-
gions towards the west. These are the two overwhelmingly
predominant, indigenous and linguistically distinct tribal clus-
ters that inhabit Meghalaya, and follow the system of matrilin-
eal descent and matrilocal residence. These two tribal clusters
are found to be genetically also quite distinct (Reddy et al.,
2007). Sandwiched between these two linguistically and ge-
netically contrasting populations of Khasi and Garo there is a
small tribe of shifting cultivators known as Lyngngam, which
inhabits the border areas of west Khasi Hills and South Garo
Hills of Meghalaya. Because of its unique geographic position
with territorial proximity to both the Khasi and Garo, the origin
of the Lyngngam has been disputed, and is claimed to be a
subtribe of both the tribes. Based on the prevalent notions, the
origin and ethnic position of the Lyngngam can be categorized
as follows:
1) Based on the physical features and linguistic similarity,
Lyngngam i
rly under the Mon-Khmer subfamily (Gurdon, 1907; Grierson,
1928; Barrett, 1982). The contemporary Khasis therefore con-
sider the Lyngngam as one of the Khasi subtribes (Rodborne,
1977).
2) Bhattacharjee (1978), Sangma (1981) and a majority of
the Garos
ibes of the Garo.
3) A mixed/hybrid group (Playfair, 1909; Bareh, 1967; Non-
gsiang, 1994), cultu
e Garos (Ehrenfels, 1955). There are only a couple of clans
that are unique to Lyngngam, many other clans have affinity
with and exogamous to certain clans of either the Khasi or Garo,
suggesting probably their evolution from a common ancestor.
Likewise, there are similar as well as distinctive socio-cultural
features of Lyngngam when compared to the neighbouring
Khasi and Garo (Langstieh & Reddy, 1999, 2004).
4) A distinct tribe, probably with an independent origin, cer-
tainly not a sub-tribe of either the Khasi or Garo (Mat
he preliminary genetic and dermatoglyphic evidences (Ahmed
et al., 1997; Thapa et al., 1998) support the Lyngngam as bio-
logically distinct from both the Khasi and Garo. Concurrent to
this most of the informants believe that they were the autoch-
thons of the present habitat in western Meghalaya. The analysis
of folk narratives of the Lyngngam, “Kon Bli”, suggests that
their ancestors were explorers and warriors who came to
Meghalaya and defended the land that they presently occupy
(Langstieh & Reddy, 1999, 2004), suggesting probably the
independent origin of this tribe.
From the foregoing information, no clear answers emerge
regarding origin and ethnic positio
e type of available data it was not possible to resolve the issue
Analysis (Swadesh, 1950, 1951, 1972) of the 200 Lyngngam
and the corresponding Khasi words collected by us suggests
that although Khasi and Lyngngam both speak the broad Khasi-
Khmuic language of the Austro-Asiatic family, their speech
forms might have been separated around 1500 years ago (CI:
1.69 M - 2.09 M years) from a common speech form (Langstieh,
2003).
Our recent exploratory studies (Langstieh & Reddy, 1999,
2004) of this small tribe based on demography, ethnohistory,
marital networks, clan structure and other population structural
measures suggest that Lyngngam as a whole forms an endoga-
mous un
ed into about 1400 households. However, 22% of the Lyngn-
gam marriages were contracted outside this tribe (Langstieh &
Reddy, 1999, 2004), a great majority of those male spouses
coming from the neighbouring Khasi and Garo. The majority of
the Khasi contributors to the Lyngngam fold hail from the
neighbouring Nongtrai, Maram, War, Bhoi and Khynriam sub-
tribes in the decreasing order of frequency and a great majority
of the 29 Lyngngam clans were involved in the exogamous
interactions. Further, the Lyngngam clans suggest a relatively
greater degree of commonness with the Khasi although a cou-
ple of Lyngngam clans could be traced as common with the
Garo as well (Langstieh & Reddy, 1999, 2004). Although the
uniquely identified Lyngngam specific clans suggest that they
might represent the founding ancestors of this admixed popula-
tion, given the Austro-Asiatic affinity of the Lyngngam dialect
and the names of Lyngngam clans suggest probable Khasi ori-
gin of this tribe. Due to its geographic position, this tribe might
have later developed marital interactions with the neighboring
Tibeto Burman Garos. Given the above scenario, there is strong
possibility that the gene pool of the Lyngngam may have dis-
tinct genetic signatures from both these putative parental popu-
lations (Khasi and Garo), while the former is likely to have
overwhelming contribution to the genetic makeup of the
Lyngngam. The results based on molecular genetic markers,
particularly the uniparental mitochondrial DNA (mtDNA) and
Y chromosome (NRY) markers, should reflect these expecta-
tions in a more conclusive way. In the present paper, we shall
outline the findings based on the analysis of molecular genetic
markers-autosomal, mtDNA and Y-chromosome-and test the
degree of correspondence between the molecular genetic evi-
dences and the patterns expected from the ethno-historic and
demographic information and estimate genetic contributions of
different source populations to the gene pool of Lyngngam.
Materials and Methods
Collection of Blood Samples
About 5 ml of intravenous blood samples were collect
epresent, besides Lyngngam and
subtribes of the Khasi tribe of Meghalay
tions and the number of subject
reened for different sets of markers are given in Table 1. As
the language of Lyngngam is known to be similar to that of the
Khasi, blood samples were also collected from all the 7 sub-
tribes of the Khasi besides the neighboring Garo. This may help
Copyright © 2012 SciRes. 183
B. T. LANGSTIEH ET AL.
\
Table 1.
Sample size, location of study and linguistic affiliation of the 9 tribal popuons of Meghalaya of the present study.
No. of subjects
lati
Populations
Auto-STRsY-STR HVS-I HVS-II occupation Meghalay
Traditional Distribution in
a Linguistic affiliation
Lyngngam 78 73 Shi 60 82 fting cultivatorsWest Khasi hills
district
Austro-asiatic
(mon-khmer)
Garo 64 67 87 89
Shifting cultivators &South Garo hill
Nongtrai* 29 18 29 29 West Khasi hills Austro-asiatic
*West Khasi hills Austro-asiatic
Khynriam* 73 82 95 100 Settled agriculturist
East Khasi hills Austro-asiatic
*Ja Austro-asiatic
Bhoi*45 32 34 33 Shifting cultivators Ri-Bhoi district Austro-asiatic
Wa si* 38 East Khasi hills Austro-asiatic
WarJaintia*23 21 22 20 Horticulturist Ja Austro-asiatic
Total 448 401 505 501
Settled agriculturist district & others Tibeto-burman
Shifting cultivators
district (mon-khmer)
Maram 48 58 72 77 Settled agriculturist
district (mon-khmer)
district (mon-khmer)
Pnar 50 40 53 53 Settled agriculturist intia hills district(mon-khmer)
(mon-khmer)
r-Kha 23 31 27 Horticulturist district (mon-khmer)
intia hills district(mon-khmer)
Note: ups of Khas
with anhe Khasi subgroups, thdence that may pr
d with written informed consent of
study has been approved by the institu-
ittee for Protection of Research Risks to
H
as isolated from the above samples following stan-
al., 1989). The extracted DNA was
method followed by verifica-
tio
allele length of DYS389I from DYS389II. Further, mtDNA
hypervariable segment I (HVS I) and hypervariable segment II
(HVS II) of the mtDNA control region were amplified and
sequenced by means of the procedures described in a recent
cs, Mishima, Japan. Pairwise FST
HVSI and HVSII sequences using
ider et al., 2000). In order to assess the
ro
*Dialectical groi.
y of te evie-
cisely help trace its origin.
Ethics Statement
The samples were collecte
all the subjects. This
tional Review Comm
umans.
Laboratory Analyses
DNA w
dard protocol (Sambrook et
quantified by spectrophotometer
n in 0.8% agarose gel (Sambrook et al., 1989). AmpFlSTR
Profiler Plus kit (ABI, Applied Biosystems, USA) (Applied
Biosystems, 2001), which consists of 9 Autosomal STR loci,
was amplified as per the manufacturers instructions. Amplified
samples were analyzed in ABI 377 automated DNA sequencer
and GeneScan and Genotyper softwares (ABI) were used to
obtain the allelic designations at the D3S1358, D8S1179,
D5S181, vWA, D21S11, D13S317, FGA, D7S820 and D18S5
loci. We have also typed the following 6 Y-STR loci: DYS19,
DYS389I, DYS389II, DYS390, DYS391 and DYS393 which
were amplified by multiplex PCR and were analyzed on ABI
3730 sequencer. The GENOTYPER software was used to ana-
lyze the fragment size. The fragment sizes of the alleles were
converted into repeat units as suggested by Butler et al. (2002).
Allele length for DYS389b was obtained by subtracting the
study (Kong et al., 2003). Sequences were edited and mutations
scored relative to the revised Cambridge Reference Sequence
(Andrews et al., 1999). Even though we have screened these
samples for both mtDNA and Y-chromosome SNPs and hap-
logroups resolved, we have already published these data in an
earlier paper (Reddy et al. 2007). The mtDNA sequence data
and the STR frequency data can be obtained from the corre-
sponding author on request.
Statistical Methods
For autosomal and Y-STR markers, the genetic distances
were computed using the modified Cavalli-Sforza distance (DA)
measure of Nei et al. (1983). These computations were per-
formed using the NJBAFD program supplied by Dr. Takezaki,
National Institute of Geneti
distances were calculated for
Arlequin ver 2.0 (Schne
le of geographic distance in the genetic relationship between
Lyngngam and the surrounding tribes of Meghalaya, we ob-
tained mantel correlations, with the help of MANTEL package
(Relethford, 1993), between the geographic distance matrix and
the genetic distance matrixes for different pairs of Meghalaya
tribes using different sets of DNA markers. Finally, multidi-
mensional scaling (MDS) of the genetic distances and the two
dimensional plots of populations in multivariate space were
obtained using SPSS version 7. We used Admix 2.0 package
Copyright © 2012 SciRes.
184
B. T. LANGSTIEH ET AL.
initially developed by Bertorelle and Excoffier (1998) for two
parental populations and extended to any number of parental
populations by Dupanloup and Bertorelle (2000), for obtaining
the admixture proportions of different putative parental popula-
tions.
Results
Phylogenetic Affinity of Lyngngam to Khasi
and Garo
In order to trace the origin of Lyngngam from among the
Meghalaya tribes we examined relative genetic distances of
Lyngngam to the Khasi and Garo populations with reference to
different sets of genetic me 2). This was done in
hasi, all
al
es and the Garo. It is intriguing to note that while
th
ng of the Lyngn-
in
y single Khasi subtribe, the overall contributions of
th
and
f the 7
pr
arkers (Tabl
two stages, first Lyngngam with the neighboring K
Khasi and Garo and then Lyngngam with the 7 individu
Khasi subtrib
e Lyngngam shows much greater affinity to the Khasi when
compared to the Garo in HVS I &II sequences-based distances
as well as in autosomal STR-based distances, it shows greater
affinity to the Garo in the Y-STR distances, suggesting di-
chotomous nature of their genetic relationship to Khasi and
Garo. To see if Lyngngam is specifically close to any particular
Khasi subgroup, the distance matrices were subjected to multi-
dimensional scaling and the plots based on the first two dimen-
sions are presented in Figure 3. This analysis suggests relative
closeness of Lyngngam to the neighboring Bhoi and Khynriam,
when compared to the other Khasi tribes as well as to the Garo
in the autosomal STRs whereas it shows closer affinity in the
decreasing order to the neighboring Nongtrai, Khynriam and
Pnar, and Nongtrai, Khynriam and War Khasi, respectively, in
case of the HVS I & II sequences. This pattern is substantiated
by the significant mantel correlation obtained between geo-
graphic and genetic distance matrices based on HVS I & II
sequences (Table 3). Given matrilineal descent, this may sug-
gest founding of the Lyngngam maternal gene pool predomi-
nantly from a common Khasi source, especially since the ma-
ternal lineages remain relatively static and the admixture is
primarily by way of males moving in from the surrounding
populations. However, in case of Y STRs, Lyngngam is rela-
tively closer to the Garo as well as to a few neighboring Khasi
tribes viz. Khynriam, Maram and Pnar.
Sharing Pattern of the Lyngngam Y-STR and mtDNA
HVS I & II Haplotypes with other Meghalaya Tribes
Y chromosome and mtDNA specific haplotypes are informa-
tive about the history of paternal and maternal lineages of a
population, respectively, hence useful in tracing the origin of
Lyngngam. The relative proportions of shari
gam Y-STR and mtDNA HVS I & II sequence based haplo-
types with those of Khasi and Garo are depicted as pie diagrams
(Figure 4), while the haplotype wise sharing pattern is furnished
Supplementary Tables S1-S3. The mutational positions char-
acterizing each haplotype of HVS I & II are given in Supple-
mentary Tables S4 and S5. Overall, it appears that Khasi con-
tribution to Lyngngam genetic constitution is overwhelmingly
greater and more heterogeneous than the Garo, especially with
reference to maternal lineages. In case of HVS I, 27 of the 40
haplotypes identified from 82 sequences are found to be
Lyngngam specific, while it shares 7 haplotypes exclusively
with Khasi and 6 with both the Khasi and Garo. Lyngngam
shares no HVS I haplotype exclusively with the Garo. Among
the 6 that Lyngngam shares with both Khasi and Garo, haplo-
type 3 and 7 are very predominantly found among the Garo,
while haplotypes 9 and 19 are more widely shared with the
Khasi. Of the 7 haplotypes that the Lyngngam exclusively
shares with the Khasi, 17 and 38 are more widely found among
the latter. Similarly, out of 35 haplotypes identified from the 73
Lyngngam HVS II sequences 20 were found unique to Lyngn-
gam, 10 shared with both the Khasi and Garo and 3 and 2 with
Khasi and Garo, respectively. It is interesting to note that nearly
60% of the Lyngngam samples represent the 10 haplotypes
common to both the Khasi and Garo, while another 14% repre-
sent 5 more haplotypes that are found either in Khasi or Garo.
Out of these 15, while haplotypes 2, 14 and 25 are widely rep-
resented by Khynriam, Nongtrai and Khynriam and Pnar, re-
spectively, haplotypes 1 and 33 are most predominantly found
in Garo.
Out of 54 Y-STR haplotypes identified from 60 male sam-
ples of Lyngngam, 30 were found to be unique to Lyngngam,
while 14 and 7, respectively, were shared with Khasi and Garo.
The remaining 3 haplotypes are shared with both Khasi and
Garo, suggesting that nearly half of Lyngngam male lineages
probably had either Khasi or Garo origin. Although Garo con-
tribution to Lyngngam male lineages outweighs the contribu-
tion of an
e Khasi (25%) seems markedly more heterogeneous as well
as outweigh the Garo contribution (12%). This finding is
somewhat at variance to the pattern observed on the basis of
Y-STR allele frequency based distances in which Lyngngam is
relatively closer to Garo. All the 7 subgroups of Khasi share
haplotypes with Lyngngam although Khynriam and Bhoi share
relatively more haplotypes when compared to others.
Contribution of the Khasi and Garo Tribes of
Meghalaya to the Genetic Constitution of Lyngngam
Using the software Admix2.0, we obtained admixture pro-
portions separately for the 9 autosomal STRs, mtDNA HVS I &
II and 6 Y-STRs. The admixture analysis was structured into 3
categories with Lyngngam assumed to be the hybrid population
and 1) Khasi and Garo, 2) “Neighbouring Khasi” (Nongtrai
Maram), “Other Khasi” and Garo and 3) Garo and each o
individual Khasi populations, respectively, as the putative pa-
rental populations. The results of each of the three analyses are
esented in Table 4. In the first case, the contribution of Khasi
is found to be much greater and much more significant to the
genetic make up of the Lyngngam, when compared to the Garo
in both autosomal STRs (82% against 18%) and mtDNA HVS I
and HVS II sequence data (78% against 22%). Furthermore, it
is evident from the results that the contribution of the
“neighbouring Khasi” subgroups (Nongtrai and Maram) is rela-
tively much greater than those farther apart namely the “Other
Khasi” groups. However, when the individual Khasi popula-
tions were considered the contribution of Garo (31%) in auto-
somal STRs is shown to be greater than any individual Khasi
population; only Maram comes closer (28%) to the contribution
of Garo. Nevertheless, given that the Garo represents the tribe
as a whole, the results of comparison with the pooled sample of
Khasi would be most apt. The situation is somewhat at variance
in the case of mtDNA HVS I & II, where the neighbouring
Nongtrai, one of the Khasi subtribes, contributes disproportion-
ately highly to the genetic constitution of Lyngngam (~53%),
Copyright © 2012 SciRes. 185
B. T. LANGSTIEH ET AL.
Copyright © 2012 SciRes.
186
Table 2.
Lyngngam genetic distances with the 3 broad Meghalaya populations.
Genetic systems (distance measures) Garo Neighboring Khasi All Khasi
Autosomal STRs (Nei’s DA) 0.073 0.062 0.044
Y-STRs (Nei’s DA) 0.052 0.066 0.066
mtDNA HVS-I (pairwise FST) 0.085 0.039 0.025
mtDN FST) A HVS-II (pairwise 0.076 0.053 0.032
Table 3.
Results of Mantel correlations between the distance matrices based on geography and different sets of DNA markers.
Geography Autosomal STR Y-STR mtDNA HVS I
Geography
Autosomal STR 0.1749
Y-STR 0.3919 0.0949
mtDNA HVS I 0.4972* 0.0398 0.4915
mtDNA HVS II 0.4974 0.0978 0.2708 0.797*
*
Table 4.
Admixture pr and their standard s (S.D.) for the autoso(9 loci), Y STR (6mtDNA HVRS I & II.
(a) Two parental populations
oportions (m)deviationmal STR loci) and
Popn N
Autosomal
(m ± S.D.) N Y chromosomal
(m ± S.D.) N
mtDNA
HVS I N
mtDNA
HVS II
m
HV
(m ± S.D.) (m ± S.D.)
tDNA
S I+II
(m ± S.D.)
Khasi 650 0.8151 ± 0.1310 274 0.3220 ± 94 ± 0.0726 344 0.6052 ± 0.1000 0.7787 ± 0.0707
0.0 0.220.390.2
(b) Three parental populations
0.1895 353 0.77
Garo 128 1849 ± 0.13167 0.6780 ± 0.1895 87 06 ± 0.0726 94 48 ± 0.1000 213 ± 0.0707
Neigh. Khasi 186 0.5122 ± 0.1395 76 0.1607 ± 1.7581 102 0.3971 ± 0.2294 106 0.0984 ± 0.2137 0.3916 ± 0.2236
Other Khasi 464 0.2382 ± 0.1583 198 0.2148 ± 1.8829 251 0.3913 ± 0.2239 238 0.6016 ± 0.2040 0.3990 ± 0.2135
Garo 128 0.2496 ± 0.1140 67 0.6244 ± 0.3211 87 0.2117 ± 0.0747 94 0.3000 ± 0.1066 0.2094 ± 0.0730
(c) Nine individual Meghalaya populations
Popn N
Autosomal
(m ± S.D.) N Y chromosomal
(m ± S.D.)
N
mtDNA
(m ± S.D.)
mtDNA
(m ± S.D.)
mtDNA
(m ± S.D.)
HVS I N HVS II HVS I + II
Nongtrai 90 0.1850 ± 0.1354 18 3005 29 0.3925 ± 0.1928 0.5310 ± 0.2821
M0.7 0.020.12 0.0
Khynriam 146 0.0177 ± 0.3536 82 0.0476 ± 2.8416 95 0.05100 0.340.03
Pnar 100 0.1131 ± 0.1652 40 0.3932 ± 3.2148 69 0.1160 ± 0.1481 58 0.1266 ± 0.1972 0.1250 ± 0.1568
Bhoi 90 0.1517 ± 0.3341 32 0.1736 ± 1.8787 34 0.0789 ± 0.0989 33 0.0884 ± 0.1983 0.0753 ± 0.0985
War-Khasi 82 0.0016 ± 0.1235 23 0.1572 ± 1.2828 31 0.0939 ± 0.1555 27 0.0168 ± 0.1302 0.0963 ± 0.1567
War-Jaintia 46 0.0216 ± 0.3448 21 0.2828 ± 1.0826 22 0.0005 ± 0.042520 0.0742 ± 0.0850 0.0001 ± 0.0423
Garo 128 0.3065 ± 0.1824 67 0.7939 ± 1.6881 87 0.1047 ± 0.1544 94 0.1509 ± 0.1380 0.1039 ± 0.1436
0.0467 ± 1.2817 30 0.5231 ± 0.
aram 96 2814 ± 0.16758 0.2386 ± 2.7037 72 67 ± 0.1975 77 624 ± 0.1370304 ± 0.205
72 ± 0.2929 66 ± 0.2691 81 ± 0.2925
Note: N = Sample size.
*
B. T. LANGSTIEH ET AL.
Figure 3.
Projection of Meghalaya tribal populations on the two-dimensional space based on the multi-dimensional scaling distances based on different sets of
markers (For MDS, the stress value and R2 for Autosomal STR, Y-STR, HVS I and HVS II are 0.124 & 0.94, 0.214 & 0.84, 0.149 & 0.93 and 0.142
& 0.92, respectively); (a) Autosomal STRS; (b) Y-STRS; (c) mtDNA HVRI; (d) mtDNA HVRII.
Figure 4.
Pattern of sharing of mtDNA and Y-STR haplotypes between Lyngngam individuals and putative parental populations, the Khasi and Garo.
the next highest contribution being from Pnar (12%) and Garo the trend observed in Y-STR haplotype sharing, suggest that
the Garo contribution (68%) to Lyngngam outweighs that of th
2%) in
r Khasi
(11%).
On the other hand, the admixture proportions based on the
allele frequency at the 6 Y-chromosome STR loci, contrary to
Khasi (32%). Garo contribution is similarly high (6
comparison to the neighbouring Khasi (16%) and othe
e
Copyright © 2012 SciRes. 187
B. T. LANGSTIEH ET AL.
groups (22%). Further, when individual Khasi subtribes are
ution of Garo turns out to be much higher (79%).
r-
i-
versity of this region ashe other regions of the
country (Clark et al., 2000; Dutt; Cordaux et al.,
20
these populations are somewhat permeable, creating possibili-
considered as putative parental populations along with Garo,
the contrib
Discussion
Northeast region of India was considered as an important
corridor for historic and prehistoric movement of populations
into and out of the Indian subcontinent (Clark et al., 2000; Cor-
daux et al., 2003, 2004; Reddy et al., 2007) and provides com-
plex population history characterized by multiple ethnic, lin-
guistic and migration backgrounds. This has resulted in eno
mous cultural (Hussain, 1991; Sharma, 1966) and genetic d
compared to t
a et al., 2002
04; Langstieh et al., 2004b; Reddy et al., 2005). Populations
of this region are predominantly of tribal origin, interspersed
with some caste populations. Composed of East Asian and
European ethnic elements, they speak languages of three major
linguistic families-Tibeto-Burman, Indo-European and Austro-
Asiatic. Unlike in the rest of India, the tribal boundaries of
ties for exchange of genes among them. The Lyngngam tribe of
Meghalaya whose genetic origins are being investigated is in
the midst of Austro-Asiatic Khasi and Tibeto-Burman Garo, the
two tribal clusters that primarily inhabit this state. Having been
affiliated to the same linguistic group, there is every indication
that the Lyngngam might have originated from the common
source as that of the Khasi populations. However, given its
geographic position contiguous to Garo and only to a couple of
Khasi subtribes, the Lyngngam has had little day-to-day inter-
action with the majority of the Khasi sub-tribes. In the above
background, despite the lack of mobility of female lineages in
this matrilocal society, the high proportions of Khasi specific
autosomal and mtDNA lineages observed in the Lyngngam and
vice versa reflect that the initial constitution/founding of female
lineages of the Lyngngam and Khasi sub-populations probably
would have been from a common source. As far as the individ-
ual Khasi populations are concerned, the Nongtrai neighbor
seems the most probable candidate to have contributed pre-
dominantly to the Lyngngam female lineages as reflected by
not only the high proportion of admixture (~53%) with refer-
Figure 5.
Plot on the first two dimensions derived from the multi-dimensional scaling of the pairwise FST distances of the populations based on
Y-haplogroups (for comparative data, refer Reddy et al., 2007). SEA = Southeast Asian; AA = Austro-Asiatic; IE = Indo-European; TB =
Tibeto-Burman; Khy = Khynriam; Lyn = Lyngngam; Wkhasi = War Khasi; Viet = Vietnamese (adapted from Reddy et al., 2007).
Copyright © 2012 SciRes.
188
B. T. LANGSTIEH ET AL.
Figure 6.
Plot on the first two-dimensions derived from the multidimensional scaling of the pairwise FST distances of the populations based on mtDNA hap-
logr an;
Wk
enc
common maternal clans found among the Nongtrai and Lyngn-
gam (Langstieh & Reddy, 2004). This is reflected partly in the
high mantel correlation between geographic and genetic dis-
tance matrices based on mtDNA sequences as well as in the
relative proximity of the Lyngngam to the Nongtrai in the MDS
plot based on mtDNA distances (Figure 3).
To sum up, the foregoing analyses of the ethnohistoric, lin-
guistic and demographic information in conjunction with the
molecular genetic evidence trace Khasi (more particularly the
Nongtrai subtribe of Khasi) as the most probable parental source
of the Lyngngam, which is consistent with the first of the four
notions concerning the origin of this tribe as outlined in the in-
troduction. Nevertheless, it is necessary to discount the possibil-
ity of Lyngngam origin from the sources outside Megha-
laya/India, particularly from the populations of Southeast Asia,
where from many Tibeto-Burman populations were known to
have migrated to Northeast India, before any rational conclu-
sion on their origin can be drawn. A strong support for Khasi
origin of the Lyngngam can be drawn from Reddy et al. (2007)
who performed multidimensional scaling analysis of the FST
distances based on mtDNA and Y-chromosome haplogroup
ustro-Asiatic
populations from the South and Southeast Asia, including the 7
Khasi subtribes, Lyngngam and Garo of the present study. The
two-dimensional plots representing the populations in the mul-
tivariate space are reproduced here for Y-chromosome (Figure
5) and mtDNA (Figure 6). The position of Lyngngam in both
the plots is relatively more proximate to the Austro-Asiatic
Khasi tribes of Meghalaya when compared to the Garo as well
as to other South Asian and Southeast Asian populations,
Austro-Asiatic or non Austro-Asiatic, ruling out the possibility
of their origin from outside Meghalaya and/or outside the
Austro-Asiatic Khasi. There is nothing in the results that goes
against concluding Khasi (particularly the Nongtrai) origin of
the Lyngngam tribe despite limited statistical power of the
study with small number of genetic loci employed.
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A
T
and G
ppendix
able S1.
Sharing pattern of the Lyngam Y-haplotypes with the neighbouring Khasiaro.
DYS DYS DYS DYS DYSDYS
Hap. No. 19 389I 389II 390 391393LynglGaroNongMaraKhynPnar Bhoi WarK WarJTota
Unique to L
1
1
1
9 10 12 1
1
1
1
1
1
1
1
1
1
1
1
Hap23 16 9 26 11 10 13 1 1
Hap24 16 10 26 11 10 14 1 1
Hap25 15 10 27 9 10 14 1
1
Hap26 17 10 27 10 10 13 1 1
yngam
Hap1 14 11 27 9 10 11
1
Hap2 16 9 26 11 10 12 2
Hap3 15 11 27 9 10 13 1
2
1
Hap4 14 9 25 10 10 13 1
Hap5 14 10 25
1
10 10 13
Hap6 15 10 27 11 10 12 1
1
1
1
Hap7 14 9 27 9 10 13 1
Hap8 15 8 29 11 10 13 1
Hap9 15 8 27
1
Hap10 12 9 26 9 10 12
1
Hap11 15 9 26 11 10 13 1
Hap12 15 9 28 11 10 13
1
1
1
1
Hap13 15 14 28 10 10 12 1
Hap14 12 9 28 10 10 14
Hap15 13 9 26 9 10 16
Hap16 16 9 27 10 11 13
Hap17 15 9 27 10 11 13
1
1
1 Hap18 15 8 27 10 10 13
Hap19 17 10 27 10 10 12
Hap20 15 10 26 11 11 12
1
1
1 Hap21 16 10 28 10 10 13 1
Hap22 15 10 27 9 11 16 1
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B. T. LANGSTIEH ET AL.
Continued
15 10 24 12 10 13 1 1 Hap27
Hap28 15 11 28 8 11 11 1
1
1
Ha30 1 1
Shared with either Khasi or Garo
Hap31 15 9 27 10 10 12 1 3 4
Hap32 14 9 25 9 10 11 1 2
3
Hap33 15 9 26 9 11 12 1 1
2
Ha 15 9 26 10 10 11 1 1
Ha 1
areith boKhasi and Ga
Hap54 15 9 26 9 10 11 2 3 1 1
7
Hap29 15 11 28 8 10 12 1
p14 9 26 10 11 11
p34 2
p35 15 10 29 11 10 12 1 2
Hap36 13 10 27 10 10 12 1 1 2
Hap37 17 9 26 10 10 11 1 1 1 3
Hap38 15 10 27 9 10 13 1 1
2
Hap39 15 9 27 9 11 12 1 1
2
Hap40 15 9 27 9 10 11 1 1
2
Hap41 14 9 26 9 10 13 1 1
2
Hap42 15 11 27 11 11 13 1 1 2
Hap43 15 10 26 11 11 13 2 1 1 4
Hap44 15 11 29 11 10 12 1 1 2
Hap45 16 11 28 11 11 12 1 2 3
Hap46 15 10 27 9 11 12 1 1 1
3
Hap47 15 11 26 11 11 13 1 1 2
Hap48 15 9 26 11 10 11 1 1 2 4
Hap49 16 10 27 11 10 12 1 1 1 3
Hap50 16 10 26 11 10 12 1 1 2
Hap51 15 10 26 9 11 13 1 3
4
Shd wth ro
Hap52 15 10 27 10 10 13 1 2 1 1 5
Hap53 15 9 27 10 10 13 3 1 1 5
Copyright © 2012 SciRes. 193
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Table S2.
Dn and uency of nallyred R I otyf Lyngam and Khasi population
pe ngngamGong aram KhriamPnahWarKhasi Waraintia
istributiofreqmater shaHVhaplpes ong with Garos.
HaplotyLy aro NtraiM ynr Boi J
n = 82 n = 87 n = 30 n = 72 n = 95 n = 69n = 34n = 31 n = 22
Unique to Lyngng Total
1 0 0 0 0 0 0 0 0 1
1 0 0 0 0 0 1
1 0 0 0 0 0 0 0 0 1
1 0 0 0 0 0 0 0 0 1
1 0 0 0 0 0 1
6 1 0 0 0 0 0 0 1
7 1 0 0 0 0 0 0 0 0 1
1 0 0 0 0 0 1
1 0 0 0 0 0 0 0 1
5 0 0 0 0 0 0 0 0 5
1 0 0 0 0 0 1
1 0 0 0 0 0 0 0 1
13 1 0 0 0 0 0 0 0 0 1
1 0 0 0 0 0 1
2 0 0 0 0 0 0 0 2
1 0 0 0 0 0 0 0 0 1
1 0 0 0 0 0 1
1 0 0 0 0 0 0 0 1
19 1 0 0 0 0 0 0 0 0 1
1 0 0 0 0 0 1
1 0 0 0 0 0 0 0 1
22 1 0 0 0 0 0 0 0 0 1
2 0 0 0 0 0 2
24 1 0 0 0 0 0 0 0 0 1
1 0 0 0 0 0 1
1 0 0 0 0 0 1
27 1 0 0 0 0 0 0 0 0 1
Sharith only
28 1 0 0 0 5 0 0 0 1 7
5 0 1 2 5 4 28
2 0 0 1 0 0 3
31 1 0 1 0 0 0 0 0 0 2
1 0 1 1 0 0 3
1 0 0 12 3 1 23
34 1 0 0 0 0 0 0 2 0 3
red wth Khasd Gar
3 10 1 0 1 1 0 0 0 16
36 9 42 3 0 0 0 0 1 0 55
14 1 4 3 4 1 30
38 3 1 3 2 0 0 0 14
39 4 2 1 0 0 0 0 0 0 7
4 1 0 1 0 0 7
am
1
2 00 0
3
4
5 00 0
0 0
8 00 0
9
10
0
11 00 0
12 0
14 00 0
15
16
0
17 00 0
18 0
20 00 0
21 0
23 00 0
25 00 0
26 00 0
ed wKhasi
29 81 2
30 00 0
32 00 0
33 60 0
Shaith boi ano
35
37 21 0
5 0
40 01 0
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B. T. LANGSTIEH ET AL.
Table S3.
Dn and uency of ternallyredR Ilotyof Lngamith G and Khasi populatio
Htype Lyng NonMm KhyPr oi Wa WarJ
istributiofreqma sha HVI happes yng warons.
Sl. No. aploGarog aran naBhrK
n = 73 n = 94 n = 29 n = 77 n = 100n = 58 n = 33 n = 27 n = 20
Unique to Lyngngam Total
1 0 0 0
2 101 0 0 0
3 1 0 0 0 0 0 0 0
4 13 1 0 0 0 0 0 0 0
5 17 1 0 0 0 0 0 0 0
6 18 1 0 0 0 0 0 0 0
7 19 1 0 0 0 0 0 0 0
8 20 1 0 0 0 0 0 0 0
9 21 1 0 0 0 0 0 0 0
122 1 0 0 0 0 0 0 0
123 1 0 0 0 0 0 0 0
128 1 0 0 0 0 0 0 0
13 29 1 0 0 0 0 0 0 0
14 30 1 0 0 0 0 0 0 0
131 1 0 0 0 0 0 0 0
132 1 0 0 0 0 0 0 0
134 1 0 0 0 0 0 0 0
135 1 0 0 0 0 0 0 0
Shareith both Khasi and Garo
11 6 19 3 0 0 0 0 0
22 8 1 1 0 9 2 1 0
23 1 2 0 0 0 2 1 0
22 9 5 1 1 1 1 1 1 0 11
214 6 1 6 0 2 2 0 0
215 2 1 1 0 0 0 0 0
216 1 2 1 1 1 1 0 1
224 1 1 0 0 2 2 0 0
27 2 4 11 17 3 1 47
227 6 1 0 0 1 2 1 1
Shared with onlyasi
24 1 0 0 0 0 2 0 0
30 5 1 0 0 0 0 0 0 0
31 6 1 0 2 2 1 0 3 0
32 11 5 0 1 0 0 0 0 0
33 0 1 0 0 0 0
Sared with onlyro
38 1 1 0 0 0 0 0 0
333 1 14 0 0 0 0 0 0
1 7 0 0 00 0 1
0 0 0 0 0 1
12 0 1
0 1
0 1
0 1
0 1
0 1
0 1
0 0 1
1 0 1
2 0 1
0 1
0 1
5 0 1
6 0 1
7 0 1
8 0 1
d w
9 0 28
0 1 23
1 0 6
0
3 0 17
4 0 4
5 0 8
6 0 6
25 7 2 0
8 0 12
Kh
9 1 4
3 4
0 9
0 6
26 2 0 0 3
h Ga
4 0 2
5 0 15
Copyright © 2012 SciRes. 195
B. T. LANGSTIEH ET AL.
Table
mtDNVRI haplotyporresponding mutated positions for the Lyngngam population.
lotypes Mutatedsitions (nucide posits 160246400)
S4.
A Hes and their c
Hap poleotion - 1
Hap1 16081T, 16168, 16311
Hap2 16168, 16311
Hap3 1, 31
Hap4
Hap5 16111,129
Hap6 1, 16172,209, 162 16244, 12del, 16
Hap7 16
Hap8 93, 16136,223, 16
Hap9 23, 16225,234, 16
Hap10 16037, 23, 16225,234, 16 16390
Hap11 23, 16225,234, 16
Hap12 057A, 16A, 1631
Hap13 160 16087C,95, 16126223, 16, 16324,362
Hap14 1609158, 16 16234,362
Hap15 16223, 16 16362
Hap16 16187, 16 16362
Hap17 37, 16187,223, 16
Hap18 16024C, 1, 16028A, 16029G037, 160 16223, 4, 1636
Hap19 16223,362
Hap20 74, 16223,362, 16
Hap21 16085G23, 16296305, 163del, 16316326, 163 16338C343T, 16, 163560, 1, 1636
Hap22 16046055, 161, 16168,311
Hap23 49, 16288,295, 16
Hap24 225, 162 16330G
Hap25 16158, 16 16234
Hap26 16093,158, 1623355A,362G
Hap27 16176183, 162 16296A324
Hap28 165, 16234,358A, 16
Hap29 16, 160406078C, 2A, 1622 16261, 14, 163116357del,362
Hap30 16l, 1602l, 16029G6223, 16 16234, 90
Hap31 1616 16223, 165, 16234, 16390
Hap32 16024 16025del, 128del, 160del, 16032l, 16061A071G, 1, 160, 16085088A,93, 1617
161836324
Hap33 160el, 16029032G,16
Hap34 1602el, 16132C223T, 16362C
Hap35 4del, 16 16129, 117, 16226261, 16
Hap37 16223,362
Hap38 1609145, 16 16261,311
Hap39 16051,168
Hap40 16158, 16 16234
160516168, 161
16168
16
1605 1639,635354
316
160 16311
162 16390
162 16354,
162 16390
160616
43, 1607, 1259 16
3, 16223, 16
311,
223,
160 16362
6025A, 1643,16272
16
161 16365
, 1620, 1129, 131,, 16349C8, 1636362G8,
2, 118T 16
162 16304
16 34,
223,
164, 16 16
2, 195,, 16
22 16390
024GA, 116093,627, 1 16
024de5de, 1225,163
2, 22
del,6029de, 166082A83AG, 16 1602,
C, 1
24dG, 16 163
4d, 16
1602037,623, 1362
16
3, 16223, 16
16
209,
Copyright © 2012 SciRes.
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Copyright © 2012 SciRes. 197
Table S5.
mtDN HVRII haplotding mutated positions for the Lyngnga population.
Haplotype Mutasitions
(np8 - 429)
Aypes and their corresponm
s ted po
s 3
Hap1 73, 150, 263, 293, 309insCT
Hap2 73, 150, 152, 153, 263, 309insT
Hap3 73,09insT
nsT
73,nsT, 316
73, 152, 2insC, 315insC
73,09insT
73, 1 309insT
T
3 8
4
5
6 T
7 42, 73, 26 320, 343, 345
8 32, 40, 57, 60, 376C, 384T, 390
9
0 64, 73,sT, 356insC
220A, 226G, 233A, 236A, 239A,, 280, 297C, 309insCCT, 329, 392G
T
5
6
7
8
9
0
1
2 insT
3
Hap35 125G, 148, 150, 309insCT
152, 234, 249del, 263, 3
Hap4 73, 152, 153, 309i
Hap5 152, 249del, 263, 309i
Hap6 63, 309
Hap7 151, 152, 263, 3
Hap8 73, 152, 195, 263, 309insT
Hap9 46, 263,
Hap10 73, 89, 92, 93, 263, 309ins
Hap11 73, 92, 93, 263, 309insT
Hap12 73, 89, 92, 263, 309insT
Hap173, 94, 263, 309insT, 36
Hap173, 199, 263, 309insT
Hap173, 199, 309insT
Hap173, 263, 309insCC
Hap13, 293, 309insCT, 317,
Hap1 63, 73, 263, 309insT, 363, 367,
Hap164, 73, 150, 263, 293, 309insCT, 317, 320G
Hap2 150, 199, 309in
Hap21 258A, 260A, 263, 270C, 272C
Hap22 73, 150, 199, 309insT
Hap23 73, 263, 309insT, 382A
Hap24 73, 152, 263, 309ins
Hap273, 263, 309insCT
Hap273, 195, 263, 309insCT
Hap273, 199, 249del, 263, 309insT
Hap273, 263, 278C, 280, 309insT
Hap273, 263, 309insCT
Hap373, 199, 249del, 263, 309insT, 382A
Hap373, 199, 249del, 263, 309insT
Hap373, 199, 263, 309
Hap373, 207, 263, 293, 309insCT
Hap34 71del, 73, 249del, 293