Molecular Genetic Perspectives on the Origin of the Lyngngam Tribe of Meghalaya, India

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

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).

182

B. T. LANGSTIEH ET AL.

secting Indian population structure has therefore been redou-

bled in recent years, especially with the proliferation of DNA

s considered as an Austro-Asiatic group, particu-

identify the Lyngngam as “Megam”, one of the sub-

rally intermediate between the Khasis and

hur, 1979).

n of the Lyngngam and given

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-

from 515 subjects, after obtaining written informed consent.

These subjects r Garo, all the 7

a. The sampled popula-

s that could be successfully

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

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)

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

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

*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

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

es and the Garo. It is intriguing to note that while

ng of the Lyngn-

y single Khasi subtribe, the overall contributions of

and

f the 7

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%),

B. T. LANGSTIEH ET AL.

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 ± 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

Popn N

Autosomal

(m ± S.D.) N Y chromosomal

(m ± S.D.)

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 0.02−0.12 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

B. T. LANGSTIEH ET AL.

groups (22%). Further, when individual Khasi subtribes are

ution of Garo turns out to be much higher (79%).

versity of this region ashe other regions of the

country (Clark et al., 2000; Dutt; Cordaux et al.,

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).

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;

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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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

9 10 12 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

Hap26 17 10 27 10 10 13 1 1

yngam

Hap1 14 11 27 9 10 11

Hap2 16 9 26 11 10 12 2

Hap3 15 11 27 9 10 13 1

Hap4 14 9 25 10 10 13 1

Hap5 14 10 25

10 10 13

Hap6 15 10 27 11 10 12 1

Hap7 14 9 27 9 10 13 1

Hap8 15 8 29 11 10 13 1

Hap9 15 8 27

Hap10 12 9 26 9 10 12

Hap11 15 9 26 11 10 13 1

Hap12 15 9 28 11 10 13

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 Hap18 15 8 27 10 10 13

Hap19 17 10 27 10 10 12

Hap20 15 10 26 11 11 12

1 Hap21 16 10 28 10 10 13 1

Hap22 15 10 27 9 11 16 1

192

B. T. LANGSTIEH ET AL.

Continued

15 10 24 12 10 13 1 1 Hap27

Hap28 15 11 28 8 11 11 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

Hap33 15 9 26 9 11 12 1 1

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

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

Hap39 15 9 27 9 11 12 1 1

Hap40 15 9 27 9 10 11 1 1

Hap41 14 9 26 9 10 13 1 1

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

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

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

B. T. LANGSTIEH ET AL.

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 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

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

2 00 0

5 00 0

0 0

8 00 0

11 00 0

12 0

14 00 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

37 21 0

5 0

40 01 0

194

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 0 1

1 0 1

2 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

3 0 17

4 0 4

5 0 8

6 0 6

25 7 2 0

8 0 12

9 1 4

3 4

0 9

0 6

26 2 0 0 3

h Ga

4 0 2

5 0 15

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

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

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

3, 16223, 16

209,

196

B. T. LANGSTIEH ET AL.

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

3 8

6 T

7 42, 73, 26 320, 343, 345

8 32, 40, 57, 60, 376C, 384T, 390

0 64, 73,sT, 356insC

220A, 226G, 233A, 236A, 239A,, 280, 297C, 309insCCT, 329, 392G

2 insT

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

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Molecular Genetic Perspectives on the Origin of the Lyngngam Tribe of Meghalaya, India

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