Population Genetic Structure in Indian Austroasiatic Speakers: The Role of Landscape Barriers and Sex-Specific Admixture

Abstract

The geographic origin and time of dispersal of Austroasiatic (AA) speakers, presently settled in south and southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. The first of these places the origin of Austroasiatic speakers in southeast Asia with a later dispersal to south Asia during the Neolithic, whereas the second hypothesis advocates pre-Neolithic origins and dispersal of this language family from south Asia. To test the two alternative models, this study combines the analysis of uniparentally inherited markers with 610,000 common single nucleotide polymorphism loci from the nuclear genome. Indian AA speakers have high frequencies of Y chromosome haplogroup O2a; our results show that this haplogroup has significantly higher diversity and coalescent time (17-28 thousand years ago) in southeast Asia, strongly supporting the first of the two hypotheses. Nevertheless, the results of principal component and "structure-like" analyses on autosomal loci also show that the population history of AA speakers in India is more complex, being characterized by two ancestral components-one represented in the pattern of Y chromosomal and EDAR results and the other by mitochondrial DNA diversity and genomic structure. We propose that AA speakers in India today are derived from dispersal from southeast Asia, followed by extensive sex-specific admixture with local Indian populations.

A Genetic Focus on the Peopling History of East Asia: Critical Views

“…However, they share common genetic features with non-Austroasiatic populations in India (at all HLA loci), but also a few characteristics with Austroasiatic populations from Southeast Asia. The analysis of Y chromosome markers indicates a high frequency of haplogroup M95 (O2a) in Austroasiatic populations including the Munda (Chaubey et al 2011;Kumar et al 2007;Sengupta et al 2006;Thangaraj et al 2003). However, based on different levels of haplotypic diversity, several independent genetic studies present opposite views regarding the geographic origin of this haplotype, which has been suggested either in India (Basu et al 2003;Kumar et al 2007) or in Southeast Asia (Chaubey et al 2011;Sahoo et al 2006;Sengupta et al 2006).…”

“…-As the Munda exhibit a high frequency and diversity of Y chromosome M95 (O2a) haplotypes Kumar et al 2007;Reddy and Kumar 2008;Sengupta et al 2006;Su et al 2000Su et al , 1999, the origin of the Austroasiatic phylum has been claimed to occur in India around 65,000 years BP according to the age estimated for this haplogroup (Kumar et al 2007), by contrast to the young age of 8,800 years previously given by Kayser et al (2003). More recently, an age of about 20,000 years has been established for O-M95, resulting in an opposite interpretation: Austroasiatic populations would have a Southeast Asian origin, and those migrating to Northeast India would have extensively admixed with Indian populations (Chaubey et al 2011). This latter view is in close agreement with our own results based on the HLA polymorphism (Riccio et al 2011).…”

Genetic analysis of novel Alu insertion polymorphisms in selected indian populations

“…These conclusions are strongly supported by other studies on STR, Alus, mtDNA, Y chromosome and other expansive genome-wide evaluations of Indian populations (Basu et al 2003;Sahoo et al 2006;Reich et al 2009;Chaubey et al 2011;Mastana, 2014;ArunKumar et al 2015). Further populations studies are required on these Alus to deconvolute the level and extent of genetic variation and population origins.…”

Retrieving Y chromosomal haplogroup trees using GWAS data

“…The 900015 markers on this chip captured 81% variation (r 2 40.8) with minor allele frequency 45% in East Asians (CHB þ JPT). Given the close relationship between East and Southeast Asians, 12 …”

“…We test our approach using data of DNA chips from populations in Myanmar (also known as Burma). Only sporadic sampling exists for Myanmar 12 and, thus, a systematic investigation of the Y chromosome diversity is wanting. In addition to providing a practical protocol of analyzing Y-SNPs from GWAS data, our work adds an essential piece to the genetic puzzle for Southeast Asians.…”