Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese

Abstract

We present 42 new Y-chromosomal sequences from diverse Indian tribal and non-tribal populations, including the Jarawa and Onge from the Andaman Islands, which are analysed within a calibrated Y-chromosomal phylogeny incorporating South Asian (in total 305 individuals) and worldwide (in total 1286 individuals) data from the 1000 Genomes Project. In contrast to the more ancient ancestry in the South than in the North that has been claimed, we detected very similar coalescence times within Northern and Southern non-tribal Indian populations. A closest neighbour analysis in the phylogeny showed that Indian populations have an affinity towards Southern European populations and that the time of divergence from these populations substantially predated the Indo-European migration into India, probably reflecting ancient shared ancestry rather than the Indo-European migration, which had little effect on Indian male lineages. Among the tribal populations, the Birhor (Austro-Asiatic-speaking) and Irula (Dravidian-speaking) are the nearest neighbours of South Asian non-tribal populations, with a common origin in the last few millennia. In contrast, the Riang (Tibeto-Burman-speaking) and Andamanese have their nearest neighbour lineages in East Asia. The Jarawa and Onge shared haplogroup D lineages with each other within the last ~7000 years, but had diverged from Japanese haplogroup D Y-chromosomes ~53000 years ago, most likely by a split from a shared ancestral population. This analysis suggests that Indian populations have complex ancestry which cannot be explained by a single expansion model.

A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations

“…Studying the Indian population history has always been a challenging task owing to its past demographic events and the complex organization of the extant human populations. Although, studies based on autosomal data reported a North to South genetic cline for non-tribal Indian populations 9 , 14 ; other studies with Y-chromosomal markers were unable to corroborate such a cline 3 , 11 , 15 . Y-chromosome based worldwide comparisons of Indian populations showed their closest affinities with some European populations 3 .…”

“…However, few haplogroups (e.g. haplogroup J) that were reported to be frequent in India are also traced to outside of the Indian sub-continent 3 . Studying the Indian population history has always been a challenging task owing to its past demographic events and the complex organization of the extant human populations.…”

Early replacement of West Eurasian male Y chromosomes from the east

“…Data Y-chromosomal data from high-coverage whole-genome sequenced samples were combined from the following publicly available or published datasets: the Simons Genome Diversity Project (SGDP) 1 , Polaris (https://github.com/Illumina/Polaris), the Human Genome Diversity Project (HGDP) 16,17 , the Andaman Islands samples 19 , haplogroup D0 samples from Nigeria and additional haplogroup D samples from Tibet 7 , Australian haplogroup C samples 18 and a haplogroup F* Singapore Malay sample SSM072 20 . Fifty low-coverage whole-genome sequenced samples from the 1000 Genomes Project dataset 14 were included to represent some of the deep-rooting lineages of haplogroups A, C, F, and H that were not present in other datasets.…”

“…We therefore set out to re-examine the early divergences within these three lineages in order to investigate the insights they can provide into male history and perhaps human history more generally in this early period. We assembled available sequences of C, D and FT lineages from worldwide surveys ensuring that common lineages were represented 1,13,14,16,17 , and supplemented them with additional sequences from known rare lineages potentially relevant to early divergences: specifically, Australian C 1,18 , West African D0 7 , Andamanese D 19 , and F chromosomes from China 1 , Vietnam 14 and Singapore 20 : 1204 sequences in all. We then focussed on the phylogenetic structure of the early divergences within these three lineages, and their geographical distributions revealed by ancient DNA and present-day analyses.…”

Past successes and future opportunities for the genetics of the human Y chromosome

“…Two original investigations document Y-chromosomal variation in the two largest populations in the world: China via typing Y-STRs in ~38,000 men (Nothnagel et al 2017) revealing a north–south gradient in the Han together with some genetically distinct ethnicities, and India via full re-sequencing of a small, but carefully chosen, set of 42 Y chromosomes (Mondal et al 2017) highlighting the unique genetics of the people from the Andaman Islands. The rest of the Special Issue offers probably the most comprehensive collection of review articles ever on the human Y chromosome.…”