Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation

Abstract

To shed light on the peopling of South Asia and the origins of the morphological adaptations found there, we analyzed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals from mainland Indian populations with different ethnic histories and with publicly available data from other populations. We show that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration. We also show that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, and this ancestry is absent from Europeans and East Asians. The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size.

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

“…1); for more information about the populations, see Mondal et al (2016). Data from South Asia from the 1000 Genomes Project was integrated in the study, resulting in a total of 305 South Asian Y-chromosome sequences.…”

“…In the present study, we have investigated the male side of Indian history by reconstructing sequence-based Y-chromosome phylogenies and analysing them from a wide set of populations, incorporating new non-tribal and tribal (including Andamanese) populations (Mondal et al 2016), together with non-tribal populations from South Asia from the 1000 Genomes Project (The 1000 Genomes Project Consortium 2015). We focused on elucidating the ancestry of South Asian non-tribal populations, as well as the divergence time of the Andamanese and Japanese haplogroup D chromosomes.…”

Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

“…However, genomic studies of ancient DNA have revealed that AMH interbred with other hominid lineages, such as Neanderthals and Denisovans, present in Eurasia up to ∼30,000-50,000 years ago Quach & Quintana-Murci, 2017;Vattathil & Akey, 2015 New studies based on current genetic diversity are suggesting that the events of archaic introgression in AMH did occur out of Africa with other hidden "ghost" archaic populations (Mondal et al, 2016). Furthermore, there is growing evidence that archaic introgression occurred also within Africa (Labuda et al, 2000;Hammer et al, 2011;Lachance et al, 2012;Hsieh et al, 2016;Xu et al, 2017; Zanolli et al, 2017), raising the exciting possibility that other unknown archaic groups may have contributed to human genetic diversity.…”

“…Figure 1. Family tree of the four groups of early humans living in Eurasia 50,000 years ago and the inferred gene flow between the groups due to interbreeding (based on Prüfer et al, 2014;Mondal et al, 2016;Hsieh et al, 2016; Medina-Gomez et al, 2017). The direction and estimated magnitude of inferred gene flow events are shown.…”

Pleistocene Hominin Fossil Femora and Humeri

“…The unpublished detailed study by the author [2] had also hinted at similar inferences. On such body adaptations, it may be reasonable to postulate that the Narmada hominins might contain the DISCUSSION common ancestors of the 'small-bodied' later Pleistocene and Holocene ancient populations that inhabited Indian mainland, including the Andaman pygmies [24 -27], who also shared mtDNA signatures until their split ~25 kya [28][29][30].…”