Genome-wide data substantiate Holocene gene flow from India to Australia

Abstract

The Australian continent holds some of the earliest archaeological evidence for the expansion of modern humans out of Africa, with initial occupation at least 40,000 y ago. It is commonly assumed that Australia remained largely isolated following initial colonization, but the genetic history of Australians has not been explored in detail to address this issue. Here, we analyze large-scale genotyping data from aboriginal Australians, New Guineans, island Southeast Asians and Indians. We find an ancient association between Australia, New Guinea, and the Mamanwa (a Negrito group from the Philippines), with divergence times for these groups estimated at 36,000 y ago, and supporting the view that these populations represent the descendants of an early “southern route” migration out of Africa, whereas other populations in the region arrived later by a separate dispersal. We also detect a signal indicative of substantial gene flow between the Indian populations and Australia well before European contact, contrary to the prevailing view that there was no contact between Australia and the rest of the world. We estimate this gene flow to have occurred during the Holocene, 4,230 y ago. This is also approximately when changes in tool technology, food processing, and the dingo appear in the Australian archaeological record, suggesting that these may be related to the migration from India.

Conservation implications for dingoes from the maternal and paternal genome: Multiple populations, dog introgression, and demography

“…Some ethnographic evidence supports this hypothesis, for example, the lack of Neolithic cultural items, such as chickens and pigs, in Australia prior to European colonization (Larson et al., 2010; Oskarsson et al., 2011), lack of human genetic signatures indicating contact between South East Asia and Indigenous Australians (Brown, 2013; Haak et al., 2010; van Holst Pellekaan, 2001, 2013; Karafet et al., 2005; McEvoy et al., 2010; Pugach, Delfin, Gunnarsdóttir, Kayser, & Stoneking, 2013), and the finding that dingoes only carry the two ancestral Amylase gene copies, consistent with their having diverged from modern domestic dogs before the agricultural era (Arendt, Cairns, Ballard, Savolainen, & Axelsson, 2016; Freedman et al., 2014). More recent molecular dating efforts based on mitochondrial divergence time suggest that dingoes could have arrived in Australia approximately 8,000–10,000 years BP (Cairns & Wilton, 2016; Oskarsson et al., 2011).…”

Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region

“…These South Asian affinities support the hypothesis of a migration path through South Asia for the ancestors of FEN groups (and other Asia-Pacific groups) as they peopled the Asia-Pacific region. [8][9][10] Ancient, Late Pleistocene affinities with Australia and Near Oceania is evident with haplogroup P. FEN group Y-STR haplotypes under haplogroups C-RPS4Y and K-M9 also were observed to have associations with Australian and Melanesian haplotypes. 14 Genome-wide SNPs also showed an ancient association between the Mamanwa FEN group and groups from Australia and New Guinea.…”

“…9 Genome-wide SNPs also show an ancient association between Australia, New Guinea and the Mamanwa FEN group, which supports the view that these populations represent the descendants of an early 'southern route' migration out of Africa. 10 Fifteen autosomal short tandem repeats (aSTRs) from 12 RC groups demonstrate limited population stratification, which supports the pooling of RC aSTR data into a single population genetic database for forensic applications. 11 A preliminary comparison of aSTR data from 12 RC groups 11 and 12 FE groups (F Delfin, MCA DeUngria and M Stoneking, unpublished data) show that the Filipino population is composed of a homogeneous set of different RC groups with separate, distinct FE groups.…”

“…14 Genome-wide SNPs also showed an ancient association between the Mamanwa FEN group and groups from Australia and New Guinea. 9,10 Overall, FE group mtDNA genetic affinities illustrate a Filipino genetic history that extends from the initial colonization of the Asia-Pacific region, 37 to the initial colonization of the Philippines, with possibly a separate postcolonization migration into the Philippine archipelago, 2 up to the time of the Austronesian expansion.…”

“…2 This link could therefore be the result of a separate migration that took place after the initial colonization of the region, possibly the same as that inferred in a recent study, which showed Holocene gene flow between India and Australia 5.7 kya. 10 Haplogroup N11b, which is still unique to the Mamanwa FEN group, presents another possible, but more ancient South Asian link that overlaps with the initial colonization of the region. These South Asian affinities support the hypothesis of a migration path through South Asia for the ancestors of FEN groups (and other Asia-Pacific groups) as they peopled the Asia-Pacific region.…”