A Mitochondrial Stratigraphy for Island Southeast Asia

Abstract

Island Southeast Asia (ISEA) was first colonized by modern humans at least 45,000 years ago, but the extent to which the modern inhabitants trace their ancestry to the first settlers is a matter of debate. It is widely held, in both archaeology and linguistics, that they are largely descended from a second wave of dispersal, proto-Austronesian-speaking agriculturalists who originated in China and spread to Taiwan approximately 5,500 years ago. From there, they are thought to have dispersed into ISEA approximately 4,000 years ago, assimilating the indigenous populations. Here, we demonstrate that mitochondrial DNA diversity in the region is extremely high and includes a large number of indigenous clades. Only a fraction of these date back to the time of first settlement, and the majority appear to mark dispersals in the late-Pleistocene or early-Holocene epoch most likely triggered by postglacial flooding. There are much closer genetic links to Taiwan than to the mainland, but most of these probably predated the mid-Holocene "Out of Taiwan" event as traditionally envisioned. Only approximately 20% at most of modern mitochondrial DNAs in ISEA could be linked to such an event, suggesting that, if an agriculturalist migration did take place, it was demographically minor, at least with regard to the involvement of women.

Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian–Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates

“…Alternatively, as pointed out in many previous studies based on both genetic (Cox 2005(Cox , 2006(Cox , 2008Karafet et al 2005;Hill et al 2007;Lansing et al 2007;Mona et al 2009) and archaeological data (Bellwood 2005(Bellwood , 2007, there is good evidence that significant Asian contact occurred in eastern Indonesia and Melanesia during the Austronesian expansion. Indeed, much of the pattern of admixture we observe in this study, especially in Wallacea and Near Oceania, may well reflect cultural processes associated with the expansion of Austronesian farmers into the territory previously occupied by Melanesian hunter-gatherers (given subsequently).…”

“…A major question emerging from this study relates to the age of the cline in eastern Indonesia. Was it established in the Paleolithic by the encounter of genetically differentiated hunter -gatherer groups (Hill et al 2007), or did it arise more recently with the mixing of Austronesian farmers and local populations in eastern Indonesia? Climatic changes following the last glacial maximum (approx.…”

Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea

“…Interestingly, Sudest showed a relatively high frequency of the AS haplogroup F1a, which was otherwise only detected sporadically (single individuals) in the eastern Calvados and in Gawa but not in any of the other Massim groups studied. The presence of haplogroup R23 in a single individual from the western Calvados was unexpected, as this haplogroup has so far only been observed much more westward in Nusa Tenggara 58 and among Cham from Vietnam. 59 AS versus NO genetic ancestry in the Massim To quantify the relative contributions of NO versus AS paternal and maternal ancestors to the gene pool of the Massim people, we assigned, based on previous knowledge, the most probable ancestral origin to each of the observed NRY and mtDNA haplogroups (Table 3).…”

Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes

“…1,18 Mutations are recorded by comparing with the revised Cambridge reference sequence (rCRS). 19 All the individuals were allocated into specific haplogroup based on their control-region information; the assignments were further confirmed by typing additional diagnostic coding-region mutations according to the reconstructed phylogenetic trees of East Asian, 1,20-25 South Asian 5,7,12,[26][27][28][29][30][31][32][33] and Southeast Asian [34][35][36][37][38] (Supplementary Table S1, Supplementary Material online). For the mtDNA sample of interest, entire genome was amplified and sequenced as described elsewhere.…”