Human settlement history between Sunda and Sahul: a focus on East Timor (Timor-Leste) and the Pleistocenic mtDNA diversity

Abstract

BackgroundDistinct, partly competing, “waves” have been proposed to explain human migration in(to) today’s Island Southeast Asia and Australia based on genetic (and other) evidence. The paucity of high quality and high resolution data has impeded insights so far. In this study, one of the first in a forensic environment, we used the Ion Torrent Personal Genome Machine (PGM) for generating complete mitogenome sequences via stand-alone massively parallel sequencing and describe a standard data validation practice.ResultsIn this first representative investigation on the mitochondrial DNA (mtDNA) variation of East Timor (Timor-Leste) population including >300 individuals, we put special emphasis on the reconstruction of the initial settlement, in particular on the previously poorly resolved haplogroup P1, an indigenous lineage of the Southwest Pacific region. Our results suggest a colonization of southern Sahul (Australia) >37 kya, limited subsequent exchange, and a parallel incubation of initial settlers in northern Sahul (New Guinea) followed by westward migrations <28 kya.ConclusionsThe temporal proximity and possible coincidence of these latter dispersals, which encompassed autochthonous haplogroups, with the postulated “later” events of (South) East Asian origin pinpoints a highly dynamic migratory phase.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-014-1201-x) contains supplementary material, which is available to authorized users.

Aboriginal Australian mitochondrial genome variation – an increased understanding of population antiquity and diversity

“…In our sample, there were individuals who carried haplogroup P1e, which was previously found in Timor and New Guinea3438, and New Guinean-specific haplogroup P23637445155. Notably, these individuals traced their maternal ancestry to the Torres Strait Islands, and may therefore have (ultimate) maternal ties to the New Guinea mainland.…”

“…This haplogroup has three known subclades; Q1, Q2 and Q3, all of which are found in New Guineans/Island Melanesians, with Q1 and Q3 being additionally present in Timorese34. To date, haplogroup Q has been found only in a single Aboriginal Australian person and it was a unique variant within haplogroup Q2, labelled Q2b9.…”

Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area

“…More P3 sequences are needed to reach a more documented decision. Although younger, the star-like radiation of P2 in New Guinea (33,5 ± 1.2 kya) extended east and westwards to adjacent islands, with indigenous branches identified in Melanesia [106] and East Timor [114], and more erratic detections beyond both sides (Additional file 1: Table S4). The presence of isolated and derived P1d1 haplotypes in Australian Barrineans [115], in the Philippines [103], and in Malaysia [116], could reflect more recent, even historic contacts.…”

“…Counting homoplasies and reversions in phylotree build 17 for each trio of mutations, we obtained a total of 45 independent events for the R12/R21 root and a total of 44 for the R21/R* alternative. On the other side, another R branch (R14) went through the Lesser Sunda islands of Bali, Flores, Lembata, Timor [114, 118, 122, 123], and Borneo and Sulawesi [121, 123], reaching the highlands [17] and lowlands [124] of New Guinea following a pattern unlike to haplogroup P. There is still another branch (R24) indigenous of the Philippines [101, 103, 125, 126], also with a younger dispersion than P9 (Additional file 1: Table S9). Recently, this clade has also been detected in northern Moluccas [121].…”

Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago

“…Shortly after, based on the rarity of mtDNA haplogroup N(xR) in India, and its continuous presence above the Himalayas, we proposed an additional northern route through the Levant [4]. Afterward, intensive and extensive research on mtDNA has been carried out, not only in populations from Central [20–23] and East Asia [24–26] but, also, from the regions covering the hypothetical southern route path as India [27–30], Mainland southeastern Asia [31–33], Island southeast Asia [34–39], New Guinea, North Island Melanesia and Australia [40–44]. The most striking global result was that while in Central and North Asia the indigenous lineages observed were derived branches of southern haplogroups, primary and independent autochthonous M and N clusters were found in every main region of meridional Asia and Australasia.…”