A Southeast Asian origin for present-day non-African human Y chromosomes

Abstract

The genomes of present-day humans outside Africa originated almost entirely from a single out-migration ~ 50,000-70,000 years ago, followed by mixture with Neanderthals contributing ~ 2% to all non-Africans. However, the details of this initial migration remain poorly understood because no ancient DNA analyses are available from this key time period, and interpretation of present-day autosomal data is complicated due to subsequent population movements/reshaping. One locus, however, does retain male-specific information from this early period: the Y chromosome, where a detailed calibrated phylogeny has been constructed. Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations. Here, we show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 50,000-55,000 years ago of all known surviving non-African male lineages (apart from recent migrants). This observation contrasts with the expectation of a West Eurasian origin predicted by a simple model of expansion from a source near Africa, and can be interpreted as resulting from extensive genetic drift in the initial population or replacement of early western Y lineages from the east, thus informing and constraining models of the initial expansion.

Fig. 1

Y-chromosomal phylogeny and haplogroup distribution. a Maximum likelihood Y-phylogeny based on 1204 samples with branch lengths drawn proportional to the estimated times between successive splits according to BEAST analysis. Y lineages currently located in Africa are coloured gold, the others black. The key lineages of D, C and F are highlighted with a blue box. Haplogroup names indicated in italics correspond to dated splits in Supplementary Table 3. b Proportion of samples carrying Y lineages shown in (a) coloured according to geographic origin using a total of 2319 samples [1204 samples used to reconstruct the phylogeny plus 1070 non-overlapping samples from the 1000 Genomes Project (Poznik et al. 2016) and 45 samples from The Singapore Sequencing Malay Project (Wong et al. 2013)] c Map showing the geographic divisions used. The approximate phylogenetic locations and geographic origins of ancient male samples living more than 30,000 years ago are shown as red symbols

Fig. 2

Presence of haplogroups C, D and F in 2302 present-day samples. The map demonstrates how many of the three haplogroups of interest (none, one, two, or all three) were found in different areas of the Old World and Near Oceania. Black dots indicate the locations of the studied populations

Fig. 3

According to serial founder model, the earliest-branching non-African lineages are expected to expand and be present closer to Africa (a), but instead have expanded in East or Southeast Asia (b). Simplified Y tree is shown as reference for colours