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.
Highlights
A consensus view has emerged that the genomes of present-day human populations outside Africa originate almost entirely from a single major migration out aroundElectronic supplementary material The online version of this article contains supplementary material, which is available to authorized users.50,000–70,000 years ago, accompanied or followed soon after by mixture with Neanderthals contributing ~ 2% to the genome of all non-Africans (Green et al 2010; Mallick et al 2016; Nielsen et al 2017; Pagani et al 2016)
We assembled available sequences of C, D and FT lineages from worldwide surveys ensuring that common lineages were represented (Bergstrom et al 2020; Karmin et al 2015; Mallick et al 2016; Meyer et al 2012; Poznik et al 2016), and supplemented them with additional sequences from known rare lineages potentially relevant to early divergences, Australian C (Bergstrom et al 2016; Mallick et al 2016), West African D0 (Haber et al 2019), Andamanese D (Mondal et al 2017), and F chromosomes from China (Mallick et al 2016), Vietnam (Poznik et al 2016) and Singapore (Wong et al 2013): 1204 sequences in all
The resulting Y-chromosomal tree (Fig. 1) depicts 50 lineages, with the African lineages represented only by the four major African haplogroups without including their subsequent branches, but with the non-African lineages represented more fully to include all those originating before 45,000 years ago and found in the sample of presentday Y chromosomes examined, together with some of the more abundant recent lineages
Summary
A consensus view has emerged that the genomes of present-day human populations outside Africa originate almost entirely from a single major migration out around. Human Genetics (2021) 140:299–307 show a steady decrease in genetic variation with travelling distance from Africa, and have been interpreted in terms of a ‘serial founder’ model which predicts such a decrease (Prugnolle et al 2005; Ramachandran et al 2005) While such a pattern may have been initially established in this way, the complexity of subsequent movements and mixing events increasingly documented by ancient DNA from more recent periods (Haber et al 2016; Yang and Fu 2018) suggests that any early pattern of population structure is unlikely to have persisted for > 50,000 years. There is, one region of the genome with the potential to inform about these events in a unique way: the Y chromosome This is because its male-specific portion provides haplotypes from which a detailed calibrated phylogenetic tree can be created (Jobling and Tyler-Smith 2017). Set out to re-examine the early divergences within these three lineages to investigate the insights they can provide into male history and perhaps human history more generally in this early period
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