Also of interest in the paper is the authors' work on the rest of the Y-chromosome tree (see Figure on the left). As always with age estimates, the details matter. From the paper:
It is worth to point out that
recently, Wei et al. published a similar study about Y chromosome sequencing of 36 individuals (mainly Haplogroup R1b and E1b), in which 3.15 or 8.83 Mbp range was sequenced 19, and they achieved a time of out-of-Africa at 57 – 74 kya using various methods, which is slightly older than our result (54 kya), although the same mutation rate of 1×10-9 substitution/base/year were employed. The difference could be ascribed to the regions chosen for date estimation; we compared the regions that Wei et al. and we studied, and found that in their study, the SNP density in the region that was sequenced only in their study is significantly higher than that in the region that both studies have sequenced (P less than 0.005) (Table S3).
It thus seems that the time estimates may be lower than true. An interesting new finding from the paper is the near-simultaneous D/CF and C/F splits. The authors comment:
It remained mysterious that how many times the anatomically modern human migrated out of Africa, since that among the three superhaplogrous C, DE and F, Haplogroup F distributes in whole Eurasia, C in Asia and Austronesia, D exclusively in Asia, while D’s brother clade E distribute mainly in Africa 62, so there are two hypotheses, 1) haplogroups D and CF migrated out of Africa separately; 2) the single common ancestor of CF and DE migrated out of Africa followed by a back-migration of E to Africa. From this study, the short interval between CF/DE and C/F divergences weakens the possibility of multiple independent migrations (CF, D, and DE*) out of Africa, and thus supports the latter hypothesis 63 (Fig. S2 a).I have argued for haplogroup E back-migration into Africa before in this blog, so it's nice to see that this idea is gaining some supporters.
Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers
Shi Yan et al.
Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-recombining region (NRY), discovered >4,000 new SNPs, and identified many new clades. The relative divergence dates can be estimated much more precisely using molecular clock. We found that all the Paleolithic divergences were binary; however, three strong star-like Neolithic expansions at ~6 kya (thousand years ago) (assuming a constant substitution rate of 1e-9/bp/year) indicates that ~40% of modern Chinese are patrilineal descendants of only three super-grandfathers at that time. This observation suggests that the main patrilineal expansion in China occurred in the Neolithic Era and might be related to the development of agriculture.