The F-series YDNA SNPs appeared at the end of last year with results from Geno 2.0, now an electronic pre-print at arXiv.org sheds some light on the discovery of these SNPs.
The paper, entitled : Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers, is freely available for download.
Some interesting (relevant to this blog) quotations from the paper follows (in blue) :
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.
Nearly all the Y chromosomes outside Africa are derivative at the SNP M168 and belong to any of its three descendent super-haplogroups – DE, C, and F 9,10,15, strongly supporting the out-of-Africa theory. The time of the anatomically modern human’s exodus from Africa has yielded inconsistent results ranging from 39 kya 16, 44 kya 10, 59 kya 17, 68.5 kya 18 to 57.0 – 74.6 kya 19.
This below explains why the F-series SNPs are for the most part found below CT-M168.
we selected 110 males, encompassing the haplogroups O, C, D, N, and Q which are common in East Eurasians, as well as haplogroups J, G, and R which are common in West Eurasians (see Table S1), and sequenced their non-repetitive segments of NRY using a pooling-and-capturing strategy.
Overall ~4,500 base substitutions were identified in all the samples from the whole Y chromosome, in which >4,300 SNPs that has not been publicly named before 2012 (ISOGG etc.). We designated each of these SNP a name beginning with ‘F’ (for Fudan University) (see Table S2). We obtained ~3.90 Mbp of sequences with appropriate quality (at least 1x coverage on >100 out of 110 samples), and identified ~3,600 SNPs in this region.
Table S2 is not available in the PDF file, the link says that all the tables are in a 'separate ancillary file', but such file is also not available, at least not at the time of the publishing of this post, and may become available when the paper is officially published. With out seeing the actual location on the Y chromosome where these SNPs are found it is hard to say how many of them are redundant SNPs relative to the PF and CTS SNPs, and how many of them are truly 'novel'.
Considering that 3.9 Mbp range constitutes only less than half of 10 Mbp non-repetitive region in Y chromosome 7, the time resolution of east Asian Y chromosome phylogeny is expected to be doubled in the near future.
To overcome the factors for uncertainty of mutation rate, a calibration with series of samples of comparable time scales might be used. For the case of mitochondrion, a recent study, in which several C-14 calibrated ancient complete sequences (4 – 40 kya) were incorporated into the tree, made the absolute dates much more convincing 41, and we expect a parallel calibration for the Y chromosome in the near future.
The authors conclude the paper with this paragraph:
Despite of the mutation rate uncertainty, we evaluate our calculation of absolute divergence time as acceptable. Firstly, our out-of-Africa date (54.1 kya) is still within the range of previous estimations (39 – 74.6 kya). Secondly, the out-of-Africa date is similar to the recent estimation of two great mitochondrial expansions outside Africa – M (49.6 kya) and N (58.9 kya) 42. Thirdly, it is not contradictory to the emergence of earliest modern human fossil out of Africa (e.g. ~ 50 kya in Australia) 43.
In the Supplementary Materials/Additional Discussions section they also mention this:
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).
Perhaps the only new material they have from this study that may strengthen the hypothesis of an extra-African origin of haplogroup E is, as they mention, the 'short interval' between the common ancestor of CF and DE and the C/F divergences, however, this 'short interval' is relative to which branch length? They did not compute the interval between the BT common ancestor and the CFDE divergence, in addition, what length of time would be considered too short to disqualify the possibility of multiple independent migrations, and how would this length of time be evaluated? next, what about the cases of DE* found in Nigeria and Guinea-Bissau that they failed to mention here, that is to say, cases found that are neither D or E but are down stream from the YAP+ insertion, how exactly are they to be explained ?
Either way, putting all these questions aside, let us assume that their proposal is correct, how then would this be reconciled with the last paragraph in the actual paper, where they associate M and N mtDNA haplogroups, with the out of Africa expansion, this would mean that if E back migrated, it would have done so with lineages downstream from mtDNA haplogroups M and N, however, many areas in Africa where E- dominates (except for East and North Africa) have, if not zero, close to zero amounts of mtDNA haplogroups M and N, wouldn't we expect to see at least some traces of the mtDNA counter part for this supposed ancient back migration in YDNA haplogroup E dominant areas of Africa other than the East and the North ? In an otherwise good and all around informative paper, I think the authors may have jumped the gun with this particular speculation, perhaps that is why they stuck it into the supplementary section of the paper and not the actual paper itself, as a testament to the highly speculative nature to their supposition.