A new paper on Y chromosome haplogroup A00 brings its split time to around the time of the emergence of modern anatomical modernity (~208ky) rather than the much earlier date inferred in the original paper. The low mutation rate (used to derive the old date) was also criticized by Wilson Sayers in an arXiv preprint, while Scozzari et al. recently argued for an old Y chromosome phylogeny (and correspondingly low mutation rate).
I suspect that (i) a good fix on the Y chromosome rate by direct methods, and (ii) ancient DNA work might help resolve this controversy fully. (i) will help us estimate times more accurately, and (ii) might document the presence/absence of lineages at particular time points.
In any case, for the time being, we should doubt that A00 represents a non-sapiens introgression event, although the occurrence of the most basal Y chromosome lineage in a West African farmer population still remains a very interesting finding. It's still possible that a finer sieve might yet detect archaic (or late pre-modern) introgressing lineages in modern humans, but A00 doesn't appear to be one of them.
Interesting (and a first?), a Youtube clip by the lead author on the paper:
European Journal of Human Genetics advance online publication 22 January 2014; doi: 10.1038/ejhg.2013.303
The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome
Eran Elhaik et al.
Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338 000 years ago (95% CI=237 000–581 000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100 000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208 300 (95% CI=163 900–260 200) years ago.