The authors make an interesting point:
Finally, our study contributes to the debate on the geographical origin of Homo sapiens in sub-Saharan Africa, providing evidence for the retention of early Y chromosome lineages in East and Central but not in Southern Africa. However, we note that the current absence of significant palaeoanthropological investigation, together with the possibility of different fossil preservation conditions in central Africa, makes the extremely long human fossil record in eastern Africa inconclusive in solving this issue. The screening of Y-chromosomal variation at an increased level of resolution, combined with additional sampling from these regions, is expected to further elucidate the early steps of Homo sapiens in Africa.
I am increasingly skeptical that Homo sapiens really "originated" in a limited geographical region within the global Homo range. Recent evidence has shown increased signs of older anatomical modernity around the world, and has rehabilitated 2/2 of the DNA-tested "archaic" hominins as relevant to the genetic diversity of modern humans. I would say that the focus on East Africa has been largely an artefact of the Great Rift Valley, rather than any strong evidence that modern humans really originated there.
Here is an interesting excerpt from the paper:
As I mentioned in How Old is Y-chromosome Adam, markers with different mutation rates ("slow" vs. "fast") give widely divergent estimates of the time depth of the human Y-chromosome phylogeny. Fast markers give very low time estimates, and the problem of saturation can indeed be important. On the other hand, using the slowest markers, where the problem of saturation is unlikely to be important results in ages of >150ky and up to 500+ky depending on which clade haplogroup A chromosomes (that are the most basal) are compared with.Given the limitation related to ASD saturation, some potentially interesting inter-lineage comparisons were beyond the available resolution dictated by the STRs we used. For example, the ASD between A and B clades, which is expected to give an estimate of the Time to the Most Recent Common Ancestor (TMRCA) of the entire human Y chromosome genealogy.
This is the first time I've seen the issue of the age of the human Y-chromosome phylogeny mentioned in a scientific paper in a long time, and hopefully it will alert people to the reality that
- we don't know how old the human Y-chromosome phylogeny is
- it could be much older than the stuff of National Geographic documentaries and the recent Out of Africa model
I have not looked into the Y-chromosome data released by the 1000 Genomes Project yet (tip me if you have), but I can't help but notice that in the Project's debut paper only the CT part of the tree (i.e., excluding Palaeoafrican haplogroups A and B) was shown.
Assuming that there are some haplogroup A and B chromosomes among the Project's African contingent, and through SNP counting-based age estimation, which is much less problematic thatn Y-STR based molecular clocks, I'm willing to bet that a lot of people will be surprised when the date of Y-chromosome Adam is finally estimated properly.
Mol Biol Evol (2011) doi: 10.1093/molbev/msr089
Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages
Chiara Batini et al.
The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad dataset of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high resolution SNP analysis with STR variation of their sub-clades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional pre-agricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies, and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.