Friday, 1 March 2013

Extremely old (237–581 kya) root of human Y-chromosome phylogeny

I had mentioned this research before, and now it has officially been published. There are three things to be excited about this new paper:
First, it forces us to consider the possibility of either (i) archaic admixture in Africa, or (ii) a much more ancient time depth of modern humans than the first fossils from Ethiopia dated to about ~200 thousand years ago.
Second, it underscores the importance of collaboration between academia and regular folk, since it was the combined contributions of academics, genetic genealogists, and the owners of the new A00 basal Y-chromosomes that made this new discovery possible.
And, third, it shows that the extraordinary can be discovered without contacting isolated tribes or seeking human bones in remote regions, but rather through careful scrutiny of large volumes of data for the proverbial needle in the haystack.
The paper developed a model of Y-chromosome mutation based on the estimate of Kong et al. Significantly, though:
If we were to use the higher mutation rate (1.0x10^-9 per base per year6) rather than a realistic range derived from whole-genome sequencing (4.39x10^-9  -   7.07x10^- 9), the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ~39 kya6 (i.e., versus ~63 kya for the mutation rate used here).
A 39kya common ancestor for Eurasian Y-chromosomes makes no sense, since we now know for sure that by that time, the differentiation of Eurasians was already well on its way and modern humans in remote parts of the Old World have been documented much earlier than that time.
A ~63kya common ancestor, on the other hand, fits nicely with my "two deserts" theory of modern human origins, according to which the ancestors of Eurasians faced an ecological crisis in Arabia when it became much drier post-70kya; that seems like a most opportune time for the major Eurasian bottleneck and the corresponding coalescence of Eurasian Y-chromosomes to a single man. And, while there is no a priori reason for Y chromosomes and mtDNA to behave similarly, the age of the "older" Eurasian ur-mother, haplogroup N at 59 thousand years, with presumably an older ancestor within mtDNA haplogroup L3 founding the Eurasian population.
Also, if modern human-Neandertal admixture had occurred  "most likely 47,000–65,000 years ago", then the expansion of modern Proto-Eurasians within a 70-60kya timeframe north Out-of-Arabia would have brought them in contact with their northern Neandertal neighbors. On the other hand, it would be incredible if modern humans experienced admixture with Neandertals but were still much later a very small population (to allow for the coalescence of their Y-chromosomes to one man ~39kya).
So, in summary, the mutation rate used by the authors seems consistent with what we know about an important calibration point of the human story.
But, who were the people in Africa responsible for the introgression of A00 chromosomes? Mendez et al. used the haplotype of the African American A00 individual and discovered his patrilineal kin among theMbo of Cameroon, who are Bantu farmers.
I have observed before that Pygmies and Bushmen represent only a tiny fraction of pre-existing African genetic diversity, the part that had not yet been absorbed into the farmers' expanding population by the time that Africa came to the attention of of modern science. We see traces of Pygmy and Bushman ancestry in some African farmers, and there were probably other groups, no longer extant as distinct ethno-cultural entities, but, nonetheless, surviving as genetic fragments in the genomes of the farmers.
Thus, while it still makes sense to study the surviving hunter-gatherers of Africa who make up perhaps a percent or less of the population of Africa, it may be equally important to study different groups of African farmers who may possess a much richer treasure trove (albeit diluted) of such "Palaeoafrican" ancestry.
Although the stochastic nature of the evolutionary process can explain the aforementioned incongruences, the extreme age and rarity of the A00 lineage point to the possibility of a highly structured ancestral population, consistent with recent work on the autosomes.40,41,43,44 This could take the form of long-standing population structure among AMH populations45 or archaic introgression from an archaic form into the ancestors of AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya.47 Further surveys in sub- Saharan Africa and in the African Diaspora might uncover more diverged basal lineages, which will help to disentangle some of the complex evolutionary processes that shape patterns of Y chromosome diversity.

AJHG 10.1016/j.ajhg.2013.02.002
An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree
Fernando L. Mendez et al.
We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

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