But, for me, the most interesting abstracts relate new developments in the Y-chromosome phylogeny world. The titles of the 3 abstracts are:
Y-chromosomal insights from large-scale resequencing
A calibrated human Y-chromosomal phylogeny based on resequencing
Insight into human Y chromosome variation from low-coverage whole-genome resequencing
and, they all seem to be from authors working at The Wellcome Trust Sanger Institute.
Researchers used 1000Genomes low coverage data (2x) and high coverage Complete Genomics data to untangle the Y chromosome phylogeny. As expected, the 1000Genomes data weer of poorer quality, and had a large number (~14-17%) of false negatives, i.e., SNPs that were actually present in the samples were not discovered.
I list the main findings from the three abstracts:
The TMRCA of the entire tree was ~115 KYA (thousand years ago), and of the lineagesoutside Africa ~60 KYA, both as expected. Additional insights included a rapid expansion of hg F~40 KYA, and of R1b in Europe ~5-10 KYA. The archaeological counterpart of the former isunclear, but the latter is likely to represent a Neolithic expansion of this lineageI would say that these results are consistent with my "two deserts" theory and the climatic history of Africa and the Near East. Of course, I don't think there was a 60ky Out-of-Africa event, for a number of different reasons that I've written about to death. With respect to Y chromosome phylogeny, it is important to highlight one more time where I'm coming from:
The GENETREE TMRCA for the complete set of chromosomes examined was 105-125KYA; times for the out-of-Africa movement were 62-79 KYA, a Paleolithic expansion 37-48KYA, and the expansion of R1b in Europe 7-10 KYA; rho times were broadly similar.
It confirmed Hg E (Bantu), O (China) and R1b (Europe) expansions associated with the Neolithic transitions in different parts of the world, and revealed that the expansion in Europe was the most extreme. One novel finding was a striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement, suggesting a previously unknown event of importance to male demography at this time.
The major African Y-haplogroup E belongs to the DE subclade of the CT clade:
I have color-coded the Eurasian lineages as "green", and the African ones as "red". Now, those who think that the age of CT corresponds to Out-of-Africa believe that this event was accompanied by a massive bottleneck which is responsible for the reduced genetic diversity of Eurasians compared to Africans.
But, the question is obvious: if there was such a massive bottleneck in Eurasian ancestors, then how come it is the Eurasians (the bottlenecked population) that ended up with most of the CT descendants?
There really is no archaeology to support a 62-79ky Out-of-Africa, the only archaeology (and anthropology) in support of Out-of-Africa relates to the pre-100ky period, with things like the Nubian complex, the Mt. Carmel hominins, Jebel Faya, and others links between Africa and the Near East.
There are no genetics to support it either: track every paper that has argued for ~60ky Out-of-Africa, and you will invariably find a 2.5x10-8/bp/generation or similar mutation rate and/or a recent human-chimp calibration hiding somewhere in the details. While the mutation wars rage, it is not certain how they will be resolved, but I would put money on the true mutation rate ending up much lower than the one dominating the literature, and, consequently, Out-of-Africa being much earlier.
Getting back to the topic, the "striking expansion of lineages F to R ~20 thousand years after the out-of-Africa movement" corresponds to the UP Revolution in west Eurasia. So, to recapitulate my thinking in bullet form:
- Pre-100ky Out-of-North Africa (Mt. Carmel, Nubian, Jebel Faya?)
- c. 70ky climate crisis in North Africa-Arabia. Reduction of Y-chromosome diversity: CT founder.
- 70-50ky. Modern human biocultural evolution accelerates as they (i) face climate crisis, (ii) face new environments as they move out of North Africa-Arabia, (iii) face archaic humans in Eurasia and Africa. Haplogroup DE is group of "southern" Out-of-Arabians heading east (D) or west (E); Haplogroup CF is group of "northern" Out-of-Arabians, some of which head east (C) or stay around (F).
- 50-40ky. Culmination of the process leads to UP/LSA Revolution:
- In East: some F descendants come to dominate over the early D and C settlers
- In West Eurasia: other F descendants break through the Neandertal bottlecap and invade Europe with UP technologies
- In Africa: E descendants (descended from DE back-migrants) kick-start the Lower Stone Age.