Bottleneck in human Y-chromosomes in the last 10,000 years

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A very exciting new paper has just been published in Genome Research on 456 full sequence Y-chromosomes from around the world. The authors date the MRCA of Y-chromosomes ("Y chromosome Adam") to 254 (95% CI 192–307) kya, find coalescences of major non-African haplogroups to 47–52 kya (which clearly corresponds to the Upper Paleolithic revolution), but also infer a second bottleneck that occurred in the last 10 thousand years.

The contrast (left) between mtDNA (red) and Y-chromosome (yellow) coalescences is quite noticeable. The little "dip" in the yellow curve in many regions on the right of the various regional plots corresponds to a the second bottleneck event (that was really not "one" event, but rather shows that many modern men descend from a small number of "patriarchs" of the Neolithic and Bronze Age worlds. The "when" of the dip is important:



Most human mythologies contain stories of "first men" and eponymous founders of nations; these were often ridiculed in recent times as invented stories whose purpose was to engender social cohesion through a story of shared descent. But, now it seems that these stories were at least in part true, and such ultra-prolific patriarchs do indeed stand at the beginning of many later lines of descent.

Figure 1 from the paper is an extremely useful overview of human Y-chromosome phylogeny.
Figure1 4

The split between DT and B2'5 is placed at around ~100 thousand years ago. This corresponds perfectly (in my opinion) to the Out-of-Africa event from which most Eurasian men are probably descended. For the next thirty thousand years, Eurasians were probably confined to Arabia and the Middle East. The next major event is the foundation of the unambiguously Eurasian CT lineage ~70 thousand years ago (coinciding with the Toba eruption and the onset of super arid conditions at the onset of MIS 4). And, the final event of the "grand picture" of Eurasian prehistory was the Upper Paleolithic at ~50 thousand years ago, when Eurasians finally got the "tech" to exhibit complex behavior, invent new tools, conquer diverse environments and ultimately colonize the entire planet while driving Eurasian archaics to extinction.

An important detail in this grand picture is the fact that the authors estimate the coalescence date between D and E1'4 to ~70,000 years, coinciding with the C/GT split from the same time. These lineages are all found in Eurasia, but only E1'4 is found in Africa. I think this points clearly to back-migration of Eurasians into Africa, perhaps as environmental refugees following the c. 70kya Arabian ecological catastrophe. In any case, the fact that two separate Eurasian-specific lineages (CT and D) coalesce to ~70kya destroys the theory that the spread of modern humans into Eurasia happened together with UP-related technologies, a theory that was already on its last legs given the evidence that pre-UP admixture with Neandertals had taken place (as such admixture would have been impossible if pre-UP Eurasians were not already present outside of Africa at that time).

Genome Research doi:10.1101/gr.186684.114 

A recent bottleneck of Y chromosome diversity coincides with a global change in culture 

Monika Karmin et al. 

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.