Genome-wide Scan of Archaic Hominin Introgressions in Eurasians Reveals Complex Admixture History
Ya Hu, Yi Wang, Qiliang Ding, Yungang He, Minxian Wang, Jiucun Wang, Shuhua Xu, Li Jin
Comments: 42 Pages, 1 Table, 4 Figures, 1 Supplementary Table, and 10 Supplementary Figures
Subjects: Populations and Evolution (q-bio.PE)
Introgressions from Neanderthals and Denisovans were detected in modern humans. Introgressions from other archaic hominins were also implicated, however, identification of which poses a great technical challenge. Here, we introduced an approach in identifying introgressions from all possible archaic hominins in Eurasian genomes, without referring to archaic hominin sequences. We focused on mutations emerged in archaic hominins after their divergence from modern humans (denoted as archaic-specific mutations), and identified introgressive segments which showed significant enrichment of archaic-specific mutations over the rest of the genome. Furthermore, boundaries of introgressions were identified using a dynamic programming approach to partition whole genome into segments which contained different levels of archaic-specific mutations. We found that detected introgressions shared more archaic-specific mutations with Altai Neanderthal than they shared with Denisovan, and 60.3% of archaic hominin introgressions were from Neanderthals. Furthermore, we detected more introgressions from two unknown archaic hominins whom diverged with modern humans approximately 859 and 3,464 thousand years ago. The latter unknown archaic hominin contributed to the genomes of the common ancestors of modern humans and Neanderthals. In total, archaic hominin introgressions comprised 2.4% of Eurasian genomes. Above results suggested a complex admixture history among hominins. The proposed approach could also facilitate admixture research across species.
Haldane's Sieve 
The findings are most interesting no doubt, however I must say that I have serious problems accepting age estimates from a study that begins with the premise of an unlikely late Pan-Homo split “approximately 5.6-7.6 million years ago” (based on papers dated to 1999-2009, which mostly just cite previous estimates in a vicious scholastic circle), contradicting the Langergraber 2012 estimate of 8-13 Ma or the Wilkinson 2010 one of c. 8 Ma, as well as the fact that Sahelanthropus tchadiensis (~7Ma.) is already in the Homo line after split with the Pan one (Bienvenu 2013). Similarly the derived claim that the African origins of the Eurasian branch of H. sapiens are only as recent as 50 Ka must be discarded as impossible on light of the archaeological evidence which places African technologies in India c. 96 Ka BP (James Blinkhorn 2013) and Homo sapiens remains in East Asia c. 100 Ka BP (Wu Liu 2010, Guanjung Shen 2013).
I’m not saying that all figures must be doubled in all cases but there is certainly a serious issue (a systemic one, for what I can see in much of the literature) with the calibration and some of the results in this aspect.
Are 50ka and 96 Ka BP dates “mutually exclusive”? Couldn’t it be that the earliest split was as early as 96 Ka, but gradually an ongoing gene flow (or even complete extinction/replacement, even though I find that more unlikely within the same species) from more recent migrations made so that it “looks as if” it was more recent?
Sort of like episodes of assimilation/introgression, but not of archaics, but the first early moderns.
I personally do not see any archaeological evidence in support of two different migrations Africa→Asia, nor I see any serious genetic evidence either (molecular-clock-o-logic speculations are not evidence). On the other hand I can see quite strong genetic evidence for a secondary expansion from SE Asia (phylo-geographic structure of mtDNA N/R and Y-DNA K(xLT)), which surely happened after the Toba catastrophe episode.
I also see no concrete reason for gradual flow Africa→Asia either. Furthermore this notion sems unparsimonious because several reasons:
1. The demographic equivalent of the communicating vessels principle. Once a population was established in Eurasia, the balance of pressures should tend to keep both populations in relative equilibrium. This is not 100% true because human ecology is more complicated and we can effectively track a “back to Africa” migration from Asia and Europe and later also significant genetic flows from Africa to Europe and West Asia. But in general terms the principle stands and both macro-populations (African and Eurasian) have remained essentially different since their consolidation some 100 Ka ago.
2. The natural windows for these Africa-Eurasia migrations were the pluvial periods. And in fact the OoA is now archaeologically documented to the Abbassia Pluvial, while the main backflow from Asia to Africa seems to correspond with the Mousterian Pluvial (earliest UP and LSA, which are surely one single phenomenon) and the bulk of the late African/West Eurasian remix seems to correspond to the early Holocene’s semi-pluvial and the Meso-Neolithic flows associated with it. In the non-pluvial periods, Tropical Africa and Eurasia were in contact only by very narrow touching points: essentially the Nile and whatever coastal canoing around the Arabian coasts could be done, which do not seem able to allow for mass-migrant phenomena. On the other hand, in the pluvial periods, the usually desert belt Sahara-Arabia surely acted as “pump”: absorbing populations in the wet periods and expelling them as it dried again – this was almost certainly the case of the OoA migrants, first established in Arabia and nearby areas (Palestine, Persian Gulf “oasis”) and then pressed to search for new lands when drier conditions returned, with some of them finding refuge in Asia (South and East) and giving birth to the “non-African” branch of modern Humankind.
In this sense the Sahara-Arabia desertic belt acted no doubt as massive natural barrier rather than permeable frontier in the dry periods which have dominated the ecological paleohistory, allowing at most for a trickle of migrants, certainly not enough to cause the mass dilution you suggest, Some Dude.
PS- The only possibily I can think of for a second “out of Africa” would be if the earliest Upper Paleolithic / LSA actually originated in Africa and implied mass migrations from Africa to Eurasia. The archaeological data for this is still not sufficiently well studied, especially in Africa, but the genetic data rather suggests an Asia→Africa flow, roughly simultaneous to the colonization of Europe and northern parts of West Asia by our species, with clearly “Asian” (and not African) genetics.