One of the interesting stories of the Neandertal Genome Project is how earlier evidence of archaic introgression into Eurasians was later confirmed when the Neandertal genome was published. It is always trickier to make a case for archaic introgression in the absence of an actual archaic genome, so I expect this paper to be subjected to a high level of scrutiny. In any case, I'm glad that it's on the arXiv so that the scrutiny process can begin by anyone who cares about the subject.
arXiv:1404.7766 [q-bio.PE]
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
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.
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6 comments:
"Furthermore, we detected more introgressions from two unknown archaic hominins whom diverged with modern humans approximately 859 and 3,464 thousand years ago".
At three and a half million years ago we are obviously dealing with introgression from some other Australopithecus species. That would indicate mixing and mingling has been going on for a considerable time, just as I have consistently maintained. In fact I am sure mixing of subspecies is one of the main drivers of evolution in most species.
Once again, agreed. I think this applies well to the discussion following the "Chris Stringer on Recent Out-of-Africa" post.
Yes.
The first admixture seems like a dead ringer for Homo heidelbergensis, particularly now that we know from ancient DNA that this Homo species is not ancestral to H. Sapiens and Neanderthals.
If both of the dating estimates are 33% too large due to some systemic error common to both estimates, this would still fit the Homo heidelbergensis archaeology and the later date, within the margin of error, could be H. Erectus, which was the first Homo species to leave Africa. Eurasian specific introgression from an Australopithecus species into both Neanderthals and Eurasians despite the lack of Australopithecus archaeology evidence in Eurasia and the presence of both H. Erectus and Homo heidelbergensis in Eurasia at times that would be right if there was systemic overestimation of 33% (most of which could arise from something as simple as a modest error in average generation length due to a difference in generation length between archaic and modern humans) the balance could be due to differences well within the margin of error in the time estimate itself.
"The first admixture seems like a dead ringer for Homo heidelbergensis"
At three and a half million years ago? Or even two and a half million years ago with 33% reduction. Even Homo erectus was yet to appear at that time. The 859,000 year date does fit H. heidelbergensis introgression of course.
"The first admixture seems like a dead ringer for Homo heidelbergensis, particularly now that we know from ancient DNA that this Homo species is not ancestral to H. Sapiens and Neanderthals. "
Andrew,
It certainly is - just not as far as mtDNA is concerned.
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