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.
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.