The Neanderthal admixture plot thickens…

Previous studies of archaic admixture from Altai Neanderthals and Denisovans into modern humans outside of Africa have put forth several lines of evidence for gene flow from Neanderthals into common ancestors of Eurasian populations, from Denisovans into ancestors of modern Oceanic and Asian populations, as well as from an unknown ancestral population into the Denisovan lineage. However, gene flow from modern humans into our extinct near relatives has yet been elusive – which Kuhlwilm et al. (2016) sought to find evidence of. By estimating regions of high and low divergence across 100 kb windows from Altai Neanderthal, Denisovan, and  more than 500 African genomes, they recover the possibility of archaic gene flow from an unknown ancestor into Denisovan genomes, and from modern humans into Altai Neanderthals. Thereon, they use demographic analyses using G-PhoCS (Gronau et al. 2011) to quantify this purported gene flow using five different population trees with Denisovans, Altai Neanderthals and two modern human populations.

"Down by the Rail Yard" by David Adams Image courtesy: Flickr Commons:

“Down by the Rail Yard” by David Adams Image courtesy: Flickr Commons:

These analyses recover previous estimates of gene flow from (1) Altai Neanderthals into modern humans out of Africa, (2) unknown archaic hominin into the common ancestor of Denisovans, and importantly (3) gene flow of modern humans into the common ancestor of the Neanderthals. This gene flow also appears to stem from a separate lineage that split from the common ancestor of all modern humans in Africa or from an ancient African lineage, a finding that they also confirm using simulations to recapitulate observed levels of divergence. Kuhlwilm et al. (2016) also estimate the age of shared haplotypes using ARGWeaver (Rasmussen et al. 2014), with findings indicating the presence of longer (and thus younger) African haplotypes in the Altai Neanderthals, than in Denisovans, coalescing back around 100,000-230,000 ybp, indicating that these haplotypes were present long before Neanderthals introgressed with humans outside of Africa.
Using newly designed probes for chromosome 21, and two newly sequenced Neanderthal genomes (from Spain and Croatia), the authors also find that the Altai Neanderthal shares more derived alleles from Africa, than the Spanish and Croatian Neanderthals. Separate analyses of gene flow using these new sequences also finds support for gene flow from modern humans into the Spanish and Croatian Neanderthals, and not directly into the Altai, but into the common ancestor. Demographic analyses also indicate population growth in the Croatian Neanderthal, but smaller population sizes compared to modern humans.

Our integrated demographic analysis of multiple archaic and present-day human genomes suggests a scenario of long-term decline in the populations of Neanderthals and Denisovans, with the consistently small Altai Neanderthal population perhaps reflecting a long period of isolation in the Altai Mountains. In addition, we provide evidence for modern human introgression into the ancestors of this population of Neanderthals, and no such evidence in the European Neanderthals.

Kuhlwilm, Martin, et al. “Ancient gene flow from early modern humans into Eastern Neanderthals.” Nature (2016). DOI: 10.1038/nature16544
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