Neanderthal-Denisovan ancestors interbred with a distantly-related hominin

Abstract

One-sentence summary We document the earliest known interbreeding between ancient human populations and an expansion out of Africa early in the middle Pleistocene.Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 mya. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that: (1) Denisovans also interbred with superarchaics, (2) Neanderthals and Denisovans separated early in the middle Pleistocene, (3) their ancestors endured a bottleneck of population size, and (4) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (5) Neanderthals interbred with the ancestors of modern humans.

Modelling the end of the Acheulean at global and continental levels suggests widespread persistence into the Middle Palaeolithic

“…In recent years, fossil and genetic evidence has confirmed the co-existence of multiple hominin species during the later Middle Pleistocene of Africa and Eurasia. Evidence of admixture between some of these species confirms a degree of interaction (Browning et al, 2018;Villanea and Schraiber, 2019;Rogers et al, 2020), while anatomical comparisons highlight manipulative and cognitive differences varying in scale and nature (e.g. Tocheri et al, 2008;Holloway et al, 2018;Détroit et al, 2019;Galway-Witham et al, 2019).…”

Morphological and phylogeographic evidence for budding speciation: an example in hominins

“…These results further underscore the need for examination at lower taxonomic scales than is typically undertaken. Overall, the picture of hominin evolution presented here represents an alignment of phylogenetic results with the heterogeneous geographic patterns observed in H. erectus and early African H. sapiens (Baab 2011, Hublin et al 2017) and the complicated network of genetic interactions (Green et al 2010, Kuhlwilm et al 2016, Villanea and Schraiber 2019, Rogers et al 2020) toward a deeper statistical understanding of the complexity in evolutionary and demographic patterns between hominin populations throughout the Pleistocene.…”

Genomic regions linked to soft sweeps approximate neutrality when inferring population history from site pattern frequencies

“…To test the effect these differences have, the site patterns for neutral and soft-sweep affected regions were used to estimate ancestral divergence times and population sizes using Legofit (Rogers, 2019). The demographic model used was taken from (Rogers et al, 2019). This model includes admixture events from Neanderthals into Eurasia, ancient humans into Nean-derthals, and from superarchaic hominins into Denisovans and the ancestor of Neanderthals and Denisovans.…”

“…This model includes admixture events from Neanderthals into Eurasia, ancient humans into Nean-derthals, and from superarchaic hominins into Denisovans and the ancestor of Neanderthals and Denisovans. Rogers et al (2019) found that the exclusion of these admixture events can strongly bias results.…”