Ancient H. erectus introgression into Denisovans and Neanderthals

A recent paper used statistical tools to look into ancient introgressions in the modern human line. The authors reported in their abastract that "We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these “super-archaic” regions—comprising at least about 4Mb—were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.".

You can read the full text of the paper here (Hubisz MJ, Williams AL, Siepel A (2020) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet 16(8): e1008895. https://doi.org/10.1371/journal.pgen.1008895).

Some higlights:

• The program they used "calls nearly 0.5% introgression from the Neanderthal into each of the African individuals. These calls are likely explained by a combination of false positives and back-migration into Africa from Europe. However, another possibility is that some regions introgressed into Neanderthals from ancient humans may be assigned the wrong direction". So they did find Neanderthal introgression in Africans but seem to write it off as a fabricaton of the program or false positives, and maybe back-migration.
• "We identify 1% of the Denisovan genome as introgressed from a super-archaic hominin—roughly double the estimated false positive rate (0.49%) for this event. Our apparent weak power for these events (another group has estimated ∼6% introgression) suggests that the super-archaic divergence may have been somewhat recent (perhaps closer to 1Mya than 1.5Mya). Still, this analysis resulted in 27Mb of sequence that may represent a partial genome sequence from a previously unsequenced archaic hominin. In addition, ARGweaver-D predicted that a small fraction of the Neanderthal genomes is introgressed from a super-archaic hominin (0.75% for Altai and 0.70% for Vindija), an event that has not been previously hypothesized. However, these fractions only slightly exceed the estimated false positive rate (0.65%), so these results are likely dominated by spurious predictions."
  This is indeed interesting. The time frame means surely an introgression from Homo erectus into Denisovans, in Asia. And also a probable admixture of H. erecrtus with Neanderthals!
• The introgression between the super-archaic into Denisovans was relatively recent: "...suggests that tmig > 225kya for the for the Sup→Den event"
• "our analysis suggests that at least about 4Mb of modern human genomes derives from an unknown but highly diverged archaic hominin, possibly Homo erectus, through at least two separate introgression events".
• The authors validate an early admixture of Humans into Neanderthals in Asia some 200 to 300 kya: "Our follow-up analysis based on the frequencies of introgressed elements among the two diploid Neanderthal genomes suggests that the Hum→Nea gene flow occurred roughly between 200 and 300kya, within the limits of accuracy imposed by our assumed demographic model, mutation rates, and generation time. As previously noted, because contact between modern humans and Neanderthals most likely took place in Eurasia, this timeline appears to be inconsistent with a genetic exchange involving the direct ancestors of most present-day Eurasians, who migrated out of Africa ∼50kya. Instead, our timeline suggests an earlier migration, occurring at least 200kya.". Yet they assume (without explaining why) that "These early migrating humans may later have gone extinct, leaving a genetic trace only in introgressed segments in Neanderthals."
• They "only detected a low rate of Sup→Afr introgression, somewhat below our estimated false positive rate." which is attributed to using a large population size, based on the assumption of their model -Africa as cradle of mankind had the largest population size.
• On ancient introgressions: "It is plausible that if Homo erectus mixed with the Denisovans, they may have also mixed with Neanderthals, perhaps in the Middle East; or perhaps DNA passed from Homo erectus to Neanderthal through the Denisovans. Altogether, given the number of gene flow events now documented among ancient hominins, it may be reasonable to assume that genetic exchange was likely whenever two groups overlapped in time and space."
• The authors did not discriminate between Africans and Non-Africans in this study: "When analyzing non-African humans, we only included the “recent” migration bands from Neanderthals and Denisovans into humans, whereas when looking for older introgression events, we excluded the “recent” bands as well as non-African humans. Throughout this paper, all humans are placed in the same population; we do not model divergences within human populations... on this time scale, the European/African split is very recent, so that we did not model the population divergence among modern humans or recent growth in out-of-Africa populations".

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