Happy New Year Homo erectus? More evidence for interbreeding with archaics predating the modern human/Neanderthal split

Happy New Year Homo erectus? More evidence for interbreeding with archaics predating the modern human/Neanderthal split
Peter J. Waddell
(Submitted on 30 Dec 2013)

A range of a priori hypotheses about the evolution of modern and archaic genomes are further evaluated and tested. In addition to the well-known splits/introgressions involving Neanderthal genes into out-of- Africa people, or Denisovan genes into Oceanians, a further series of archaic splits and hypotheses proposed in Waddell et al. (2011) are considered in detail. These include signals of Denisovans with something markedly more archaic and possibly something more archaic into Papuans as well. These are compared and contrasted with some well-advertised introgressions such as Denisovan genes across East Asia, archaic genes into San or non-tree mixing between Oceanians, East Asians and Europeans. The general result is that these less appreciated and surprising archaic splits have just as much or more support in genome sequence data. Further, evaluation confirms the hypothesis that archaic genes are much rarer on modern X chromosomes, and may even be near totally absent, suggesting strong selection against their introgression. Modeling of relative split weights allows an inference of the proportion of the genome the Denisovan seems to have gotten from an older archaic, and the best estimate is around 2%. Using a mix of quantitative and qualitative morphological data and novel phylogenetic methods, robust support is found for multiple distinct middle Pleistocene lineages. Of these, fossil hominids such as SH5, Petralona, and Dali, in particular, look like prime candidates for contributing pre-Neanderthal/Modern archaic genes to Denisovans, while the Jinniu-Shan fossil looks like the best candidate for a close relative of the Denisovan. That the Papuans might have received some truly archaic genes appears a good possibility and they might even be from Homo erectus.

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1 thought on “Happy New Year Homo erectus? More evidence for interbreeding with archaics predating the modern human/Neanderthal split

  1. I wonder about the error margin of such scenarios, considering things like incomplete lineage sorting, and past episodes of introgression and admixture.

    Intuitively it seems logical that, if modern Africans are the most structured populations, and chimpanzees are way, way more structured, earlier hominids used to be in between both; initially more structured, gradually becoming somewhat less and less perhaps approaching the level of modern Africans, but maybe never reaching it, except on Homo sapiens itself.

    If that were in a graph, I think that instead of a tree of “pure” single lines (Recent African Origin + introgression), or a homogeneous widespread “trellis” (classic multiregional), we’d have something like a tree that looks like the one from a “pure lines” RAO diagram, but instead of being drawn with a single lines for each lineage, each line is itself “narrow”, heterogeneous “trellis-line”. Sapiens doesn’t have a “clean split” with archaics, nor archaics among themselves. And then there could have been varying degrees of archaic inheritance shared in the different sub-branches of the sapiens’ trellis-line, initially more according to geography, but then obfuscated by the history of migrations, population decline, regrowth, and “mini extinctions, and further admixture and replacement with other sapiens lines. Then perhaps the “admixture” that there was never was from “textbook hybrids” but from a smoother gradation, not much unlike the gradation that is supposed to have happened chronologically in each line.

    Feels somewhat idiotic to describe that since theoretically is what the study ruled out, but it just feels weird that it’s even possible to do, given that not long ago it was still argued that even though genes and mtDNA strongly suggested a recent African origin, it could still have been the result of a much longer history of worldwide gene flow. If that was indeed a possibility from what was known, just feels weird that a much milder version can be safely ruled out. Can the “ruling out” method itself be tested, does it “okays” things like the pattern of incomplete lineage sorting between humans, chimps, gorillas and orangutans? Well, that perhaps begs the question, as it could still be that those splits were messier as well. Not long ago there was even a papers suggesting a 1-2mya episode of hybridization of hominids and chimpanzees.

    God, I shouldn’t really care about it enough to write that much, it bears absolute no relevance in my life and here I am, wasting time. Damn.

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