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Stem-human gene flow into Neanderthals


The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals:

Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.

The standard model is that 500-750,000 years ago the ancestors of African (modern) stem humans and Neandersovans diverged, and that’s that before the recent admixture and assimilation. But it’s pretty clear there were contacts between stem lineage and Neandersovans before the recent expansion of the African lineage. Neanderthals acquired lots of neat genes from our lineage, and we probably acquired stuff from them too.

(note that I think there were old modern lineages that disappeared)

10 thoughts on “Stem-human gene flow into Neanderthals

  1. It seems that genes shuffling presents at all levels from meiosis all the way to subspecies. Vector virus might also contribute the shuffling even between different species.

    At end, evolution is really ongoing genetic lottery, in which the best combination for the specific environment or ecosystem will win the day. And such recombination shuffling lottery will continue into future. No body can be certain which combination or mutation will win (roaches win, dinosaure lost).

    Like economy or stock market, no expert can precisely predict outcome.

    “I have never met a man who could forecast the market.” – Warren Buffett.

  2. what is the meaning of “stem humans” in the phrase “African (modern) stem humans”?

  3. In addition to the analyses of this specific protein, there are the recent findings of Neanderthal Y and mtDNA being introgressions from a modern human lineage. Has anyone tried modeling what percent “modern-ish” autosomal DNA Neanderthals actually had? Were they 10%, 20%, 30% human and the rest something more ancient (and cladal with Denisovans)?

    I’ve always been somewhat skeptical that Nean Y and mtDNA could really both be 200-300k human introgressions. What could possibly cause such a significant sweep of the native uniparentals in favor of more African shifted ones, and what is realistically the lowest amount of African autosomal DNA they could have if their uniparentals were swept in favor of African types?

  4. One other thought – it’s really interesting to see papers like this detecting very ancient signals of introgression across species going way back in time by looking at specific haplotype distributions. One of the great obstacles of aDNA research is being able to actually retrieve aDNA samples, since there’s only so many potential fossils currently out there in museum collections or still in the ground to dig up. I am wondering if researchers can take the haplotype analysis of this paper as a model and try and tease out possible admixture scenarios between the ancestors of East and West Eurasians, or between Eurasians and Africans, from the time 40,000-80,000 years ago, where fossils become rarer and we may never have the enough of the raw material to resolve potential deep modern human admixture scenarios.

  5. @Mick

    Not very relevant to what you wrote I must admit, but why would there be admixture between the ancestors of East and West Eurasians prior to 40kya? As far as I know, they had not really diverged yet, or were just diverging and admixture in early divergence phase (60-50kya) probably was continual until it decreased later on.

    Regarding the paper this post was based on, I can’t judge their methods but it seems reasonable, I think there had been some evidence for an earlier OOA about 200kya for some time now, that probably affected some Neanderthals a bit but mostly died out.

    I also think that Nean Y and mtDNA being 200kya (or so) human introgressions is odd at its face but it seems a robust finding and likely due to pervasive selection.

    It is also interesting that this gene flow may not have affected all Neanderthals, but unless I am mis-remembering the names, mostly European ones.

  6. “What could possibly cause such a significant sweep of the native uniparentals in favor of more African shifted ones”

    Hybrids who remained living with Neanderthal groups and who were more reproductively successful.

  7. @James

    Well, Tianyuan was 40,000 years old and already an obvious East Eurasian. And 45,000 year old sample from all the way from Bulgaria, Bacho Kiro, apparently may have been a very early type of East Eurasian as well.

    I guess I was thinking more along the lines of figuring out the nature of apparently hybrid West-East samples like Yana, Salkhit, and the whole concept of Ancestral North Eurasian. How exactly did these blended populations come to form, etc. Where exactly did West and East Eurasians form, period – the Bacho Kiro sample was real surprise to me, if we have some sort of proto-East Eurasian sample all the way in Bulgaria 45,000 years ago, where the heck were West Eurasians?

    @John Massey

    “Hybrids who remained living with Neanderthal groups and who were more reproductively successful.”

    Yes, of course that’s the literal explanation, but why were they more reproductively successful. What benefits did modern human Y and mtDNA have over the native Neanderthal uniparentals that caused the former to be so strongly positively selected for that they wiped out the latter?

  8. @Mick

    >Well, Tianyuan was 40,000 years old and already an obvious East Eurasian. And 45,000 year old sample from all the way from Bulgaria, Bacho Kiro, apparently may have been a very early type of East Eurasian as well.

    Tianyuan was a mixture of two populations, one which I call Outer Crown Eurasian (Bacho Kiro) and the other I call Inner Crown Eurasian (more specifically Inner Crown Clade B). The IUP population was an outgroup to most of Tianyuan’s remaining ancestry as well as other Inner and Middle Crown Eurasians. Hypothetically you could say Bacho Kiro is East Eurasian, but since all other Eurasians are below it in the phylogenetic tree, essentially all Eurasians except basals will be termed as East Eurasians in this schema and so the word “East” become redundant, and all Eurasian = East Eurasian (excluding basals). But then you will still have the job of classifying the different subclades so you’ve come right back to square one.

    I think this is a better schema:
    https://imgur.com/a/cOpSfR0
    I did not make the model, I simply added additional labels. Crown begins at Neanderthal admixture, the Middle Crown is most of Ust Ishim’s ancestry. Anything before the Ust Ishim split is Outer Crown Eurasian and anything after Ust Ishim’s primary ancestry is Inner Crown Eurasian. The Inner Crown Eurasian splits into two clades: Inner Crown Clade A (ancestral to “Western Eurasians”, a word that I will be using less often in these kinds of situations), and Inner Crown Clade B (ancestral to “East Eurasians”, again, will not be using that term). The reason why I call Tianyuan’s ancestral Inner Crown clade B is because it contributes 61% of ancestry to Tianyuan (the non-IUP in Tianyuan) and Tianyuan man is mtDNA B, so it is easier for me to remember it. The A vs B thing can be placed the other way around as well, but once you have placed it your way, continue to use it that way.

  9. Fits with the few records known by now of anatomically modern humans in Eurasia before the main Out of Africa event. Later contacts have left observable gene flow behind, so why not also any earlier contacts? Except of course observed to be only in the other direction, since in Mid-Pleistocene Eurasia, it was the Neanderthals that survived and the African humans that eventually died off.

    @marcel: in biology, the “stem” of a group of organisms is the historical lineage between its own splitting-up into known descendants, and its splitting apart from its more distant sister lineages. So “stem African humans” are humans that diverged from the lineage leading to us, but after the lineage leading to the (extinct but relatively long-surviving) Neanderthals had already split off. Similarly e.g. the extinct dinosaurs are “stem birds” — not strictly birds, but closer relatives of birds than anything else around today is.

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