Neanderthal Y chromosomes are paleo-modern?

I don’t have time to blog in detail today so I’ll point you to Ann Gibbon’s story, How Neanderthals lost their Y chromosome. You can find the link to the paper in there. The big issue here is that both mtDNA and Y chromosomes were replaced due to introgression from a population closer to modern humans than the Neandersovans, though basal to any modern humans alive today. This new group may actually be basal to the “basal human” group hypothesized by some scholars (there are suggestions of its existence in autosomal admixture into Neanderthals).

The probability of fixation of a newly introduced allele is the frequency of that allele, so how is it that these paleo-modern variants swept into Neanderthals? Perhaps on one locus, but two? One solution offered is naturals selection. This seems plausible, but the possibility of natural selection on Y and mtDNA lineages has always been a “wild card” that would make us rethink a lot of our phylogeography in general.

Finally, though it looks like the vast majority of modern ancestry outside of Africa is derived from a relatively recent (60,000 years ago) rapid expansion, it is clear that the picture at any given time is more complex than the signal we see today. It seems more and more likely that there was more a continuum between the African and Neandersovan lineages, and I strongly suspect that some of the paleo-modern lineages will at some point be detected in some modern groups once we have ancient DNA (the closer genetic distance and low fraction makes it hard for these segments to be identified in extant modern lineages using standard inference).

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4 thoughts on “Neanderthal Y chromosomes are paleo-modern?

  1. They admit the sample size is very low. And they’re using modern-human yDNA to reconstruct the Neander yDNA.
    I’d wait for more results and for better-preserved samples before making a call either way.

  2. Lazaridis and John Hawks have some good comments about this on their Twitter. Just on a quick look does seem more likely to me to have originated in some para-AMH lineage (split with AMH at some point after AMH split with NeanderSovan), though Laz seems agnostic on that.

    But selection seems like no evidence *for* it really. Yes, rising to high frequency through drift seems unlikely given low AMH contribution to Neander, with significant caveat that this y is from AMH sister group to AMH… but shifts in y from low frequencies to high due to repeated sex biased and social process do influence uniparental dynamics in humans, so not purely a contest between drift and genetic selection. And there’s no direct evidence of LoF on an originally Neander y.

    Certainly, with all extant y-groups (at least for main haplos) we don’t really have good evidence, or indeed any evidence, of phenotypic difference – no evidence of trait differences that I know of when looking at between y group differences in autosomally homogenous populations, nor of discovering these differences through systematic male:female siblings / population differences. (There’s still a fair amount of burbling about which I see online about how I2 ydna must be causally linked to height in Dinaric Alps… But females in the populations have about the same standard deviation height advantage – I’m unsure how the people making this claim imagine that I2 ydna in males makes their sisters equally tall, relative to female norms!). This should be low hanging fruit for biobanks and large studies… We also tend to see punctuated transition for y-dna groups in the adna record, and parallel starburst expansions of subclades from different branches under shared social process at the same time (R1b-M269 and R1a-M417) which doesn’t really speak to genetic selection…

  3. Color me skeptical. The analysis makes several big conceptual leaps that shouldn’t be taken as Gospel truth. There are other plausible narratives to explain the result that may turn out to be correct.

  4. The usual way is that the dominant males take the conquered females.
    I always wondered how the Neandertals could withstand the supposedly much larger and more developed meta-population to the South which led to Homo sapiens. Probably they didn’t, but got overwhelmed on a regular basis, but this didn’t led to their extinction, but just regular upgrades which ran in a cline through the Neandertal populations.

    I think we don’t know enough about the Neandertal population and their interaction with sapiens in the Near East. A lot is open. I heard we get Palaeolithic DNA from the Near East soon? Might help to solve this.

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