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Neanderthals as a reservoir of paleo-modern human heritage

A new preprint reports on the peculiar Y chromosomal patterns that one finds in Neanderthals, Denisovans, and modern humans. Spencer Wells has told me that Y and mtDNA are actually much more informative now that we have an ancient DNA autosomal scaffold. I think that’s right. The strange result from Neanderthals is both their Y and mtDNA lineages seem to form a clade with modern humans, while Denisovans the outgroup, though the whole genomes cluster Denisovans with Neanderthals. This reminds us that we put way too much weight on mtDNA during the molecular ecology heyday of the 2000s.

Here’s the preprint, The evolutionary history of Neandertal and Denisovan Y chromosomes:

…Here we present sequences of the first Denisovan Y chromosomes (Denisova 4 and Denisova 8), as well as the Y chromosomes of three late Neandertals (Spy 94a, Mezmaiskaya 2 and El Sidrón 1253). We find that the Denisovan Y chromosomes split around 700 thousand years ago (kya) from a lineage shared by Neandertal and modern human Y chromosomes, which diverged from each other around 370 kya. The phylogenetic relationships of archaic and modern human Y chromosomes therefore differ from population relationships inferred from their autosomal genomes, and mirror the relationships observed on the level of mitochondrial DNA. This provides strong evidence that gene flow from an early lineage related to modern humans resulted in the replacement of both the mitochondrial and Y chromosomal gene pools in late Neandertals. Although unlikely under neutrality, we show that this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.

First, the first author gives due credit to the bench scientists who managed to get usable Y chromosomal sequences out of ancient DNA. That’s not a trivial task. Second, confirming both earlier autosomal and mtDNA work, it does seem that the Neanderthal lineage experienced Y and mtDNA turnover during the last 400,000 years, with the donor population being an outgroup to most modern humans, albeit closer to that lineage than the Denisovan clade (the Y evidence suggests it’s an outgroup to all modern humans, but the autosomal work is more difficult to pin down in terms of dating of divergence). Third, the replacement of the Y and mtDNA aren’t random, but a function of fitness differences due to the accumulated burden of deleterious alleles. Using simulations they show that very small differences can give notable selective advantages and result in likely replacement of mutation burdened lineages. Finally, we see a different dynamic with Denisovans.

In fact, the Denisovan Y divergence is suspiciously concordant with the autosomal divergence dates in some models.

Many years ago John Hawks pointed out to me that some of the patterns in human evolution may simply be a consequence of large population sizes for Homo in Africa. When it comes to Neanderthals this seems to be a reasonable way to think about it. The genetic and non-genetic evidence points to huge fluctuations in population size of Neanderthals, so the accumulation of deleterious mutations is plausible, and, impact by more numerous southern Homo lineages seems likely. But what about “Denisovans”? I think this work will be part of a tradition that shows Denisovans exhibit fundamentally different population dynamics as compared to Neanderthals.

While Neanderthals seem to have been a coherent population from the Altai to Europe, undergoing repeated bottlenecks, I think Denisovans were a diverse array of populations that exhibited a wide range in population sizes (this is genetically supported by recent work which shows diverse Denisovan contributions to East, South, and Southeast Asians). Additionally, the region of the Old World that seems to be second to Africa in being suitable ape habitat is Southeast Asia.

Finally, due to the reality that colder climates present better opportunities for DNA preservation, we may obtain some of our best understanding of the genomics of paleo-modern humans outside of Africa from Neanderthals as more and more data accumulates. The non-African populations today seem to be almost exclusively descended from an African or Africa-adjacent expansion that dates to ~50,000 years ago. But archaeology and suggestive genetic clues indicate that there were other African lineages which ventured out 100 to 200 thousand years ago. These did not leave a major impact on today’s populations, but with enough Neanderthal genomes, one might be able to reconstruct these people.

We live in interesting times!

3 thoughts on “Neanderthals as a reservoir of paleo-modern human heritage

  1. “this replacement is plausible if the low effective population size of Neandertals resulted in an increased genetic load in their Y chromosomes and mitochondrial DNA relative to modern humans.”

    I wonder if the lack of replacement in Denisovans is due to Razib’s theory that had much larger populations and therefore were able to find better Y and mtDNA without requiring a donating population. (Pls ignore intentionality in my description).

  2. “The non-African populations today seem to be almost exclusively descended from an African or Africa-adjacent expansion that dates to ~50,000 years ago. But archaeology and suggestive genetic clues indicate that there were other African lineages which ventured out 100 to 200 thousand years ago.”

    How would “out of Africa” ca. 50kya be distinguishable from “out of Southwest Asia” or “out of India” at that time depth?

    Also, what ever happened to the phylogenetic analysis of Y-DNA showing most of the branches in the Y-DNA F clade (including Y-DNA R and Q) deriving from Southeast Asia in the mid- to late Upper Paleolithic era?

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