The evolutionary history of Neanderthal and Denisovan Y chromosomes

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A new paper out this week in Science reports the sequencing and analysis of Y chromosome ancient DNA (several hundred kilobases to a few megabases from interior, non-recombining regions of the chromosome) from multiple Denisovan and Neanderthal individuals.

https://science.sciencemag.org/content/369/6511/1653

Abstract

Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.

After doing some tricky genotyping, the authors using genetic variation in the 2 Denisovan and 3 Neanderthal Y chromosomes (combined with data from modern humans) to do some demographic analysis:

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The phylogeny on the left shows the inferred relationships between the Y chromosomes. Unlike what is seen in autosomes, here the Neanderthals are more closely related to the modern human (represented by several non-African individuals and the A00 haplogroup, a particularly important African Y chromosome lineage) than to Denisovans.

The figure on the right shows the estimated coalescent times of modern non-African Y chromosomes and the other Y chromosomes used in the analysis. The human-Neanderthal split is somewhat more recent than estimates from previously sequenced exonic aDNA , possibly due to improvements in the way that errors in aDNA sequencing were managed in this analysis (requiring a 90% or greater consensus among sequencing reads in order to genotype a variant, among other things).

It’s a neat, if short, paper. What’s truly amazing, though, is that it feels kinda “ho-hum”*…like of course we can get multiple megabases of DNA from individuals who lived tens of thousands of years ago. It’s a testament to how amazingly fast the aDNA field is moving.

@swamidass is there anything here that is relevant to GAE?

*This is of course not at all a criticism of the work the authors did. From what I can tell as an outsider, aDNA is a giant pain to work with.

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Or perhaps the autosomes are suffering from incomplete lineage sorting, while the Y and mt, having a much smaller effective population size, are not. Introgression is also an option, which they appear to pick. Is that right?

My sole attempt (as a grad student) at ancient DNA ended up amplifying lab contamination from someone else’s work months previously. Of course I didn’t have a dedicated ancient DNA lab with obsessive protocols like they do these days.

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Yeah, they go with the introgression scenario:

The Denisovan–modern human Y chromosome TMRCA estimates agree with population split times inferred from autosomal sequences, suggesting that the differentiation of Denisovan Y chromosomes from modern humans occurred through a simple population split ( 19 ). By contrast, the young TMRCA of Neanderthal and modern human Y chromosomes and mtDNAs suggest that these loci have been replaced in Neanderthals through gene flow from an early lineage closely related to modern humans (Fig. 3A) ( 7 ). Previous work indicates that the rate of gene flow from modern humans into Neanderthals was on the order of only a few percent ( 20 , 21 ). Because the fixation probability of a locus is equal to its initial frequency in a population ( 22 ), the joint probability of both Neanderthal mtDNA and Y chromosomes being replaced by their introgressed modern human counterparts starting from a low initial frequency is even lower. However, owing to their low N e and reduced efficacy of purifying selection, Neanderthals have been shown to have accumulated an excess of deleterious variation compared with modern humans ( 16 ), and it has been suggested that introgressed DNA was not neutral ( 23 , 24 ).

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Do they consider the ILS scenario?

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They do some simulations to corroborate the scenario of Y chromosome replacement via introgression. I’m not sure if ILS was considered in this simulation; most of the methods are, of course, in the supplemental, and I haven’t read most of it. Here is a figure summarizing their preferred scenario:

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Not that I can see, but there is a lot that is relevant to the conversation on human origins with RTB and WLC.

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Oh, nice! I confess that I have not kept up with that conversation (not even sure if it’s public).

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