The New York Times and other general audience media outlets are reporting on a new genetics study in the Journal Science, examining the gender dynamics of Neanderthal admixture. The editor's summary and abstract and citation are:
Editor’s summaryAlthough a low level of Neanderthal ancestry is present in most humans, these regions are not uniformly distributed. A handful of regions in the autosome are entirely devoid of such ancestry in essentially all living humans, and the X chromosome is strongly depleted across its sequence. Platt et al. modeled the possible demographic processes and selection that could have produced this pattern. They found that these patterns are most consistent with Neanderthal contributions to human populations being heavily male biased. The concurrent additional depletion in functional regions on the X chromosome suggests that the effects of this skew may have been strengthened by negative selection on Neanderthal variants. —Corinne SimontiAbstractSex biases in admixture and other demographic processes are recurrent features throughout human evolution. For admixture between Neanderthals and anatomically modern humans (AMHs), sex bias has been proposed as an explanation for the relative lack of Neanderthal ancestry in modern human X chromosomes compared with that in modern human autosomes. By observing a 62% relative excess of AMH ancestry in Neanderthal X chromosomes, we characterized the interbreeding between the two groups as predominantly male Neanderthals with female AMHs. Analytic and numerical modeling presents mate preference as a more parsimonious cause of the sex bias than purely demographic processes with differential patterns of male and female migration.
While I don't dispute the genetic data that the study discloses and bases its narrative upon, I don't think that the narrative that the general audience presentation and even the study itself have chosen a narrative that is anything close to being the most plausible one.
I've previously discussed the narrative that I think is closer to the truth, using just the Y-DNA, mtDNA, and overall autosomal genetic data previously available, without the X chromosome specific data from both admixed modern humans and admixture in Neanderthal ancient DNA that this study brings to the table.
In a nutshell, my prior analysis was that admixed Neanderthal-modern human hybrid children ended up in the communities to which their mothers belonged, and that Haldane's rule (which provides as relevant to this context, that cross-species hybrids are disproportionately female, perhaps sometimes sterile males, and only rarely fertile males) was also a key factor in why there are no modern humans with Neanderthal Y-DNA, there is no Neanderthal ancient DNA with modern human Y-DNA, why there are no modern humans with Neanderthal mtDNA, and why there is no Neanderthal ancient DNA with modern human mtDNA.
I also suggests that hybrid children may have often been the product of rape or episodic hookups, rather than long term marriage-like relationships embedded in a modern human or a Neanderthal tribe.
While the X chromosome data may require some fine tuning of that analysis, I don't think that it justifies a wholesale paradigm shift from it. I think that the new study's narrative gives insufficient consideration of these priors from that data when evaluating when kind of narrative makes the most sense to interpret its X chromosome based data, and focusing on a sexual selection and attraction based narrative instead.
The default assumption of the simple, uniparental DNA driven paradigm with Haldane's law paradigm is that the X chromosome would have the same proportions of Neanderthal and modern human DNA as other chromosomes, since almost all of the fertile hybrid children would have one Neanderthal X chromosome and one modern human X chromosome.
Admixture in X chromosomes could be reduced in early modern human communities if they had an influx of "basal" modern human populations (i.e. introgression from modern humans with no Neanderthal admixture) and that introgression was female biased because the Neanderthal admixed population was usually (at least with its own species pairing in marriage-like ways) patrilocal and recruited brides from outside its tribe in a way that had a significant basal modern human component. This kind of marriage pattern was common in the Neolithic Age, the Bronze Age and the Iron Age, including in herder populations who were culturally more similar to ancestral modern human hunter-gatherer societies, so it is quite plausible.
The lack of modern human mtDNA in Neanderthal ancient DNA strongly constrains the extent to which the mothers of hybrid individuals in Neanderthal communities were modern humans, although the fact that Neanderthal effective populations were falling at the time of Neanderthal-modern human contact means that it would be easier to lose low frequency modern human mtDNA variants in Neanderthal communities than it would be to lose low frequency Neanderthal mtDNA variants in human communities.
But, one still has to explain the new data point that there is an excess of modern human DNA in the ancient DNA of admixed Neanderthal X chromosomes. But that data still has to be reconciled with the lack of modern human mtDNA in any Neanderthal ancient DNA.
Since the Neanderthal ancient DNA sample, unlike the modern human DNA sample, is a small one, the statistical significance of this excess also needs to be examined as well as possible selective genetic fitness based explanations for some of the modern human X chromosome excesses relative to Neanderthal genes at those loci. But the number of genes per chromosome is great enough and 62% is a significant enough excess, that statistical flukes probably don't explain that much of the excess.
The first possible explanation that comes to mind for the excess modern human genes in admixed Neanderthal ancient DNA is that the effective population size of Neanderthals in that era was much smaller than the effective population size of modern humans in that era. In other words, the Neanderthals were more inbred.
This would make children in Neanderthal communities with pure Neanderthal source X chromosomes more vulnerable to harmful X chromosome based recessive diseases than hybrid Neanderthal children who would enjoy hybrid fitness. Over time, at multiple generations and not just the first one, this would favor individuals in Neanderthal communities with hybrid ancestry over those with pure Neanderthal ancestry. And the effect would be strong on the X chromosome than on the other autosomal chromosomes, because Neanderthal boys would not be at risk of suffering from harmful X chromosome based recessive diseases, while unadmixed Neanderthal girls would be at risk of suffering from these diseases.
This factor alone, depending on the prevalence of X chromosome based recessive diseases in much more inbred Neanderthal gene pools, might very well have been enough to explain the excess of modern human X chromosomes in the ancient DNA of admixed Neanderthals, without requiring modern human woman who have hybrid children to frequently live in and raise their children in Neanderthal communities (leaving us with the problem of explaining why there is no modern human mtDNA in these admixed Neanderthal individuals in Neanderthal communities).
I'll update this post with more analysis as time permits, after I've had more time to read the paper and consider its analysis.
