Two new preprints on Neanderthals, A high-coverage Neandertal genome from Chagyrskaya Cave and 100,000 years of gene flow between Neandertals and Denisovans in the Altai mountains.
The first preprint is an empirical one focused on a new high-coverage Neanderthal genome, which allows for more powerful inferences. To me, the most interesting insight is that Neanderthals seem to have been a highly structured population. This is something we knew from other research, but they used the fact that European Neanderthals seem to have medium-length runs of homozygosity to get a better sense of it. One modern group with lots of medium length runs of homozygosity are Ashkenazi Jews, who went through a very modest bottleneck and were highly endogamous. This suggests that Neanderthal subpopulations did now have much gene flow between them and that their demes were rather viscous.
Additionally, the contribution of Neanderthal ancestry to modern humans seems to come from one particular subpopulation. This reiterates that even if there were multiple admixtures (there were), in non-African humans the vast majority of the Neanderthal admixture comes from a single pulse.
The second paper focuses more on broad population genetic questions and theory. Using an HHM-based framework the author looks at various Neanderthal and Denisovan genomes and infers long-lasting and repeated instances of reciprocal gene flow between the two populations in the Altai. This is entirely expected. But, the author notes that Denisovan ancestry isn’t present in European Neanderthals. This is in keeping with the earlier preprint, which highlighted a strong degree of population structure. Presumably the Altai was a zone of contact between these two Eurasian hominin populations, but it did not serve as a mediator of gene flow due to high structure in both groups, and repeated local extinction (later Altai Neanderthals are very different from earlier Altai Neanderthals).