Previous studies of DNA extracted from Neanderthal remains revealed that these Eurasian hominids were much more inbred and less genetically diverse than modern humans. For thousands of years, the Neanderthal population size remained small, and mating among close relatives seems to have been common.There is something odd about this analysis, that I think the writer is getting wrong. While it is quite true that drift has an outsized role in small populations—leading to founder effect in some populations (such as Ellis van Kreveld on the Pitcairn Islanders), when deleterious mutations reach a larger population, they don't get weeded out, they get masked. Most really bad alleles are recessive and only express themselves in the presence of a parent with a like allele. In the presence of a dominant allele, they don't express themselves.
Then, 50,000-100,000 years ago, groups of anatomically modern humans left Africa and moved to the homelands of their distant Neanderthal cousins. The two groups interbred, mingling their previously distinct genomes. But though a small fraction of the genome of non-African populations today is Neanderthal, their genetic contribution is uneven. Neanderthal sequences are concentrated in certain parts of the human genome, but missing from other regions.
"Whenever geneticists find a non-random arrangement like that, we look for the evolutionary forces that caused it," says [Kelley] Harris.
Harris and her colleague Rasmus Nielsen (University of California, Berkeley / University of Copenhagen) hypothesized that the force in question was natural selection. In small populations, like the Neanderthals', natural selection is less effective and chance has an outsized influence. This allows weakly harmful mutations to persist, rather than being weeded out over the generations. But once such mutations are introduced back into a larger population, such as modern humans, they would be exposed to the surveillance of natural selection and eventually lost.
I will be curious to read the research that derives from this.