The Genetic Cost of Neanderthal Introgression - Genetics According to a paper recently published in GeneticsPDF, interbreeding between modern humans and Neanderthals in Eurasia may have been much more common that the small quantity of Neanderthal DNA in modern non-African peoples suggests. The two populations may even have behaved like a single breeding group, in which Neanderthals were eventually genetically swamped by Homo sapien DNA.
The team led by Kelley Harris, of Stanford University used computer simulation of mutation accumulation during Neanderthal evolution to model how humans were affected by imported neanderthal genes. The simulations used known data on mutation rates and population dynamics of hominids.
Since the population of modern humans was probably some ten times that of Neanderthals, if they behaved like a single breeding group the resulting population would be expected to have about 10% Neanderthal DNA rather than the approximately 2% seen today in Eurasian people. However, Neanderthal DNA in the modern humans is concentrated in a few parts of the genome but entirely absent from others. All things being equal we should expect to see a random distribution, not this highly non-random pattern.
This non-random pattern is probably the result of natural selection depleting the Neanderthal DNA in the modern genome because alleles now found themselves not only in competition with more advantageous versions but in an environment in which the probability of a more beneficial allele arising by chance were greatly increased. There is recent evidence that the proportion of Neanderthal DNA in early Homo sapiens population was higher than today. The authors suggest that this was the result of Neanderthals existing in small, highly inbred populations until the influx of H. sapiens from Africa. This inbreeding led to a lack of genetic diversity such that Neanderthals may have been up to 40% less fit in reproductive terms than modern humans and so 40% less likely to breed successfully.
The cause of this is that, in a small population the probability of a beneficial allele arising in any generation is smaller than in a large population. In a population of a million, a million to one chance should occur once every generation on average; in a population of only a thousand, a million to one chance occurs only every thousand generations on average. So, with less competition from other alleles, a harmful mutation, provided it isn't massively harmful, can actually increase in the local genepool by genetic drift, so chance plays a much larger part in evolution in small inbred populations.
Abstract
Approximately 2–4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis. We also predict a residual Neanderthal mutational load in non-Africans, leading to a fitness reduction of at least 0.5%. This effect of Neanderthal admixture has been left out of previous debate on mutation load differences between Africans and non-Africans. We also show that if many deleterious mutations are recessive, the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population. This might partially explain why so many organisms retain gene flow from other species and appear to derive adaptive benefits from introgression.
So, having evolved in isolation in Eurasia, during which they evolved adaptations to northern cloudy and cold conditions, such as pale skin, and an immune system suitable for their environment, Neanderthals might simply have merged into the emergent Eurasia H. sapiens population, their DNA eventually losing out in the general evolutionary struggle between competing alleles and leaving us with the good bits; the less good bits being discarded by natural selection.
The legacy may be a modern Eurasian population derived from H. sapiens x neanderthalensis, adapted to northern temperate conditions but with a still slightly reduced fitness.
As a nod to my creationist readers, note how the entire paper depends on an understanding and acceptance of evolution as the explanatory theory underpinning change over time. There is no hint here of a theory in crisis and nor is there in any known scientific publication. Perhaps a creationist who believes that the Theory of Evolution is a theory in crisis which is being increasingly rejected as a valid scientific theory could point my normal readers to a reference for this repetitive claim. Just a single peer-reviewed publication by a working biologist would do.
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The fact that the Neandertal population was ~10% of the Cro Magnon doesn't necessarily mean that the breeding was at equivalent levels. We don't know the social dynamics of Neandertal cultures, of which there were more than one. Some cultures even in the same ethnic group are much more tolerant of outbreeding than others; all we have to do is look at Semitic people today and contrast Jews and Arabs in that respect. Also, Neandertal and sapiens sapiens groups were, by modern standards, still very small and scattered. They simply may not have interacted that often, even when in contact, like modern day tribes in the Amazon or SE Asia. Of course that doesn't invalidate the rest of your essay.
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