The genome of Neanderthals contained harmful gene variants that made them around 40 percent less reproductively fit than modern humans. And non-Africans inherited some of this genetic burden when they interbred with our extinct cousins, say genetic researchers.
Neanderthal. Image credit: Trustees of the Natural History Museum, London.
Several previous studies revealed that Neanderthals 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.
Then, between 100,000 and 50,000 years ago, anatomically modern Homo sapiens left Africa and moved to the homelands of their distant 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,” said Dr. Kelley Harris of Stanford University.
Dr. Harris and her co-author, Dr. Rasmus Nielsen from the University of California, Berkeley, and the 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.
To quantify this effect, the scientists used computer programs to simulate mutation accumulation during Neanderthal evolution and to estimate how humans were affected by the influx of Neanderthal genetic variants.
“To assess the fitness effects of Neanderthal introgression on a genome-wide scale, we used forward-time simulations incorporating linkage, exome architecture, and population size changes to model the flux of deleterious mutations across hominin species boundaries,” the scientists said.
The results, published in the journal Genetics, suggest that Neanderthals carried many mutations with mild, but harmful effects.
The combined effect of these mutations would have made Neanderthals at least 40 percent less fit than Homo sapiens in evolutionary terms.
The team’s simulations also suggest that humans and Neanderthals mixed much more freely than originally thought.
Today, Neanderthal sequences make up approximately 2 percent of the genome in people from non-African populations. But the scientists estimate that at the time of interbreeding, closer to 10 percent of the human migrants’ genome would have been Neanderthal.
Because there were around 10 times more humans than Neanderthals, this number is consistent with the two groups acting as a single population that interbred at random.
Although most of the harmful mutations bequeathed by our Neanderthal ancestors would have been lost within a few generations, a small fraction likely persists in people today.
The team estimates that non-Africans may have historically had approximately 1 percent lower reproductive fitness due to their Neanderthal heritage.
This is in spite of the small number of Neanderthal gene variants thought to be beneficial today, including genes related to immunity and skin color.
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Kelley Harris & Rasmus Nielsen. 2016. The Genetic Cost of Neanderthal Introgression. Genetics, vol. 203, no. 2, pp. 881-891; doi: 10.1534/genetics.116.186890
