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Neanderthal inbreeding left mark on our genome

Neanderthals are the real-life version of aliens from another planet, different but also fascinatingly intelligent and similar to us. Now it’s starting to look as if they fascinated our ancestors thousands of years ago just as much as they fascinate us today. New research on the genomes of Neanderthal humans and modern humans supports the very likely possibility that the two species had kids together regularly — not just sporadically, as previous research has suggested.

The results surprised Kelley Harris, PhD, a Stanford postdoctoral research fellow in genetics, because modern humans carry very little Neanderthal DNA — none in Africa and only 2 to 4 percent in other parts of the world. Such low numbers have strongly implied that interspecies mating was infrequent and possibly limited to a single brief period around 50,000 years ago.

Now, computer simulations by Harris and her colleague Rasmus Nielsen, PhD, professor of statistics and integrative biology at UC-Berkeley, indicate that our species once carried much more Neanderthal DNA than we do today.

“The most exciting result was that the Neanderthal admixture in the human genome is likely to have decreased over time,” said Harris. Her computer simulations suggest that during the time the two species intermingled, perhaps 10 percent of modern human DNA was of Neanderthal origin.

And, to Harris’s delight, she says, recent empirical work by a group at Harvard supports that prediction. Harvard geneticist David Reich, PhD, and his team looked for Neanderthal DNA in the genomes of ancient human remains, and found that the proportion of Neanderthal genes started out high at about 3 ­– 6 percent 45,000 years ago and declined to about 2 percent in more recent times.

Why did we lose all that Neanderthal DNA? Harris and Nielsen, whose research was published today in the journal Genetics, have a possible answer to that as well. The Neanderthal lineage diverged from the modern human lineage nearly 600,000 years ago and flourished in Europe for 250,000 years, mostly alone in small populations in far flung parts of Spain, Siberia, Croatia, and Germany; modern humans didn’t arrive in Europe until about 45,000 years ago.

When modern humans did arrive, they moved persistently north into Neanderthal lands, breeding with but also pushing out the Neanderthal humans. The history of the Neanderthals' demise is, to a surprising degree, written in their genes — in their long-buried bones, in our own ancestors’ bones and in our living genomes.

A key part of Neanderthal genetic history is how inbred they were. Only a few individuals settled in Europe to begin with, creating a genetic bottleneck. On top of that, their habit of living in small, widely dispersed populations meant further inbreeding.

As a result, they were inbred and their genomes were likely riddled with mildly harmful gene variants. Using computer simulations, Harris and Nielsen quantified this accumulation of harmful mutations. They estimated that, thanks to a heavy load of harmful gene variants, the offspring of human ­– Neanderthal matings had about 40 percent fewer children than the modern humans who ultimately displaced them.

As the two kinds of humans intermarried, the mild genetic damage was passed to modern humans. In us, Harris says, natural selection has gradually weeded out most of those harmful variants, leaving the low numbers of Neanderthal genes we now have.

Even today, report Harris and Nielsen, Neanderthal genes might put non-African human lineages at a slight disadvantage compared to African lineages, which carry no Neanderthal genes.

And so, although we think of love as ephemeral, the love affairs between our ancestors and Neanderthals left its faint mark on our genomes.

Previously: Ask Y: Modern humans lack Neanderthal Y chromosomeHumans owe important disease-fighting genes to trysts with cavemen
Photo by suchosh

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