Study shows no long-term removal of Neandertal DNA from Europeans

January 16, 2019 by Bob Yirka, Phys.org report
Comparison of Modern Human and Neanderthal skulls from the Cleveland Museum of Natural History. Credit: DrMikeBaxter/Wikipedia

A team of researchers at the Max Planck Institute for Evolutionary Anthropology has found evidence that suggests there has been no long-term removal of Neandertal DNA from modern Europeans. In their paper published in Proceedings of the National Academy of Sciences, the group describes using whole-genome simulations to trace the history of Neandertal DNA in the human genome and what they found.

Over the past several years, multiple teams of researchers have conducted studies with the goal of learning more about what has happened with the Neandertal DNA that became mixed with human DNA approximately 45,000 years ago. Most have agreed that introduction of DNA from Neandertals underwent negative selection and thus has slowly diminished—at least in modern Europeans. In this new effort, the researchers have found evidence that suggests these earlier results were wrong, and that there is no evidence of negative selection. They further contend that the reason the other researchers got it wrong was because they made incorrect assumptions about between non-Africans (Europeans) and Africans.

To learn more about the fate of Neandertal DNA introduced into the , the researchers started by obtaining DNA from two actual long-dead Neandertals—one from Mongolia, the other from a site in Croatia. They used that data to create a whole- simulation of introgression in modern human DNA. Doing so allowed them to follow the level of Neandertal DNA in the human genome over the time of first introduction until now. They report that the levels remained nearly constant.

The researchers were also interested in learning more about the impact of Neandertal DNA on functional classes of genomic sites. To find out more about it, they separated the human genome by functional annotation and by primate conserved areas, and made comparisons. They found no noticeable depletion of Neandertal contribution in protein-coding sequences. They did, however, find depletions in conserved and promoter regions.

The researchers suggest their results are likely transferable to other cases in which one species introduces its DNA to another. Over time, reductions in DNA would likely not occur, and if they did, it would be due to admixture with other populations.

Explore further: The genomes of five late Neandertals provide insights into Neandertal population history

More information: Martin Petr et al. Limits of long-term selection against Neandertal introgression, Proceedings of the National Academy of Sciences (2019). DOI: 10.1073/pnas.1814338116

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rderkis
5 / 5 (1) Jan 17, 2019
Neanderthals are NOT extinct they live in us! :-)
torbjorn_b_g_larsson
5 / 5 (3) Jan 20, 2019
Ha, so Pääbo - 2nd author - was correct in that Neanderthals (and by implication Denisovans) *were* different species. He had a seminar that was web posted last year continuing saying this despite the collecting number of papers claiming to see gradual selection against incompatible alleles, so perhaps he was in the midst of this work. The paper strikes the earlier papers down in one fell swoop, showing them to be artifacts of recent gene flow (mostly back to Africa).

The data is consistent with first 1/10 Neanderthal introgression based on the differences in effective population sizes, then decrease with to 1/4 of that within 10 generations based on fitness differences. I would have to run some simulations to understand the process but one very loose estimate would be that the relative fitness was below 0.5 for Neanderthal alleles (as homozygotes). And while I have no other example handy, let me provisionally take that as "another species".
Da Schneib
3.7 / 5 (3) Jan 20, 2019
The really interesting thing is, as far as we can tell, you could sit down next to a Denisovan or a Neanterthal in a bar, have a brewski and a chat with them, and never know they weren't as human as you are.

You'd have to take a tissue sample to find out.
rderkis
not rated yet Jan 20, 2019
The really interesting thing is, as far as we can tell, you could sit down next to a Denisovan or a Neanterthal in a bar, have a brewski and a chat with them, and never know they weren't as human as you are

On the other hand using the loose definition the way you just did we aren't human either. :-)
eric_in_chicago
not rated yet Jan 20, 2019
"you could sit down next to a Denisovan or a Neanterthal in a bar, have a brewski and a chat with them, and never know they weren't as human as you are."
...except for the fact that he will beat you in an arm wrestle, he is smarter than you and he looks like a "caveman"
We bred them out through prostitution. They were better hunters, better in the field than the pretty homo sapiens so we traded sex for meat.
torbjorn_b_g_larsson
not rated yet Jan 21, 2019
one very loose estimate would be that the relative fitness was below 0.5 for Neanderthal alleles (as homozygotes). And while I have no other example handy, let me provisionally take that as "another species".


So I figured loosely how to model this, with the 2.5 % remaining alleles under near neutral drift (as in the paper) because they are so diluted. And my estimate was totally off, it is enough with 10 % lower relative fitness to get there in the time given by the paper model.

So yeah, Pääbo has pointed out a partial species interbreeding barrier on incipient speciation, but I don't necessarily need to subscribe to the subspecies - as I want to see them as the null model - having been sufficiently separated to merit different species designation. Even small rising barriers seem to give a drastic difference in a few generations.

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