Friday , June 5 2020

Neanderthals may have interbred with a much older human lineage, Ars Technica


      Twisted family trees –


The result is likely to be disputed, as it relies on a novel technique.




/ OK, which one of you is the father? Shortly before the publication of the first Neanderthal genome, a number of researchers had seen hints that there might be something strange lurking in the statistics of the human genome. The publication of the genome erased any doubts about these hints and provided a clear identity for the strangeness: a few percent of the bases in European and Asian populations came from our now-extinct relatives.

But what if we did not have the certainty provided by the Neanderthal genome? That’s the situation where we find ourselves now, as several studies have recently identified “ ghost lineages “- hints of branches in the human family tree for which we have no DNA sequence but find their imprint on the genomes of populations alive today. The existence of these ghost lineages is based on statistical arguments, and so it is very dependent upon statistical methods and underlying assumptions, which means they’re prone to being the subject of disagreement within the community that studies human evolution.
Now, researchers at the University of Utah are arguing they have evidence of a very old ghost lineage contribution to Neanderthals and Denisovans ( and so, indirectly, possibly to us). This is undoubtedly going to be a claim that others in the field contest, in part because the evidence comes from an analysis that would also revise the dates of many key events in human evolution. But it’s interesting to look at in light of how scientists deal with a question that may never be answered by definitive data. Looking for ghosts
Ghost lineages have made their presence known in two ways. In the first, sequences of DNA from different populations can reveal shared ancestry groups. Native Americans, for example, have sequences that descended from an ancestral population that contributed DNA to modern East Asians, as well as another population that contributed to modern Siberians. In West Africans, we’ve found a significant contribution from a population that doesn’t seem to have contributed to any other existing population (along with contributions from groups that do have current descendants).

of time to build up their own variations that are distinct to their lineage and not found in modern human populations.

Enlarge / Neanderthals contributed DNA that had developed its own distinct variations after hundreds of thousands of years of reproductive isolation.
John Timmer
Thus, the DNA Neanderthals contributed to Eurasian groups included variants that fall well outside the range of the variation we see in other parts of the genome. And, while we know about Neanderthals, it’s possible you can get a similar contribution from a group we don’t know about.
The problem is that this sort of branching is impossible to identify at the single-base level. There’s no way to distinguish a variant that has arisen recently due to mutation from one that was brought in from a more distantly related lineage. In the diagram below, we take some known branches of the recent human family tree and add a potential ghost lineage. We can imagine an example where, at a specific location in the genome, modern humans and Neanderthals have an A, while Denisovans have a G.

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Neanderthals were different because their genes were regulated differently, Ars Technica

Neanderthals were different because their genes were regulated differently, Ars Technica

out with the old — Inferring what ancient humans were like by examining gene control sequences we didn't get from them. Diana Gitig - Oct 31, 2019 7:45 pm UTC A modern human and Neanderthal skull face off.John Capra, a research scientist at Vanderbilt University, wants to know how evolution has shaped our genomes and…

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