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Study Proves Human Mutation Rate Is Slower Than Believed Posing New Date For Human-Neanderthal Separation

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By Christina Troelsen / Science Daily

Researchers from Aarhus University, Denmark, and Copenhagen Zoo have discovered that the human mutation rate is significantly slower than for our closest primate relatives. The new knowledge may be important for estimates of when the common ancestor for humans and chimpanzees lived - and for conservation of large primates in the wild.

Human Mutation Rate Slowing Down

Over the past million years or so, the human mutation rate has been slowing down so that significantly fewer new mutations now occur in humans per year than in our closest primate relatives. This is the conclusion of researchers from Aarhus University, Denmark, and Copenhagen Zoo in a new study in which they have found new mutations in chimpanzees, gorillas and orangutans, and compared these with corresponding studies in humans.

Using whole- genome sequencing of families, it is possible to discover new mutations by finding genetic variants that are only present in the child and not in the parents.

Electropherograms are commonly used to sequence portions of genomes. (Tom David / Public Domain)

Electropherograms are commonly used to sequence portions of genomes. (Tom David / Public Domain )

"Over the past six years, several large studies have done this for humans, so we have extensive knowledge about the number of new mutations that occur in humans every year. Until now, however, there have not been any good estimates of mutation rates in our closest primate relatives," says Søren Besenbacher from Aarhus University.

Carl, an alpha-male chimpanzee, one of the participants in the study. (David Trood / Aarhus University)

Carl, an alpha-male chimpanzee, one of the participants in the study. (David Trood / Aarhus University )

The study has looked at ten families with father, mother, and offspring: seven chimpanzee families, two gorilla families, and one orangutan family. In all the families, researchers found more mutations than would be expected on the basis of the number of mutations that would typically arise in human families with parents of similar age. This means that the annual mutation rate is now about one-third lower in humans than in apes.

Time of Speciation Fits Better with Fossil Evidence

The higher rates in apes have an impact on the length of time estimated to have passed since the common ancestor of humans and chimpanzees lived. This is because a higher mutation rate means that the number of genetic differences between humans and chimpanzees will accumulate over a shorter period.

If the new mutation rates for apes are applied, the researchers estimate that the species formation (speciation) that separated humans from chimpanzees took place around 6.6 million years ago. If the mutation rate for humans is applied, speciation should have been around 10 million years ago.

"The times of speciation we can now calculate on the basis of the new rate fit is much better with the speciation times we would expect from the dated fossils of human ancestors that we know of," explains Mikkel Heide Schierup from Aarhus University.

The skeleton of a Neanderthal. (gerasimov174 / Adobe)

The skeleton of a Neanderthal. ( gerasimov174 / Adobe)

The reduction in the human mutation rate demonstrated in the study could also mean that we have to move our estimate for the split between Neanderthals and humans closer to the present.
Furthermore, the results could have an impact on conservation of the great apes. Christina Hvilsom from Copenhagen Zoo explains:

"All species of great apes are endangered in the wild. With more accurate dating of how populations have changed in relation to climate over time, we can get a picture of how species could cope with future climate change."

The study " Direct estimation of mutations in great apes reconciles phylogenetic dating " has been published in Nature Ecology and Evolution and is a collaboration between researchers from Aarhus University, Copenhagen Zoo, and Universitat Pompeu Fabra in Barcelona.

Modern Human and Homo Erectus Man Compared. (AlienCat / Adobe)

Modern Human and Homo Erectus Man Compared. ( AlienCat / Adobe)

Top image: DNA molecule spiral structure with unique connection. Source: solvod / Adobe

The article, originally titled ‘ Human mutation rate has slowed recently ‘ was first published on Science Daily.

Source: Søren Besenbacher, Christina Hvilsom, Tomas Marques-Bonet, Thomas Mailund, Mikkel Heide Schierup. Direct estimation of mutations in great apes reconciles phylogenetic dating . Nature Ecology & Evolution , 2019; DOI: 10.1038/s41559-018-0778-x

References

Søren Besenbacher, Christina Hvilsom, Tomas Marques-Bonet, Thomas Mailund, Mikkel Heide Schierup. Direct estimation of mutations in great apes reconciles phylogenetic dating . Nature Ecology & Evolution , 2019; DOI: 10.1038/s41559-018-0778-x

Comments

So I note that the site self describes as a Pop Archaeology site, which is fair context but rubs me personally the wrong way even though the article lifted from Science Daily is fine in itself. Specifically the site is not sufficiently professional to lift photos from stock without checking their origin and relevance. I am no archaeologist but the photo labeled "The skeleton of a Neanderthal" looks entirely too well preserved and modern skeleton too me, besides the bronze arm ring complication.

Without taking the time to locate the original source who has been labeled "Neanderthal" in several stock data bases, I found a partial properly labeled "Exhumation" from mostly graveyards on Shutterstock [ https://www.shutterstock.com/search/exhumation ; https://www.shutterstock.com/sv/image-photo/skeleton-ancient-man-archaeo... ].

This may be an unfortunate mistake, but let us not make another one: I will likely not return here.

And it strikes me that my analysis was generic, while specifically chimps evolved in Africa while Neanderthals and Denisovans bot evolved in Asia/Europe.

The only way introgression would be possible is by the back flow of modern humans into Africa. That would mean a putative rather late (the last few thousand years), still localized and diluted introgression of such alleles which would be practically impossible to discover.

Not specifically alleles from those relatives, but I have seen attempt at estimating how long the populations in the chimp/human ancestral split interbred without finding much evidence either way.

There are - to my knowledge - no alleles that can be interpreted as a more modern interbreeding either way. The later human splits are 10 times younger, at some 0.5 Myrs vs 6 Myrs, and while it is an open question if we should consider them species (as most paleontologists seem to do) or subspecies the low introgression speak of incipient speciation. Pääbo was among the authors of a recent paper that used the two whole genome sequenced Neanderthals in a comparison test (since one is related to the human introgressions, the other not). They could show that the amount of Neanderthal DNA is the same 2.5 % or so all over, with the back flow into Africa likely screwing earlier assessments up to erroneously show differences across Asia,

So the interbreeding happened early when Africans left, but more importantly they see little signal of selection after the first 10 generations. I.e. the difference between population sizes would imply that we should see some 10 % Neanderthal alleles. But we see 1/4 of that due to "a species barrier" being in progress. That said, the fitness difference is not tremendous, it would suffice with 10 % lower progeny until the remaining alleles were too diluted (at 2.5 %) to matter. That is IIRC similar to what people see when some - but not all - mammal species are inbreeding but still technically the same species.

The point being that, besides the moral issues and despite the ability of especially plants and birds but also mammals to make hybrids long after speciation events, I would not expect to see such alleles as you ask about.

Neanderthal and Denisovan DNA have been found in human DNA. Has anyone looked at whether Neanderthal and Denisovan DNA been found in apes or chimps? If so, what were the results? I read that human DNA contains less than 4% Neanderthal DNA. Curious.

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