F Rosa Rubicondior: Human Evolution - Sex With Neanderthals

Thursday 23 October 2014

Human Evolution - Sex With Neanderthals

Neanderthal DNA specialist Svante Pääbo examines the anatomically modern human femur, found near Ust'-Ishim in western Siberia.
Photograph: Bence Viola/MPI EVA
Thoroughly modern humans interbred with Neanderthals - life - 22 October 2014 - New Scientist

A little more light was shed on the fascinating human story the other day when an international team from America, Asia and Europe led by Svante Pääbo and Janet Kelso of the Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, published their findings from the DNA sequenced from the oldest human fossil so far. And the picture is emerging of not only several periods of interbreeding between fully modern humans and Neanderthals but that there may have been several waves of modern human migration out of Africa and into Euro-Asia, not all of which were successful in the long run.

The fossil is the anatomically modern human femur found at Ust'-Ishim in Siberia and dated to about 45,000 years old. This fossil was found quite by chance in 2008, sticking out of the bank of the Irtysh river by Nikolai Peristov, a local artist and ivory carver, looking for fossilised mammoth tusks to make jewelry from. Nothing more is known of the remains which appear to have been deposited in the alluvial silt produced by flooding of the Irtysh river.

We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.

Irtysh River, Siberia, Russia.
Basically, what this technical jargon means is that by looking at the length of segments of Neanderthal DNA in the genome, and allowing for the rate at which a length of DNA gets chopped up and mixed with the rest of the DNA at each generation, they were able to calculate that the femur came from a man whose ancestors had bred with Neanderthals between 230 and 400 generations, or between 7,000 and 13,000 years earlier, taking us back to between 50,000 and 60,000 years when this man's ancestors came into contact with Neanderthals in Euro-Asia.

But they also found longer sequences than expected, probably from later interbreeding, indicating that interbreeding might have been more frequent especially during periods when there was significant overlap between the two populations.

The other significant finding to emerge from this study is that this fossil was from a population which was as closely related to Europeans as it was to Southeast Asians, but it doesn't appear to be directly ancestral to either.

This suggests this particular population was not successful in the long run and died out, raising the possibility that human colonization of Euro-Asia may he been a hit and miss affair with some populations failing. This view is consistent with the view that the 100,000 year-old remains of early modern human found in a cave in what is now Israel may not have been ancestral to the people of New Guinea and Australia as some had proposed. The fact that they have similar amounts of Neanderthal DNA to other non-African people suggests they picked up their Neanderthal DNA like the rest of us during a migration through Neanderthal territory. The population that left their bones in a cave in the Middle-East might simply have been another failed colonisation from Africa.

And none of this detracts from the view that, at this period in our evolutionary history, the various diversified forms of humans, some of which may have progressed to the status of a distinct biological species such as Neanderthals and Denisovans, acted like a ring-species much as you would expect of an evolving, widely-dispersed species, consisting of incompletely isolated population, each interbreeding with it's neighbours on the edges of its range. At a later stage in our history, these local populations then merged to form a single gene-pool but with distinct local characteristics.

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  1. @Rosa: Do you know if Neanderthals and Homo sapiens mated peacefully or the main explanation is involuntary sex, i.e. rape. And in that case, who was the rapist? Was it the Neanderthal male or the human man? Or maybe both? (Cf. sexual intercourse with animals.)

    1. I'm no expert, but I don't see how we could possibly know that based on the available evidence. It would depend on the culture and sexual habits of Neanderthals and Cro-Magnons at the time, which we also have no way of knowing much about.

    2. Can it be, Rosa, that part of the answer to the questions you bring up is to be found in this blog of yours: http://rosarubicondior.blogspot.se/2014/01/the-legacy-of-sex-with-neanderthals.html ?

      Here are the last paragraphs of your article: They also found an almost complete absence of any Neanderthal genes on the sex-determinant X chromosome, suggesting that, when these were passed on they may have caused infertility and so would have been quickly eliminated. This is a common problem when related but distinct species interbreed, reinforcing the idea that Neanderthals had evolved into a distinct species, not a subspecies or merely a local variant, as had earlier been thought.

      Because Neanderthal DNA is clustered in the H. sapiens genome rather than being more evenly admixed within it, this suggests that inter-breeding was a rare event. Sriram Sankararaman goes so far as to estimate that it may have happened only four times.

      If this is so, it may well be that it was always H. sapiens male mating with H. neanderthalensis females since Neanderthal Y chromosomes, which are always inherited only from the father, have never been recovered from modern humans. Of course, this could also be because they are so rare that we just haven't found one yet - which doesn't square with Neanderthal DNA being found in all non-African humans. It could also indicate that a Neanderthal father and an H. sapiens mother always produced offspring with reduced fertility, or even sterile offspring.

    3. The problem there is that we should find Neanderthal mitochondrial DNA in some modern humans but the evidence seems to be that all the 'seven' varieties found by Bryan Sykes in 'Seven Daughters of Eve' seem to form a well-defined evolutionary tree from a single original 'mitochondrial Eve'. Of course, Mitochondrial Eve COULD predate the common ancestor of H.sapiens and H. neanderthalensis and that one of our seven IS a Neanderthal mitochondrion. Fascinating stuff and the picture is still developing.

  2. The interbreeding between humans belonging to Homo sapiens and Neanderthals occurred just for a relatively short period of time, around 54,000 years ago. This is confirmed by another research group, whose study was conducted by an international team of researchers from the University of Copenhagen and the University of Cambridge. See more at: http://www.cam.ac.uk/research/news/ancient-dna-shows-earliest-european-genomes-weathered-the-ice-age-and-shines-new-light-on .

    As far as I can understand it, both research groups came to, in principle, the same conclusions, since the Kostenki 36,000 years old genome also contained a small percentage of Neanderthal genes. So the studies definitely give support to and corroborate each other.

    Both studies show there was a so-called admixture event rather early in the human colonization of Eurasia: and during that relatively short period Neanderthals and the first humans (Homo sapiens) to leave Africa for Europe briefly interbred.

    Both research groups also estimate this admixture event occurred around 54,000 years ago, i.e. before the Eurasian population of Homo sapiens began to separate. This means that, even today, anyone with a Eurasian ancestry – from Chinese to Scandinavians and most North Americans – has a small element of Neanderthal DNA in his or her genome.

    However, despite Western Eurasian humans shared the same European landmass with Neanderthals for another (estimated) 10,000 years, no further periods of interbreeding seem to have occurred. This is really mystifying.

    What can the reason be? Were Neanderthal populations dwindling much faster than previously believed by scientists? Did the Neanderthals avoid encounters with humans or vice versa? Or what happened? And why?

    Can it be that the offspring of sexual encounters between the two species had reduced viability? What about the phenomenon called Hybrid inviability; see: http://en.wikipedia.org/wiki/Hybrid_inviability ? I know to little to be able to answer that question.

    Here's a quote from that Wikipedia post: The barrier of hybrid inviability occurs after mating species overcome pre-zygotic barriers (behavioral, mechanical, etc.) to produce a zygote. The barrier emerges from the cumulative effect of parental genes; these conflicting genes interfere with the embryo's development and prevents its maturation. Most often, the hybrid embryo dies before birth. However, sometimes, the offspring develops fully with mixed traits, forming a frail, often infertile adult. This hybrid displays reduced fitness, marked by decreased rates of survival and reproduction relative to the parent species. The offspring fails to compete with purebred individuals, limiting genes flow between species.

    So what do you think, Rosa (and others)? Can the explanation be "simple" hybrid inviability? Or am I totally wrong?

    1. It could be. I assume this inviability increases as the species diverge so it could be that offspring were at least viable enough to interbreed with H. sapiens earlier on but became less viable over time. We might have killed off a variety of Neanderthals that we could interbreed with leaving other varieties that we couldn't interbreed with.

      Lots of speculation and few answers at the moment. More data needed. :-)

  3. Maybe we'd contact Ken Ham and other creationists and beg them to give us a clarification? At least the creationists should try to explain to us heathens if humans with some elements of Neanderthal DNA in their genome really are allowed to enter the Pearly Gates of Heaven. God Almighty might consider them unworthy hybrids (= not created by Him).

    Most GOP voters and creationists in the US surely need to rewrite their pedigree and counterfeit their CVs or else they won't come to Heaven in their afterlife. But there's a tricky catch AFAIK: If their God is omniscient, then He immediately will detect and disclose their filthy lies.


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