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The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans:

Some present-day humans derive up to ∼5% …of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals…We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry…In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10−7 to 3.2 × 10−7 for Denisovan and 2.2 × 10−3 to 2.9 × 10−3 for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.

Take a look at the supplements for the functional stuff. I am not going to address that. Much of those results have been circulation or in other papers over the years. Rather, I want to highlight the variation in patterns of Denisovan admixture in non-Oceanian groups. Here is an important section:

Taken together, the evidence of Denisovan admixture in modern humans could in theory be explained by a single Denisovan introgression into modern humans, followed by dilution to different extents in Oceanians, South Asians, and East Asians by people with less Denisovan ancestry. If dilution does not explain these patterns, however, a minimum of three distinct Denisovan introgressions into the ancestors of modern humans must have occurred.

You see it on the figure above. The South Asian groups consistently jump well above the trend line for inferred Denisovan as a function of shared ancestry with Australians non-West Eurasian ancestry. Also, if you look at the admixture patterns for Denisovan ancestry in South Asia you see they follow the ANI-ASI cline. That is, it seems to come into the South Asian populations through the “Ancestral South Indians.” Interestingly, the Onge sample of Andaman Islanders has less Denisovan than low caste South Asian groups, reminding us that though the Onge and their kin are the closest modern populations to the ASI, they are not descended from the ASI. The highest fraction of inferred Denisovan is in the Sherpa people of Nepal.

sherpa The figure to the right is from Admixture facilitates genetic adaptations to high altitude in Tibet, and the authors find that the Sherpa are at one extreme in an ancestry cline in comparison to other East Asians. The figure is hard to make out, so I will tell you that many of the Sherpa are fixed for the red component, while other Tibetans are in positions in the middle, and most East Asians have low fractions of the red, with the Dai having none. The Gujarati sample form the HapMap have low fractions of both East Asian components. This is almost certainly an artifact of the shared ancestry of all eastern Eurasians (and perhaps Oceanians), of which the ASI were one descendant group. The proportion of Denisovan in low caste South Asians indicates that the fraction in ASI was about at the same level as the Sherpa. I suspect that ASI and the Tibetan groups got their Denisovan via different paths, but it doesn’t seem like we know yet.

Overall I do marvel at what ancient DNA can tell us. Without it we wouldn’t be talking about any of these admixture events; they’d be signals too weak to have left an obvious mark in the genome.

• Category: Science • Tags: Denisovan, Neanderthal 
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In antiquity what we term Tunisia and Tripolitania were part of “African province.” Just as “Asia” originally referred to the margins of what we now term Asia (regions of Anatolia), so “Africa” originally denoted a subset of the northwest fringe of the continent which became Africa. In biogeography this segment of the continent is actually not part of Africa (it is part of the Palearctic ecozone). And yet the vicissitudes of early modern cartography are such that continent had to be bounded by water on as many sides as possible, and today we clumsily make recourse to the term “Sub-Saharan Africa” to distinguish that region from the northern littoral, which is really part of the Mediterranean world.

This context is somewhat relevant when we evaluate a new PLoS ONE paper, North African Populations Carry the Signature of Admixture with Neandertals. This paper makes little sense unless you’ve read an earlier one, Genomic Ancestry of North Africans Supports Back-to-Africa Migrations. In that paper authors make the case that a majority of the ancestry of modern Maghrebis seems to date back to before the Neolithic, from a late Pleistocene migration of Eurasians. Though the indigenous North African element is naturally somewhat diverged from other West Eurasian components, it nevertheless comes out of the West Eurasian milieu, on the order of 10-40,000 years before the present.

In the PLoS ONE paper the authors show that the Neandertal admixture in the modern Mahgrebis is consistent with the ancient event on the order of ~60,000 years before the present. I was curious to see that the paper was careful to observe that the balance of scholarship is still shifting toward a Eurasian admixture model, instead of ancient population structure within Africa. And these findings push it further in that direction, in particular showing that Neandertal admixture is not contingent upon European or West Asian admixture, but was found in large proportions even among predominantly North African groups.

There are some qualms I have about the number of SNPs, but I can’t say much more until I try and replicate (it may be that 50-100,000 SNPs is sufficient for their questions). What I am confused about is what they expected. After all, it is well known that the peoples of North Africa are part of greater Eurasia. What Sub-Saharan African admixture exists seems to be mostly a function of the Islamic era. As such, we’d expect to see Neandertal admixture, in particular because a previous group already argued that the indigenous substrate of North Africa derives from an Ice Age migration out of Eurasia.

More importantly the “true answer” for the question of weather the affinity to Neandertals among Eurasians is due to ancient African population structure (so that the African ancestors of Eurasians happened to be closer to Neandertals than the Africans left behind) will require Sub-Saharan data sets. With whole genome coverage and thicker sampling of the continent I’m moderately optimistic. I do know that there is some evidence of Neandertal admixture in Kenyan Masai. This is probably another clue to an ancient back migration rate, though at some point someone will try and see where African and non-African Neandertal ancestry relate to each other on a phylogenetic true (preliminary data I’ve heard about seem to indicate that it’s intrusive to the continent).

• Category: Science • Tags: Anthropology, Neanderthal 
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So asks a commenter below in relation to the question above. First, why would one even presume that they were red-haired, see my 2007 post, or the paper in Science: A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals. In humans loss of pigmentation can usually be thought of as loss of function on genes. That’s probably one reason that there are several different genetic architectures for light skin, but only one for very dark skin. There might be only one way for an engine to operate as designed, but there are many different ways you can tweak a part and render it broken.

The reason that scientists have posited that Neanderthals were red-haired is that they examined the region around a melanocortin receptor gene which serves as something of a master regulator in terms of melanin production. Their sample was of two Neanderthals, one from Italy and one from Spain, and both exhibited signs of loss of function within this region. An N = 2 is small, but one must recall the fact that they are independent draws as they were sampled from different regions. Also, since then from what I recall in the Denisovan paper the authors noted that all four of their Neanderthals, from Spain, to Italy, to Croatia, to the Caucasus, seem to have a shared recent common history back to an extreme population bottleneck. If Neanderthals were relatively genetically homogeneous spatially, they may also have exhibited phenotypic similarities (thought perhaps not, due to the power of natural selection to reshape populations).

But back to the question about what Neanderthal looked like. I’m sure you’ve heard the old chestnut that if you made a few hygienic changes and had a Neanderthal don modern clothing no one would bat an eye. I’ve obtained an artist’s reconstruction of a red-haired Neanderthal in contemporary dress after a visit to a barber:

Image credit: Hoggarazzi Photography

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We’re all a bit of a Neanderthal:

As a result, between 1pc [percent] and 4pc of the DNA of non-African people alive today is Neanderthal, according to the research. The discovery emerged from the first attempt to map the complete Neanderthal genetic code, or genome. It more or less settles a long-standing academic debate over interbreeding between separate branches of the human family tree. Evidence in the past has pointed both ways, for and against modern humans and Neanderthals mixing their genes.

Prof Svante Paabo, of the Institute for Evolutionary Anthropology in Leipzig, Germany, said: “Those of us who live outside Africa carry a little Neanderthal DNA in us.”

eva-green-picture-1I will have a thorough write-up when I get a hold of the paper, which should be soon. As I said, this is a story of genomics, not just genetics. 1-4% is not trivial. The Daily Telegraph has more:

They were surprised to find that Neanderthals were more closely related to modern humans from outside Africa than to Africans.

Even more mysteriously, the relationship extended to people from eastern Asia and the western Pacific – even though no Neanderthal remains have been found outside Europe and western Asia.

The most likely explanation is that Neanderthals and Homo sapiens interbred before early modern humans struck out east, taking traces of Neanderthal with them in their genes.

Professor Svante Paabo, director of evolutionary genetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the international project, said: “Since we see this pattern in all people outside Africa, not just the region where Neanderthals existed, we speculate that this happened in some population of modern humans that then became the ancestors of all present-day non-Africans.

“The most plausible region is in the Middle East, where the first modern humans appeared before 100,000 years ago and where there were Neanderthals until at least 60,000 years ago.

“Modern humans that came out of Africa to colonise the rest of the world had to pass through that region.”

Several genes were discovered that differed between Neanderthals and Homo sapiens and may have played important roles in the evolution of modern humans.

They included genes involved in mental functions, metabolism, and development of the skull, collar bone and rib cage.

Image Credit: United Press International

Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"