More Archaic Admixture Data

More Ancient Neanderthal Genomes

An article in Nature provides great understanding of Neanderthal admixture by adding five new autosomal Neanderthal genomes to our pool of knowledge:

Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. 

Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. 

Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

The bottom line is that most Neanderthal admixture in modern humans can be traced to the Out of Africa era in a population that would have been basal to almost all non-African modern humans, even Papuans who together with Australian Aborigines who diverge from other non-African modern humans at the most basal point, probably around 65,000-70,000 years ago. If modern humans made it into Asia and Europe before then, and Altai Neanderthal admixture dated to ca. 100,000 years ago suggests that this did happen somewhere, they have not left much of a genetic trace in modern humans.

This makes sense. First wave modern humans in Europe and Siberia mostly went extinct in an ice age about 20,000 years ago, so any subsequent admixture in the Neanderthals European homeland would have been lost. By the time that modern humans recolonized Europe, Neanderthals were extinct.

Inferred Archaic Admixture In Africans

There is essentially no Neanderthal admixture or Denisovan admixture in sub-Saharan Africans that can't be traced to Eurasian back migration to Africa. But, that doesn't mean that the ancestors of today's sub-Saharan Africans didn't also experience admixture with archaic hominins. It just means that they admixed with different hominins from whom we have no ancient DNA, in part due to poor conditions for preserving it, and in part due to insufficient resources devote to looking for potential samples.

But, it is possible to reliably estimate ancient admixture from "ghost populations" of hominins by statistically analyzing patterns in the genomes of people who are alive today and these methods have been validated by comparing their results to those obtained from direct comparisons to ancient homin genomes.

What have scientists found?

According to a new preprint at bioarXiv that largely confirms a couple of prior studies along the same lines:

Analyses of Neanderthal and Denisovan genomes have characterized multiple interbreeding events between archaic and modern human populations. 

While several studies have suggested the presence of deeply diverged lineages in present-day African populations, we lack methods to precisely characterize these introgression events without access to reference archaic genomes. We present a novel reference-free method that combines diverse population genetic summary statistics to identify segments of archaic ancestry in present-day individuals.  

Using this method, we find that ~7.97±0.6% of the genetic ancestry from the West African Yoruba population traces its origin to an unidentified, archaic population (FDR [false discovery rate] ≤20%). We find several loci that harbor archaic ancestry at elevated frequencies and that the archaic ancestry in the Yoruba is reduced near selectively constrained regions of the genome suggesting that archaic admixture has had a systematic impact on the fitness of modern human populations both within and outside of Africa.

This admixture percentage rivals that of Papuans and aboriginal Australians. It is equivalent to a situation at the time shortly after archaic introgression had ceased, in which the average person had 1.5 great-grandparents who were archaic hominins. This is roughly four times the archaic admixture proportion found in Europeans, and a somewhat lower multiple of Asians who have no Papuan ancestry. It is similar to the total amount of archaic admixture in Papuans. 

But, in this case, it involves West Africans who, unlike early of of Africa modern human populations and proto-Papuan populations, did not experience a really severe population bottleneck in their demographic history that the other populations did.

The study controlled for admixture with highly diverged African populations like Biaka Pygmies.

It is kind of nuts that we can see this huge amount of archaic admixture, and yet have no meaningful idea what kind of hominin was those source of this admixture, just as it is pretty crazy that we can document Denisovan admixture so well while having no real idea what a Denisovan looked like.

As in other cases of archaic admixture, with Neanderthals and Denisovans, it also appears that natural selection has weeded out archaic ancestry from our genomes in areas where modern human genes provide a fitness advantage relative to archaic hominins, who were, on average, less fit than modern humans. But, as in other cases of archaic admixture, there are a few loci where archaic admixture is elevated, suggesting that the introgressed genes provided their descendants with selective advantages involving those loci.

Other studies have found a distinct source of archaic admixture in a different sub-Saharan African Paleo-African population.

While this method was superior in identifying particular loci where archaic introgression did or did not take place, unlike prior studies of this type, the paper does not expressly identify how deeply diverged the archaic population is from the modern humans who admixed (other than that they are much more diverged than the most divergent modern human populations), nor does it identity how long ago this admixture event probably took place, something that prior studies have put shortly before the Holocene era (i.e. more than 10,000 years ago, but not that much earlier than that; certainly in the Upper Paleolithic era).

A finding for the West African Yoruba has wide relevance to sub-Saharan Africa because almost all populations except for a handful of relicts, gained substantial Bantu admixture in the mid-Holocene era, and the Bantu have origins geographically close to that of the Yoruba.