Archaic admixture in Africa confirmed

I have been somewhat of a broken record in arguing for archaic admixture in Africa over the last few years. My reasons for doing so have been stated many times, but here they are, once again:

1. African populations are structured today, why would they be otherwise at the time of the emergence of Homo sapiens?
2. Africa has a great deal of ecological variability, so the emergence and spread of H. sapiens from some region of the continent is consistent with the presence of other H. species elsewhere
3. Africa has an extremely long hominin record, and a diverse climate. It is inconceivable that archaic H. forms there would simply vanish, as they were well-adapted in their particular niches
4. African populations of today show the greatest genetic diversity: but, to what extent is that a consequence of them being the ur-humans, and to what extent is it the product of admixture between distantly related H. populations in a multiregional model?
5. The palaeoanthropological record has important lacunae in much of tropical Africa where conditions for preservation are extremely unfavorable; so, it is possible that there are as of yet undetected H. populations that lived there
6. Even the fossils we do have do not paint a picture consistent with the naive Out-of-Africa model. For example, H. sapiens idaltu (Herto) was hailed as our ~150ky ancestor when it was published, only to lose that title by the redating of Omo to ~195ky. Omo is more modern than Herto anatomically, so this is consistent with the idea of modern humans not being the "only game in town", when they make their entrance
7. Indeed, unquestionably modern, but archaic-looking forms persist in the available record down to a few thousand years ago, such as the Fish Hoek and Boskop samples

All of the above, however, amount to nothing, without a real genetic smoking gun. In Africa, because of climate, we are unlikely to ever extract DNA from really ancient hominins, as it was possible in Eurasia with Neandertals and Denisovans. Moreover, in tropical regions, such as the jungles of Central Africa, the odds are stacked against finding (m)any H. specimens. So, the evidence has to come from modern genomes.

Hence, I was pleasantly surprised to see a new paper appear in PNAS whose title pretty much summarizes what I've written about for so long. At present, the paper is not "live" on the PNAS site, so I will refrain from blogging about its actual contents. There is already a story in Nature:

Hammer and his colleagues argue that roughly 2% of the genetic material found in these modern African populations was inserted into the human genome some 35,000 years ago. They say these sequences must have come from a now-extinct member of the Homo genus that broke away from the modern human lineage around 700,000 years ago.

and a press release:

Hammer said that even though the archaic DNA sequences account for only two or three percent of what is found in modern humans, that doesn't mean the interbreeding wasn't more extensive.

"It could be that this represents what's left of a more extensive archaic genetic content today. Many of the sequences we looked for would be expected to be lost over time. Unless they provide a distinct evolutionary advantage, there is nothing keeping them in the population and they drift out."

In a next step, Hammer's team wants to look for ancient DNA regions that conferred some selective advantage to the anatomically modern humans once they acquired them.

"We think there were probably thousands of interbreeding events," Hammer said. "It happened relatively extensively and regularly."

We must note that detection of archaic admixture is a bit like detective work. For ancient DNA, it involves dealing with contamination and damaged DNA; for inferring admixture from modern DNA it involves statistical modeling and is inhibited by drift (which removes all evidence of admixture) and recombination (which breaks up archaic segments that introgressed long ago into small chunks in present-day humans).

These factors are often not emphasized enough:

• Small chunks of DNA are more difficult to assign to a modern or archaic origin; a long stretch of DNA with multiple substitutions relative to most modern humans can be proven not to have arisen by simple mutation in a conventional OoA timeframe, but this becomes increasingly difficult the smaller the segment
• Recombination breaks up DNA into smaller chunks with the passage of time; given enough time there are no longer any identifiable archaic segments but only inconspicuous remnants of archaic DNA that no longer "stand out" as peculiar against the background
• Drift gets rid of modern and archaic DNA alike. A million years from now most of our DNA will be extinct because of it. Archaic admixture that happened a long time ago can no longer be detected.

Just like a detective doesn't catch most criminals but makes sure that the one he catches are criminals, so does the genetic detective try to catch real archaic DNA, but, in the process misses a lot of archaic DNA if there is no evidence for it, or it has gone missing by drift and recombination.

The conclusion is obvious: archaic admixture is adding up: a few percent in Africa, a few in Eurasia, a few in Australasia. All this is the tip of the iceberg. With the next ancient hominin to be unearthed, with the next collection of full human genomes, with the next suite of more powerful statistical tools, archaic admixture is only bound to go up.

I will post the abstract, and any further comments specific to the paper itself as an update here.

UPDATE:

From the paper:

Interestingly, the Mbuti represent the only population in our survey that carries the introgressive variant at all three candidate loci, despite the fact that no Mbuti were represented in our initial sequencing survey. Given that the Mbuti population is known to be relatively isolated from other Pygmy and neighboring non-Pygmy populations (26), this suggests that central Africa may have been the homeland of a nowextinct archaic form that hybridized with modern humans.

...

The emerging geographic pattern ofunusual variants discovered here suggests that one such introgressionevent may have taken place in central Africa (wherethere is a very poor fossil record). Interestingly, recent studiesattest to the existence of Late Stone Age human remains witharchaic features in Nigeria (Iwo Eleru) and the DemocraticRepublic of Congo (Ishango) (30–32). The observation that populations from many parts of the world, including Africa, showevidence of introgression of archaic variants (6, 16, 19) suggeststhat genetic exchange between morphologically divergent formsmay be a common feature of human evolution.

The most interesting thing, to me at least, is not that Africans too admixed with archaic humans, but rather the time depth of the separation of the admixing groups: 0.7My, which contrasts with the 270-440ky estimated for the modern-Neandertal split by Green et al. So, it appears that archaic admixture may extend even beyond the H. heidelbergensis clade which is ancestral to modern humans and Neandertals, and may encompass late H. erectus populations.

We are not in classical multiregional territory quite yet (the multiregional model posits a single interbreeding species within the Homo genus throughout its history, consisting of multible regional populations), but Hammer et al. have certainly joined the Neandertal/Denisovan papers into showing that the central prediction of multiregional evolution, namely that there was no reproductive isolation between Homo populations long before the advent of "anatomically modern" humans.

Of course it should be noted that we should not necessarily envision direct intermixture between sapiens and erectus populations. The archaic segments may well have been transmitted via an intermediate erectus-admixed form to the sapiens population.

UPDATE II: A poster at dna-forums makes a rather good point:

So now we are required to believe that homo sapiens interbred first in Eurasia (and the north of Africa) and only afterwards with their closest African neighbors?

It is certainly counterintuitive that admixture with archaics would have happened in Africa after it happened in Eurasia. The latter event was initially theorized to coincide with the first exit of anatomically modern humans to the Levant more than 100,000 years ago, but has been lately redated to 37-86ky BP.

It is difficult to believe that Homo sapiens waited 160ky to mix with his archaic neighbors in Africa (=the period between Omo and 35ky BP) and yet started hooking up right away with Eurasian archaics.

PNAS doi: 10.1073/pnas.1109300108

Genetic evidence for archaic admixture in Africa

Michael F. Hammer et al.

A long-debated question concerns the fate of archaic forms of the genus Homo: did they go extinct without interbreeding with anatomically modern humans, or are their genes present in contemporary populations? This question is typically focused on the genetic contribution of archaic forms outside of Africa. Here we use DNA sequence data gathered from 61 noncoding autosomal regions in a sample of three sub-Saharan African populations (Mandenka, Biaka, and San) to test models of African archaic admixture. We use two complementary approximate-likelihood approaches and a model of human evolution that involves recent population structure, with and without gene flow from an archaic population. Extensive simulation results reject the null model of no admixture and allow us to infer that contemporary African populations contain a small proportion of genetic material (≈2%) that introgressed ≈35 kya from an archaic population that split from the ancestors of anatomically modern humans ≈700 kya. Three candidate regions showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size are identified and the distributions of introgressive haplotypes surveyed in a sample of populations from across sub-Saharan Africa. One candidate locus with an unusual segment of DNA that extends for >31 kb on chromosome 4 seems to have introgressed into modern Africans from a now-extinct taxon that may have lived in central Africa. Taken together our results suggest that polymorphisms present in extant populations introgressed via relatively recent interbreeding with hominin forms that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene.

Link

Related:

• Fossil evidence for the origin of Homo sapiens
• Is multi-regional evolution dead?
• Deep ancestors of human DNA compatible with structured African population
• Is Jebel Irhoud the Father of mankind?
• Human population history from single human genomes (Li & Durbin 2011)
• Homo heidelbergensis and the Ceprano calvarium