February 17, 2016

Ancestors of Eastern Neandertals admixed with modern humans 100 thousand years ago

If true, this is very hard to reconcile with late (60kya) out of Africa and may be a smoking gun for pre-100kya presence of anatomically modern humans in Eurasia. From the paper:
The inferred demographic model confirms and provides quantitative estimates of previously inferred gene flow events among modern and archaic humans2, 3 (Extended Data Fig. 1). These include Neanderthal gene flow into modern humans outside Africa (3.3–5.8%) and gene flow from an unknown archaic hominin into the ancestors of Denisovans (0.0–0.5%). Interestingly, we also detect a signal of gene flow from modern humans into the ancestors of the Altai Neanderthal (1.0–7.1%). The precise source of this gene flow is unclear, but it appears to come from a population that either split from the ancestors of all present-day Africans or from one of the early African lineages, as significant admixture rates are estimated from San as well as Yoruba individuals. This introgression thus occurred in the opposite direction from the previously reported gene flow from Neanderthals to modern humans outside Africa
However, it is clear that the source of the gene flow is a population equally related to present-day Africans and non-Africans (Extended Data Fig. 3). We conclude that the introgressing population diverged from other modern human populations before or shortly after the split between the ancestors of San and other Africans (Fig. 3a), which occurred approximately 200,000 years ago11.
The implications of this inference (if correct) for modern human origins are potentially monumental as they suggest a Eurasian modern human lineage (only detected in the Altai Neandertal) that diverges from other modern humans as early (if not earlier) than any two African ones.

If the new discovery checks out, it will no longer be possible to assert that the deepest split in our species, H. sapiens, involves African populations. A modest interpretation of these results would assert an earlier (pre-100kya) exodus of our species from Africa, and a more bold one would seek to re-examine the geographical origin of H. sapiens itself. I don't know if anyone is working on getting DNA from the progressive Neandertals of the Near East, but they should.

Things are bound to get more interesting.

Nature (2016) doi:10.1038/nature16544

Ancient gene flow from early modern humans into Eastern Neanderthals

Martin Kuhlwilm, Ilan Gronau, Melissa J. Hubisz, Cesare de Filippo, Javier Prado-Martinez, Martin Kircher, Qiaomei Fu, Hernán A. Burbano, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajkovic, Željko Kucan, Ivan Gušic, Tomas Marques-Bonet, Aida M. Andrés, Bence Viola, Svante Pääbo, Matthias Meyer, Adam Siepel & Sergi Castellano

It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000–65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.



capra internetensis said...

A sample of Middle Paleolithic modern human DNA, basically. Sweet. Indirect and tricky to analyze, though, so caution is in order.

*If* the authors are right about the phylogenetic position and it isn't any closer to non-Africans than to Africans, that has interesting implications. Either 1) everyone (including Africans) is (mostly) descended from them, or 2) no one (including Eurasians) is (mostly) descended from them.

I am somewhat sympathetic toward your Out-of-Arabia position, Dienekes, because of the lack of any clear archaeological evidence for a recent (early MIS 3) Out-of-Africa which you have pointed out, and the considerable evidence for an MIS 5 Out-of-Africa (which this study further supports). But there isn't any clear archaeological evidence for a Back-to-Africa migration either. And a big Back-to-Africa migration carrying tons of uniparental lineages which almost all die out outside of Africa that doesn't leave a trail is a heck of a lot less convincing than a little Out-of-Africa migration carrying a small subset of uniparental lineages leaving behind loads of surviving relatives that doesn't leave a trail. There is after all clear evidence of a massive expansion of closely-related modern humans through Eurasia at the beginning of the Upper Paleolithic starting from *somewhere*.

tl;dr this is evidence *for* Recent Out-of-Africa (with incomplete replacement and ongoing gene flow in and out, not the forcefield-across-the-Sinai version).

German Dziebel said...

Reposting from Eurogenes: "[The paper provides] another completely artificial interpretation. A more simple interpretation is that Altai Neandertals carry a set of derived alleles shared with all of modern humans and a set of alleles shared only with non-Africans. Africans end up being just a subset of the EurasianHuman-Neandertal variation."

Ilan Gronau said...

I'm not sure I would say that this completely re-writes the current view of human migration out of Africa. Let me try to clarify the hypothesis we are trying to put forward:

~100 ka a group of early modern humans interbred with Neanderthals (could have been earlier, but not much later than 100 ka). This population diverged from the ancestors of present-day humans much earlier (~ 200 - 300 ka). If you want to place the divergence event geographically, then it likely happened in Africa, unlike the interbreeding, which likely took place in the Near East. So sometime in between, there was migration of humans out of Africa. Now, according to the genetic evidence, this population of early modern humans does not have any descendants in present-day humans. So they likely stayed very isolated in the Near East and never spread much in Eurasia. This is why we were trying to point out the Skhul and Qafzeh humans as a possible link.

I would say that this actually complements archaeological evidence of the presence of early modern humans out of Africa around and before 100 ka by providing the first genetic evidence of such populations.

--Ilan Gronau (co-author of Kuhlwilm et al)

Dienekes said...

If you want to place the divergence event geographically, then it likely happened in Africa, unlike the interbreeding, which likely took place in the Near East.

Yes, it's possible that the divergence event happened in Africa.
It's also possible that it happened in Asia. I see no reason to prefer one or the other.
After all, the main piece of evidence in favor of Out-of-Africa is that Eurasians are nested within African genetic variation.
If this paper is right, this is no longer the case: Africans are nested in Eurasian variation as a whole, inclusive of both modern Eurasians and the mystery population.

Mark Moore (Moderator) said...

So are the mysterious "Basal Eurasians" linked to this other mystery population in any way? I seem to remember them as also being described as "African-like but not African" in their genome. I understand these two populations are separated by tens of thousands of years in time, but the description of the two has some similarities. The difference is that the EEF/Basal Eurasian populations have LESS Neanderthal admixture than everybody else outside of Africa. That implies that the Basal Eurasians that mixed with the EEF were from a population which did not admix.

Rob said...

Hopefully, large initiatives like the Green Arabia programme will shed more archaeological (? and aDNA) light on the MP of the near east

Kurti said...

I had the same thoughts for quite some time now. What if modern Africans are just a migration from a very early Eurasian group that is nowadays extinct in Eurasia itself and modern Eurasians are merely a little piece of the once bigger Eurasian genetic variation. With other words similar to what happened with EEF in the Near East. It expanded to Europe and was washed out in the Near East itself by a related component. So what if a broad ancient Eurasian population with all it's diversity reached Africa and just after some time when they reached Africa, got almost completely "wiped out" by just one straign of Eurasians.

Another possible scenario is that we are dealing with a "backmigration" from Africa into Eurasia after earlier an "proto Eurasian" population moved into Africa.

Grey said...

"But there isn't any clear archaeological evidence for a Back-to-Africa migration either."

Perhaps there didn't need to be.

If north central Eurasia is/was an iodine desert and the population there (human/archaic) developed some kind of compensatory adaptations e.g. iodine retention, and those adaptations didn't make them smarter than other groups but only prevented retardation then there'd be no reason for a mass back migration.

However what if those adaptations once removed to a higher iodine region did make ppl smarter?

So for example average Altai woman marries average guy who lives around a nice lake with lots of fish and their kids end up a little smarter than either original populations.

So the migration is silent because the adaptations only create the bonus effect away from the source region.

eurologist said...

It seems to me that there could be an answer to this conundrum by looking more closely at the derived alleles found in the Altai specimen, but also across extant Eurasian AMH populations. In other words, if (as many of us think likely) AMHs not only made a futile ooA exit ~ 120,000 to 105,000 ya, but subsequently had a significant impact on extant populations, then we should be able to see such a signature, if we are interested in clarifying this issue at all and are willing to demonstrate that researchers are not biased one way or another...

AndyC said...

The interbreeding event is dated 100kya, and the age of the Altai Neandertal is estimated by the excavation team to be between 50-30kya. That is a 50,000 year gap. It is pretty hard to say anything about where the interbreeding event occurred, given that huge gap.

If we consider the Denisovans and Oceanians who have their genetic legacy, the fossil and the people are separated by a huge distance. The simplest explanation is that the Denisovans were more widespread than just Denisova cave. Likewise, the Altai Neandertals' range may have been extensive and overlapping with the Levant -- at least we have archeological evidence for Neandertal presence there.