Have you taken my Steppelandia Quiz yet?
A new ‘must read’ paper on Neanderthals, Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry:
Modern humans appeared in Europe by at least 45,000 years ago but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania and Siberia who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.
There are two primary points of interest:
- More evidence of ubiquitous ‘admixture’ between Neanderthals and ‘modern humans’ who may have been in contact with them.
- These earliest European modern humans in Southeast Europe seem to be more closely related to (possibly ancestral to?) people in East Asia than modern Europeans.
On the first point, twenty years ago there were some paleoanthropologists who were arguing there was no admixture between Neanderthals and modern humans. That is, no fertile offspring. To not pussyfoot around it, Neanderthals were barely acknowledged as human in the early years of this century by many scholars. This is evident in Richard Klein’s The Dawn of Human Culture, written in 2002. With hindsight much of this is ridiculous. It really didn’t make any sense that the Neanderthal and modern human lineage were not inter-fertile when you dug into the literature on mammalian hybridization. There just wasn’t that much time for them to be totally incompatible.
In 2010 when it was found that Neanderthal ancestry seems to be found in non-Africans, we updated many of our priors. I think it is clear on some level Neanderthal humanization is driven by the fact of Neanderthal admixture. Nevertheless, there was a plausible case this admixture was rare. Perhaps a single Neanderthal tribe was mixed into expanding modern humans? Perhaps a single Neanderthal? These were ideas that were mooted.
With what we know now I’m not sure this is tenable. There are two primary issues. First, there is variation in Neanderthal ancestry among non-African populations which does not seem to be due to African admixture. East Asians have more Neanderthal admixture (~25% more last I checked) than Europeans who have more than West Asians. South Asian Neanderthal admixture is proportional to their distance from East Asians. The less West Eurasian the South Asian, the more Neanderthal.
There are a few ways to understand this. A simple explanation is that there was a secondary admixture event that impacted people migrating to eastern Eurasia. Another hypothesis is that natural selection reduced the Neanderthal fraction over time, but East Eurasians were less impacted by this due to small effective population size. Then, there is the idea that a non-African population, “Basal Eurasians”, that did not have much Neanderthal admixture later mixed into West Asians and Europeans, reducing the original Neanderthal fraction.
Because of the small fractions and the paucity of ancient DNA more than 10,000 years old, there are still arguments around this. These results increase the probability that there were multiple Neanderthal admixture events. At least in my way of thinking.
The authors found that the Neanderthal fraction seems to have decreased from a higher level relatively early on. Rather than a gradual decrease, the authors found suggestions of strong effective selection in the first few generations. Though there is still room for the Basal Eurasian model, I’m not sure it’s quite as necessary now. Along with Oase, and the existence of a Neanderthal-Denisovan hybrid from Denisova cave, the likelihood of frequent admixture between ancient hominin lineages seems pretty high.
I believe the primary issue at this point is that the admixture event seems to be dated to a narrow time period, before the extinction of Neanderthals, but not too ancient (before 60,000 years ago), and the Neanderthal ancestry is quite similar. Perhaps there isn’t the power to detect multiple secondary admixtures at “around the same time.” From the perspective of today, 45,000 v. 50,000 years ago is “around the same time.” But the reality is 5,000 years is a long time.
A few days ago a collaborator of one of the authors above posted this preprint (last author), An extended admixture pulse model reveals the limits to the dating of Human-Neandertal introgression:
In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models. In contrast, the duration of the gene flow is much more difficult to recover, except under ideal circumstances where gene flow is recent or the exact recombination rate is known. We conclude that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.
The second major finding of this paper is that the very first modern humans to settle in Europe are more genetically close to East Asians than to modern Europeans. This is in contrast to the Oase sample from Romania, just to the north, and a few thousand years later, that was no closer to East or West Eurasians. Or, a new 45,000-year-old sample from Czech Republic, which also shows no connection to any modern people.
If you read the first paper, you know that years ago the GoyetQ116-1 sample from Belgium that dates to 35,000 years before the present, and which seems to have some ancestral connection to the later Magdalenian people of Pleistocene Europe, had an East Eurasian affinity. Additionally, earlier mtDNA work showed eastern affinities in some Pleistocene Europeans. The authors above make the connection between these eastern-affinity early Europeans and the “Initial Upper Paleolithic” (IUP), which seems to have expanded across a broad swath of Eurasian, from Europe all the way to western Mongolia.
The implication then is that some of the ancestry of East Eurasians comes from a migration that took a route through Europe, and around the Black Sea littoral. This is a bit more complicated than a pure “southern route”, but it’s not crazy, and has long been proposed.
I think at this point we need to take a step back, and acknowledge that the period between 40 and 60 thousand years ago is important, but we look through the glass darkly. Something happened, as all the ancient Eurasian hominin lineages were absorbed by the “Out of Africa” population (which may not have been expanding out of Africa!), and the phylogenetic relationships of some of these people do not make sense in light of the phylogeography of the present.
It is entirely feasible to me that the ancient non-African or proto-non-African populations had already started to develop some internal structure. The putative Basal Eurasian v. “the rest” is one key bifurcation, but there may already have been divisions between the western and eastern branches of Eurasians in northeast Africa or the Near East. We just don’t know yet. Basically, ancient substructure that is getting “blown up” with rapid radiation.
Finally, here’s the first author with a write-up, Ancient genomes and stone age encounters.