Assuming you haven’t been sleeping under a rock, you have probably heard that a Nature paper came out on an F1 Neanderthal-Denisovan hybrid. The major new science in my opinion from the results of the genome itself is to be found in the figure above. It confirms that there was a lot of population turnover among Neanderthals, as this individual’s mother is more closely related to European Neanderthals who flourished ~40,000 years later than conspecifics from the same region 30,000 years earlier. This is not surprising in light of what we know about the genetics and paleoecology of this group, though it confirms what we know and increases our confidence.
Rather, what is surprising is that this paper was published because they found an F1. From their conclusion:
It is notable that one direct offspring of a Neanderthal and a Denisovan (Denisova 11) and one modern human with a close Neanderthal relative (Oase 1) have been identified among the few individuals from whom DNA has been retrieved and who lived at the time of overlap of these groups…In conjunction with the presence of Neanderthal and Denisovan DNA in ancient and present-day people…this suggests that mixing among archaic and modern hominin groups may have been frequent when they met.
The number of ancient genomes from these species/groups/lineages is literally in the range a handful. And among the early finds is an F1! This seems highly unlikely. It could be a fluke. Or, as inferred above, F1’s may have been very common when different hominin lineages met.
But that makes one ask: how is it that Neanderthals and Denisovans remained some genetically distinct over hundreds of thousands of years? The two reasons offered are that the lineages were geographically very distant from each other on the whole, and, that hybrid individuals had very low fitness. I think the former is the primary dynamic to focus on.
For my assertion to make sense, consider some context in the published literature and theory. From 2004 and 2011 respectively, Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe and Strong reproductive isolation between humans and Neanderthals inferred from observed patterns of introgression.
From the first paper:
…we estimate that maximum interbreeding rates between the two populations should have been smaller than 0.1%. We indeed show that the absence of Neanderthal mtDNA sequences in Europe is compatible with at most 120 admixture events between the two populations despite a likely cohabitation time of more than 12,000 y. This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species.
And the second:
Recent studies have revealed that 2–3% of the genome of non-Africans might come from Neanderthals, suggesting a more complex scenario of modern human evolution than previously anticipated. In this paper, we use a model of admixture during a spatial expansion to study the hybridization of Neanderthals with modern humans during their spread out of Africa. We find that observed low levels of Neanderthal ancestry in Eurasians are compatible with a very low rate of interbreeding (<2%), potentially attributable to a very strong avoidance of interspecific matings, a low fitness of hybrids, or both.
Models are models, and they have assumptions. Don’t have the player, hate the model assumption and revisit your priors.
There are 22 ancient genomes from 40,000 years ago or before. One of them is an F1 between Neanderthals and Denisovans. And another, Oase 1, has a Neanderthal in their very recent ancestry. The sampling locations may not be totally representative. The Denisova cave is likely to be special because it’s at the nexus of the ranges of the two Eurasian archaic lineages. But with that out of the way, it seems very unlikely to me that very low fitness or very low likelihood of mating when it close contact is the reason that the lineages remained distinct. After less than half a dozen samples from Denisova, cave researchers hit on an F1. What are the chances?
And yet, if matings between the lineages occurred when they were in close contact, and they were genetically distinct nevertheless over such long periods, then that demands an explanation. Denisova hominins and Neanderthals were genetically closer than modern humans are to either. At the time that F1 was conceived the two lineages had been distinct for ~300,000 years. This is not qualitatively much longer than some modern human groups (e.g., Khoisan vs. everyone else) have been diverging. And yet, like the Denisovan-Neanderthal split, modern humans have a lot of population structure and evidence of isolation (also, note that modern humans show no evidence of reduced reproductive fitness from offspring and purification of admixture, as has been inferred for Neanderthal genomic regions in modern human genomes).
All this leads me to conclude that in Pleistocene hominins allopatry and metapopulation dynamics are the solutions to this quandary. The population density of archaic hominins was on average low, but you need to go beyond average. The distribution was possibly highly patchy and with large zones of little habitation. Gene flow across populations may have occurred, but they would run up to a wall of emptiness equivalent to the Atlantic ocean. Additionally, both Neanderthal and modern human ancient indicates a recurrent pattern of location population extinction and replacement. My hypothesis is that populations which were liminal to the range of both lineages, and so likely to have a higher load of admixture from the other lineage, were also in a marginal territory and most likely to go extinct and leave no descendants. Then, less admixed populations with larger numbers close to the core of the lineage range would repopulate the liminal region.
If the model is correct, I think the Altai was resettled by Neanderthals from the west after the Eemian interglacial.
A contrasting method to maintain genetic separation from allopatry (physical distance and barrier) are group cultural identities which maintain very strict endogamy. We see this over 2,000 years in India, where populations are co-localized but almost totally unrelated in any way you’d predict from geography. But 2,000 years is a blink of an eye geologically. The explanation for why Neanderthals and Denisovans, and various African human lineages, remained separate for hundreds of thousands of years as coherent populations despite some gene flow on the margins, has to be geology, geography and ecology. Domains where hundreds of thousands years of stasis on quite possible.
Strictly speaking, observing one F1 among a few dozens similarly ancient genomes isn’t a strong reason to believe that interbreeding was common. One-off observations are just as compatible with low incidence as with high one. We’d need considerably more observations than one to put a tighter bracket on the incidence numbers.
Also if F1s were infertile or not allowed to breed, then even higher relative numbers of F1s may not mean much introgression?
please acknowledge oase 1. if you don’t know what i’m alluding to (it’s in the post), please google it. also, why are you saying ‘similarly ancient.’ they’re older than 40K but all over the place age-wise.
Also if F1s were infertile or not allowed to breed, then even higher relative numbers of F1s may not mean much introgression?
infertile? what relevance does this have for this post? we know that hominins were interfertile.
your general point is well-taken. but unless i’m confused as to the details of your comment it’s kind of stupid tbh.
I wasn’t sure if we want to count Oase man because it wasn’t F1, and the interbreeding act which yielded that lineage may have also yielded dozens or even likely hundreds descendants with similarly elevated / historically recent Neanderthal ancestries. What should we put for denominator there, anyway? Of course the new Denisova Cane girl doesn’t represent the “only” attested cross-species hybridization event, it’s just the one known F1. The hominin DNA in contemporary humans came from numerous Neanderthals and Denisovans, so of course there must have been a number of interbreeding occurrences.
All my inner statistician was trying to point out is that if you observe 1 outcome in a pool of say 50 events, then it’s a fallacy to infer that this outcome happened at a 1/50 frequency. We just don’t have enough statistical data yet; the CI spans close to zero, and the true frequency may turn out to be much lower.
Well done, Razib! Make love not war hasn’t been invented in the Sixties, and your arguing about population density is convincing.
This is quite a bit outside my field, but you mention that at the time of the F1, Denisovans and Neanderthals had been distinct for ~300 kyears. But the latest I read was Rogers, Bolender and Huffs “Early history of Neanderthals and Denisovans” which estimate that the lineages diverged 744 – 632 kyears ago, with the earlier divergence seeming more probable. Is there something new here?
Also, I’ve generally understood that West Asian Neaderthals had greater genetic diversity than later European ones. Does not this argue for Europe being resettled from the east, rather than the other way around?
If the F1 and Oasis showed that interbreeding was very common, then why is there not one modern human with Neanderthal or Denisovan mtDNA or Y-DNA? And not only that (Because maybe it could have been explained by some sort of massive founder effect in a more modern population or maybe there were a few but simply drifted from the population, not unlike Y-DNA C or mtDNA M in Paleolithic Europe) but we don’t see any Neanderthal or Denisovan mtDNA or Y-DNA in ancients either. Not one example.
Because maybe it could have been explained by some sort of massive founder effect in a more modern population or maybe there were a few but simply drifted from the population
drift. small Ne means shorter time to coalescence. the vast majority of ancient lineages are going to go extinct. if the vast majority of ancestry is NOT neanderthal or denisovan, then it makes sense (there’s a blog post on this i put up). john hawks pointed this out years ago. though with the Y, A00 might be introgression from a non-modern lineage (within africa).
But the latest I read was Rogers, Bolender and Huffs “Early history of Neanderthals and Denisovans” which estimate that the lineages diverged 744 – 632 kyears ago, with the earlier divergence seeming more probable.
yeah, i’ve talked to alan about this. they might be right. or not. depends on the details of their model specification. they are working on some updates (presented at AAPA).
Also, I’ve generally understood that West Asian Neaderthals had greater genetic diversity than later European ones. Does not this argue for Europe being resettled from the east, rather than the other way around?
biogeographically europe and northern west asia are the same.
@Razib
If it’s drift we should find a Neanderthal uniparental in ancient AMH samples of Asia or Europe, I’d say. We did find mtDNA M in ancient samples, which may serve as an example of that. Also, the massively admixted AMH Oase 1 apparently left no ancestry in modern Europeans.
PS: Although, as you said, you could theorize that the original pool of mtDNA M must have been much larger than the tiny pool of Ne uniparental genes.
Also, the massively admixted AMH Oase 1 apparently left no ancestry in modern Europeans.
yes. that drops the Ne in general.
If it’s drift we should find a Neanderthal uniparental in ancient AMH samples of Asia or Europe, I’d say. We did find mtDNA M in ancient samples, which may serve as an example of that.
(and a lot of these old mt and Y are basal/gone too)
we don’t have that many ancient samples (pleistocene). the admixture fraction was less than 10%. eg look at fu et al. where they have about 10 from before 10,000 years ago: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4943878/
Surprised that anyone still remembers that old LaTour song…
Are there words in genetics to distinguish between two populations with a shared ancestral population at (at least) the genus or taxonomic family level, that are long separated and phenotypically distinct, that produce (1) fully fertile hybrids in gender balance, (2) that produce hybrids subject to Haldane’s law (i.e. fertile hybrids are predominantly homozygotes), (3) that produce generally infertile hybrids (e.g. donkeys and horses producing mules), and (4) that do not sexually produce offsprings?
Loose definitions of the word species could encompass all four, while very narrow ones could include only (4), but there seem to be at least four possibilities that each deserve a word.
Also my impression is that these four possibilities are tightly linked to the number of generations to a most recent shared ancestor, even if there is a weak general trend, and that it isn’t uncommon to leap frog some of the categories in the course of evolution. Is that correct?
Also, the common name “Denny” for the female Denisovan-Neanderthal hybrid individual is cute and appropriate and informative.