The Y chromosome of Neanderthals

A paper published in Science (The evolutionary history of Neanderthal and Denisovan Y chromosomes by Martin Petr et al. SCIENCE 25 SEP 2020 : 1653-1656), reports that "interbreeding between early humans and Neanderthals and selection replaced the more ancient Denisovian-like Y chromosome and mitochondria in Neanderthals".

The paper includes this tree:

Caption for image: "A) Neighbor-joining tree estimated from the Y chromosome genotype calls, excluding C-to-T and G-to-A polymorphisms, rooted with a chimpanzee as the outgroup (14). Numbers show bootstrap support out of 100 bootstrap replicates. Terminal branch lengths are not informative about the ages of specimens (Fig. 1A), owing to differences in sequence quality. (B) Estimates of TMRCA between Y chromosomes along the x axis and a panel of 13 non-African Y chromosomes. Each dot represents the TMRCA with a single non-African Y chromosome, with error bars showing 95% CI from a resampling of branch counts (14). Black horizontal lines show the mean TMRCA calculated across the full non-African panel (dashed lines) with resampling-based 95% CI (solid lines) (14).".

I have written about Neanderthal Y chromosome in two posts (May 2014 and May 2018), so I found this paper really intersting.

It suggest that:

• Denisovans, Neanderthals and Humans lie on three separate phylogentic branches ("the Denisovan Y chromosomes form a separate lineage that split before Neanderthal and modern human Y chromosomes diverged from each other (Fig. 2A). Notably, all three late Neanderthal Y chromosomes cluster together and fall outside of the variation of present-day human Y chromosomes"). This is what one would expect.
• Split dates: "The two Denisovan Y chromosomes split from the modern human lineage around 700 ka ago ... By contrast, the three Neanderthal Y chromosomes split from the modern human lineage about 370 ka ago". Which also seems quite normal to me.
• They conclude that "The Denisovan–modern human Y chromosome TMRCA estimates agree with population split times inferred from autosomal sequences, suggesting that the differentiation of Denisovan Y chromosomes from modern humans occurred through a simple population split"
• And find the 370 ky TMRCA too recent for the Neanderthal Y chromosome. They authors write: "By contrast, the young TMRCA of Neanderthal and modern human Y chromosomes and mtDNAs suggest that these loci have been replaced in Neanderthals through gene flow from an early lineage closely related to modern humans."

So they concluded that a line of modern humans admixed into Neandethals, and they completely replaced Neanderthal Y chromosomes and that is why the split seems so recent. Instead of reflecting the older age they expected. This is summarized as "Autosomal genomes show that Neanderthals and Denisovans are sister groups that split from modern humans between 550 thousand and 765 thousand years (ka) ago. By contrast, the mtDNAs of Neanderthals and modern humans are more similar to one another [time to the most recent common ancestor (TMRCA) of 360 to 468 ka ago] than to the mtDNAs of Denisovans."

They add: "We conclude that the Y chromosomes of late Neandertals represent an extinct lineage closely related to modern human Y chromosomes that introgressed into Neanderthals between ~370 and ~100 ka ago. The presence of this Y chromosome lineage in all late Neanderthals makes it unlikely that genetic changes that accumulated in Neanderthal and modern human Y chromosomes before the introgression led to incompatibilities between these groups".

Now, they only sampled 3 male Neanderthals. Perhaps a larger sample may result in a different outcome. An introgression 370 ka would mean that these humans "closely related" modern humans left Africa -assuming the Out Of Africa theory is correct- 370 ka in an ancient migration and mated with Neanderthals. Since their Y chromosome is distinct from ours, these "closely related" people must have died out in Eurasia.

But looking at the tree and the dates, why conclude an admixture from "closely related" humans into Neanderthals? An admixture that erased old Neanderthal Y chromosomes?

Occam's razor approach suggests: the Neanderthals have a different Y chromosome to us and to Denisovans (fig. above, B) it lies on a different branch. Which ratifies the conclusion. So is the age an issue? 370 ka is too recent?

Why not look into the assumptions that lead to this date? Such as the mutation rate (they estimated 7.34 × 10⁻¹⁰ per base pair per year) or the age they adopted for the "oldest Y lineages" (A00): ~249 ka ago.

I am agree with the authors when they state " Furthermore, we predict that the ~400-ka-old Sima de los Huesos Neanderthals should carry a Y chromosome lineage more similar to that of Denisovans than to that of later Neanderthals", it is reasonable, and does not impact on their supposed Y chromosome replacement theory. Sima de los Huesos chromosomes may also have evolved into what we find in later Neanderthals.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall © 

Ancient H. erectus introgression into Denisovans and Neanderthals

A recent paper used statistical tools to look into ancient introgressions in the modern human line. The authors reported in their abastract that "We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these “super-archaic” regions—comprising at least about 4Mb—were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.".

You can read the full text of the paper here (Hubisz MJ, Williams AL, Siepel A (2020) Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genet 16(8): e1008895. https://doi.org/10.1371/journal.pgen.1008895).

Some higlights:

• The program they used "calls nearly 0.5% introgression from the Neanderthal into each of the African individuals. These calls are likely explained by a combination of false positives and back-migration into Africa from Europe. However, another possibility is that some regions introgressed into Neanderthals from ancient humans may be assigned the wrong direction". So they did find Neanderthal introgression in Africans but seem to write it off as a fabricaton of the program or false positives, and maybe back-migration.
• "We identify 1% of the Denisovan genome as introgressed from a super-archaic hominin—roughly double the estimated false positive rate (0.49%) for this event. Our apparent weak power for these events (another group has estimated ∼6% introgression) suggests that the super-archaic divergence may have been somewhat recent (perhaps closer to 1Mya than 1.5Mya). Still, this analysis resulted in 27Mb of sequence that may represent a partial genome sequence from a previously unsequenced archaic hominin. In addition, ARGweaver-D predicted that a small fraction of the Neanderthal genomes is introgressed from a super-archaic hominin (0.75% for Altai and 0.70% for Vindija), an event that has not been previously hypothesized. However, these fractions only slightly exceed the estimated false positive rate (0.65%), so these results are likely dominated by spurious predictions."
  This is indeed interesting. The time frame means surely an introgression from Homo erectus into Denisovans, in Asia. And also a probable admixture of H. erecrtus with Neanderthals!
• The introgression between the super-archaic into Denisovans was relatively recent: "...suggests that tmig > 225kya for the for the Sup→Den event"
• "our analysis suggests that at least about 4Mb of modern human genomes derives from an unknown but highly diverged archaic hominin, possibly Homo erectus, through at least two separate introgression events".
• The authors validate an early admixture of Humans into Neanderthals in Asia some 200 to 300 kya: "Our follow-up analysis based on the frequencies of introgressed elements among the two diploid Neanderthal genomes suggests that the Hum→Nea gene flow occurred roughly between 200 and 300kya, within the limits of accuracy imposed by our assumed demographic model, mutation rates, and generation time. As previously noted, because contact between modern humans and Neanderthals most likely took place in Eurasia, this timeline appears to be inconsistent with a genetic exchange involving the direct ancestors of most present-day Eurasians, who migrated out of Africa ∼50kya. Instead, our timeline suggests an earlier migration, occurring at least 200kya.". Yet they assume (without explaining why) that "These early migrating humans may later have gone extinct, leaving a genetic trace only in introgressed segments in Neanderthals."
• They "only detected a low rate of Sup→Afr introgression, somewhat below our estimated false positive rate." which is attributed to using a large population size, based on the assumption of their model -Africa as cradle of mankind had the largest population size.
• On ancient introgressions: "It is plausible that if Homo erectus mixed with the Denisovans, they may have also mixed with Neanderthals, perhaps in the Middle East; or perhaps DNA passed from Homo erectus to Neanderthal through the Denisovans. Altogether, given the number of gene flow events now documented among ancient hominins, it may be reasonable to assume that genetic exchange was likely whenever two groups overlapped in time and space."
• The authors did not discriminate between Africans and Non-Africans in this study: "When analyzing non-African humans, we only included the “recent” migration bands from Neanderthals and Denisovans into humans, whereas when looking for older introgression events, we excluded the “recent” bands as well as non-African humans. Throughout this paper, all humans are placed in the same population; we do not model divergences within human populations... on this time scale, the European/African split is very recent, so that we did not model the population divergence among modern humans or recent growth in out-of-Africa populations".

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2020 by Austin Whittall ©