On the Apportionment of Archaic Human Diversity:
The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution of archaic ancestry in modern populations can be leveraged to better understand the interaction between our species and its archaic relatives, and the impact of natural selection on archaic segments of the human genome. Resolving these interactions can be difficult, as archaic variants in modern populations have also been shaped by genetic drift, bottlenecks, and gene flow. Here, we investigate the apportionment of archaic variation in Eurasian populations. We find that archaic genome coverage at the individual- and population-level present unique patterns in modern human population: South Asians have an elevated count of population-unique archaic SNPs, and Europeans and East Asians have a higher degree of archaic SNP sharing, indicating that population demography and archaic admixture events had distinct effects in these populations. We confirm previous observations that East Asians have more Neanderthal ancestry than Europeans at an individual level, but surprisingly Europeans have more Neandertal ancestry at a population level. In comparing these results to our simulated models, we conclude that these patterns likely reflect a complex series of interactions between modern humans and archaic populations.
The method is pretty neat. Read this closely. Here are some takeaways:
– European Neanderthal ancestry is lower than East Asian, but more diverse
– South Asians clearly have different Denisovan ancestry than East Asians
– Population structure matters…South Asian rare allele frequency is due to admixture between divergence groups
Basically, Neanderthal and Denisovan admixture is more complex than our simple stylized models.
The parallel between this and the other this week large scale archaic ancestry variant paper (https://advances.sciencemag.org/content/7/29/eabc0776 – “An ancestral recombination graph of human, Neanderthal, and Denisovan genomes”) is of course “We also detect an excess of Neanderthal and Denisovan haplotype blocks unique to South Asian genomes.”. They used a lot of the SGDP project genomes (which has 142 populations with typically two individuals from each, sacrificing a relatively large sample size in population that HGDP has for more diversity in coverage), so it doesn’t seem like the finding in that paper and this one would be due to a lack of coverage of some populations in 1000 Genomes (used in this paper). It seems instead like the AASI ancestry is relatively deep splitting and so harbours more unique geographically restricted variants, whilst SA also “benefits” from the rest of the rest Eurasian variant pool through migration (i.e. the end result is that the AASI linked haplotype blocks are mostly somewhat restricted to India, despite low level geneflow across SEA and Central Asia, while West Eurasian variants are found in South Asia, and the Americas etc so are not unique to the region). Graphically – https://imgur.com/a/BAACb08.
Curious thing about that paper is that seems to classify radically less of Oceanian ancestry as Denisovan origin, in their Table S2. If I remember rightly I thought that was 2-3% or so, but this supplement provides as only 0.43%, still about 1 in 250 ancestors but only a factor of 4x East Asian (around 0.1%). Which is curious. Partly mediated by the “ambiguous” (that they can’t call between Denisovan and Neanderthal) but still leaves Oceanians as relatively less enriched in archaic ancestry than they might have seemed from other works (as here they have about as much Neanderthal ancestry as other populations with a top-up of 1% Denisovan+ambiguous, only about 1% higher archaic ancestry, short of 2-3% extra from Denisovan).
(On the linked paper that’s the subject of the post, as an aside I noted it had a short section in praise of Lewontin. It seemed unnecessary to any understanding the paper, and I guess sort of a thing of his supporters wanting to put in a shout-out to solidify him in the firmament in that dangerous period where reputations can be forgotten after death, but fine. Although that did make me did kind of wonder whether Lewontin actually was the first to run those statistics on human genetics and publish on them, or if he was simply the first to do so in aid of making a particular political argument.)