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The last glacial maximum bottlenecks and human phylogeny

I’ve mentioned The genomic origins of the world’s first farmers a few times. It’s an intense model-based paper that revises some expectations and models of the origins of diverse human groups on the cusp of the Holocene:

The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.

A few things to note about this paper. First, no mention of Basal Eurasians. This research group doesn’t believe they’re necessary. As you may know, Basal Eurasians were hypothesized because Mesolithic Europeans seem genetically closer to eastern non-Africans than to incoming Early European Farmers (EEF) from Anatolia. One model that can explain this is that there was a population somewhere in N. Africa and W. Asia that split off first from other non-Africans, perhaps more than 60,000 years ago and that eventually merged back with West Eurasians at some point. Lazaridis et al. also believe this might explain why some W. Asia groups have less Neanderthal ancestry; the Basal Eurasians did not admix with them.

The problem, so far, is that nearly a decade after they were hypothesized we haven’t found a mostly Basal Eurasian sample. And, Basal ancestry is found in West Eurasia pretty early. Perhaps they’ll always remain a statistical construct?

Why doesn’t everyone think Basal Eurasians are necessary? If you read the above paper, the key issue is the distortionary impact that bottlenecks can have on the inferred branch lengths of a given phylogeny. They argue that a very strong bottleneck during the LGM 20,000 years ago inflated the divergence of European foragers from other populations and that subsequently, the populations bounced back very well so that their census sizes were likely large. And, they also argue that some of the distinctiveness of EEF from Anatolia is a function of their own bottleneck far more recently, around the beginning of the Holocene. Combined with these bottlenecks there are also various migrations between the branches in the typology, branches differentially impacted by these bottlenecks.

I don’t know how this aligns with earlier models, but I think it’s a serious contender. The key question I wonder is how this fits in with earlier ancient DNA and archaeology.

4 thoughts on “The last glacial maximum bottlenecks and human phylogeny

  1. I don’t see how LGM bottlenecks can work at all. Upper Paleolithic Europeans are also modelled as lacking Basal Eurasian relative to Iran_N, where Basal Eurasian is defined by reduced phylogenetic sharing with Ust Ishim, i.e. f4(African_Outgroup, Ust_Ishim,X,Y). Which is also true comparing post-Neolithic Europeans with East Asians (reduced sharing with Ust Ishim).

    So anything that explains the effect via LGM timed bottlenecks in either of Anatolian or post-LGM Europeans seems not plausible.

    It may be something else, like some phylogenetic relation between Ust Ishim and Upper Paleolithic people from much of Eurasia, of course.

    I think the main reason why they didn’t find Basal Eurasian could just be because of a lack of using Ust Ishim in their model. Why they didn’t, I don’t know; he’s high enough coverage as I understand it. (I did even suggest they could try it at the preprint comments on biorxiv).

  2. @Matt,

    On AG, some members argue that Basal Eurasian isn’t actually real, but a fstats artifact. According to them Basal Eurasian correlates with SSA in modern Eurasians with the highest amounts of BE ancestry. It appears they have a valid point here.

  3. @eyes of the tiger, it’s seems hard to test in a way, to eliminate the influence of Neanderthal ancestry.

    Like to test whether Near Eastern farmers share more derived changes (a signal of actual geneflow) with Africans, we could in theory use the test statistic.

    f4 (Chimpanzee, SS African (from any group); EEF, HG)

    With Chimpanzee as the proxy for the common ancestor that SS African and Eurasian split from.

    To prove geneflow, you need to show a shift in the derived state from the common ancestor in the EEF/Near Eastern group.

    But this problem is that this would be confounded by flow from Neanderthal -> HG, if it existed, which would inflate sharing between Chimp->HG (or rather, deflate the degree to which HG/Africans share the human ancestral variant frequencies). So a single stat is difficult.

    I think when it comes to qpGraphs though, which use multiple stats, that try to look at the possibility of whether EEF actually show any derived changes with any African groups, it always comes down to it being simpler to have flow from some group that forms a clade with Eurasian Upper Paleolithic HG but has less Neanderthal ancestry. Thus the Basal Eurasian solution. Geneflow from Africans that brings in derived frequency/variant changes specific to any African group doesn’t ever seem to be the right/preferred solution.

    I haven’t really tested this myself though. Possibly the anthrogenicans have something different via their qpGraphing or something.

  4. Considering that it isn’t just a matter of genetic distances that appear too high to be true for peoples that are equally derived, in their large majority, from West Eurasians (which accelerated drift caused by dramatic bottlenecks followed by intense founder effects could explain), but also a matter of considerably differentiated levels of Neanderthal admixture (AFAIK), I think this hypothesis can only work if they find evidences that there were various instances of Neanderthal input into the gene pool of West Eurasians, explaining the difference between Middle Easterners (lowest %), modern Europeans (higher %) and Paeolithic Europeans (highest %). Instead of dilution by Basal Eurasian-admixed Near Easterners (ANF, CHG, Iran_N, Levant_N), it would be the ancestors of Late Paleolithic Europeans the ones who would’ve acquired extra Neanderthal ancestry.

    Otherwise, what would explain it? Some strong indigenous African input in the entire Near East, from as early as Late Pleistocene, aside from the North African (Iberomaurusian-related) admixture in some of them, e.g. the Natufians, and AFAIK not yet identified in Epipaleolithic/Neolithic Anatolians? I don’t know if that’s feasible, because even Natufians aren’t very strongly shifted toward any indigenous African cluster, let alone Neolithic Anatolians and EEF.

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