Razib Khan One-stop-shopping for all of my content

One of the somewhat surprising things we have learned over the last decade is that massive admixture and homogenization has occurred between distinct human lineages over the last 10,000 years. By this, I mean that we’re not talking simply about continuous gene-flow between neighboring populations, but massive expansions of small groups and assimilation of very different groups from the expanding groups. As a stylized fact, it looks like “Early European Farmers” we as distinct from Mesolithic hunter-gatherers as modern Northern Europeans are from Han Chinese (pairwise Fst ~0.10). The fusion of these two groups later merged in much of Europe with migrants from the east, the western edge of the forest-steppe.

The empirical pattern seems to be that cultural innovations (e.g., agriculture) trigger demographic revolutions, which homogenize and admix vast regions. This is a story of demographic history. Phylogeography.

But there is another aspect, natural selection. Humans are not exempt from this. Selection operates upon genetic variation, which is preexistent (“standing variation”), or, comes from new mutations (de novo).

It seems plausible that cultural innovation has resulted in a great deal of selection over the last 10,000 years. So where did the raw material come from? One argument that has been playing out is between those who argue that it’s from variation within human populations that is ancestral and shared, and new variation. This is where admixture comes into play.

A new preprint on bioRxiv uses the 1000 Genomes data in the New World to suggest that admixture resulted in the introduction of a lot of adaptive alleles into populations of mostly European and Native background from African ancestry. Basically, it seems likely that the American tropics were colonized by African tropical diseases, which entailed adaptations which were already existent within African populations. Admixture-enabled selection for rapid adaptive evolution in the Americas:

Background: Admixture occurs when previously isolated populations come together and exchange genetic material. We hypothesized that admixture can enable rapid adaptive evolution in human populations by introducing novel genetic variants (haplotypes) at intermediate frequencies, and we tested this hypothesis via the analysis of whole genome sequences sampled from admixed Latin American populations in Colombia, Mexico, Peru, and Puerto Rico. Results: Our screen for admixture-enabled selection relies on the identification of loci that contain more or less ancestry from a given source population than would be expected given the genome-wide ancestry frequencies. We employed a combined evidence approach to evaluate levels of ancestry enrichment at (1) single loci across multiple populations and (2) multiple loci that function together to encode polygenic traits. We found cross-population signals of African ancestry enrichment at the major histocompatibility locus on chromosome 6, consistent with admixture-enabled selection for enhanced adaptive immune response. Several of the human leukocyte antigen genes at this locus (HLA-A, HLA-DRB51 and HLA-DRB5) showed independent evidence of positive selection prior to admixture, based on extended haplotype homozygosity in African populations. A number of traits related to inflammation, blood metabolites, and both the innate and adaptive immune system showed evidence of admixture-enabled polygenic selection in Latin American populations. Conclusions: The results reported here, considered together with the ubiquity of admixture in human evolution, suggest that admixture serves as a fundamental mechanism that drives rapid adaptive evolution in human populations.

The period after 1492 is easy for us to think about. But what ancient DNA has shown us is that it’s not as uncommon a phase as we might have thought.