The 4,000 year explosion


The figure above shows a most interesting result from a new preprint, FADS1 and the timing of human adaptation to agriculture. It shows the allele frequency change using ancient Eurasian genomes for the derived allele at FADS1.

In case you don’t know why FADS1 is important, it’s been implicated in variation long-chain polyunsaturated fatty acids (LC-PUFA) metabolism. The derived allele, embedded in haplotype D in the above preprint, seems more optimized for plant-based diets, because of the higher activity of synthesis of LCPUFAs (which one might otherwise obtain from marine resources, as is likely among Inuit).

So the standard model is that the Neolithic changed things, as humans began to adapt to cereal-based diet diets. This preprint suggests maybe not:

Our analysis shows that selection at the FADS locus was not tightly linked to the development of agriculture. Further, it suggests that the strongest signals of recent human adaptation may not have been driven by the agricultural transition but by more recent changes in environment or by increased efficiency of selection due to increases in effective population size.

The authors are explicit that the derived allele at FADS1, which is at ~60% in modern Europeans, was under strong selection during the Bronze Age. In fact, this allele, which is common in Africans, may have been absent in most Paleolithic Eurasians. Using various methods they infer in fact that the ancestors of non-Africans may have been subject to selection for the ancestral variant. Their timing estimates indicate that this predates the standard expansion period starting ~60,000 BP (there was also an older selection event for the derived variant within Africa). Additionally, the authors posit that the derived variant was introduced into Europeans due to the Basal Eurasian ancestry in farmers.

They posit two dynamics that might drive the Bronze Age selection events. First, they suggest that the change in environment was actually more dramatic than that during the Paleolithic-Neolithic transition. Second, they suggest that effective populations were much smaller before the Bronze Age, so selection was not as efficacious (or, more precisely, drift effects were dominant in shaping variation).

This idea that the Neolithic isn’t quite as important, or singular, is somewhat of a surprise. But we may need to consider it. Another line of research, using high-quality modern day sequences rather than ancient genotypes, implies that there has been a lot of recent selection, and that’s likely going on today.

Second, one of the major takeaways from The Fate of Rome is that pandemics probably weren’t a feature of Neolithic small-scale societies. Rather, pandemics relied on long-distance trade and movement, as well as concentrations such as urban centers. Though certain endemic diseases probably arose in the Neolithic, the periodic sweep of pandemics required greater social and cultural complexity and overall human density.

The analogy then is rather straightforward. Just as microbes can move faster and more efficiently in an interconnected world, so such a world is much closer to a panmictic one. Earlier work suggested that effective population size of Neolithic farmers was not particularly small, but perhaps there are dynamics being missed by that simple summary value when it comes to the interconnectedness of the Eurasian landscape triggered by the emergence of pastoralism, and the necessary reaction of larger-scale polities.

A simple test of this would be to compare selection signals in a place like Papua New Guinea, which did not seem to undergo the same sort of pressures as Bronze Age Eurasian societies in relation to reduced diversity. I presume that New World societies as well would be an interesting test.

5 thoughts on “The 4,000 year explosion

  1. Razib: Second, they suggest that effective populations were much smaller before the Bronze Age, so selection was not as efficacious

    That’s really quite interesting; really hope they can use methods to directly reconstruct population size estimates from Neolithic genomes so that we can test this.

    This is also important to understanding the demographic history; if populations in North-Central European Neolithic were not so large, maybe replacement (even 90%) is not so surprising as it might seem.

    I’m a bit skeptical about strong population substructure in Neolithic Europe, because when we look at populations from east to west along Europe, there doesn’t seem to be isolation from each other and rather the picture looks quite clinal (e.g. the British Neolithic and Globular Amphora in Central Europe looks to be intermediate more westerly and easterly Neolithic populations in Spain and Balkans).

    Less sure as well about how idea of small population size can be sustained for Neolithic SE Europe specifically (opposed to NC Europe) given social complexity and settlement size of “Old Europe” cultures there.

    Additionally, the authors posit that the derived variant was introduced into Europeans due to the Basal Eurasian ancestry in farmers.

    It could be this, but at the same time, ancient Middle Eastern populations from the West Eurasian branch that contributed to early farmers could also have preserved the variant? It seems like generally variant must have been preserved to some degree by more Southern Eurasian populations without Basal Eurasian ancestry, or East Eurasians couldn’t have it without having any Basal Eurasian. (I believe derived variant frequency also goes higher from North->South in East Eurasia as well, from Yellow River down to SE Asia?).

  2. Urban Revolution vs. Neolithic Revolution? V. Gordon Childe really does seem to get it right even after all these years.

  3. @ Matt

    “It could be this, but at the same time, ancient Middle Eastern populations from the West Eurasian branch that contributed to early farmers could also have preserved the variant? It seems like generally variant must have been preserved to some degree by more Southern Eurasian populations without Basal Eurasian ancestry, or East Eurasians couldn’t have it without having any Basal Eurasian. (I believe derived variant frequency also goes higher from North->South in East Eurasia as well, from Yellow River down to SE Asia?).”

    Are you referring to the Anatolian foragers who became ancestors of Neolithic Anatolians, sans the Levantine-related admixture found in the latter?

  4. A limited but decisive number of SNPs is on the 23andme data.

    One of the most important problems right now is that the phenotypical consequences of a lot of this genetic variation is poorly understood. If you know too little about the full impact of an allel, the interpretation might be way off.

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