There’s a new preprint on bioRxiv that is very interesting, Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals:
…To learn about the frequency and evolutionary history of founder events, we introduce ASCEND (Allele Sharing Correlation for the Estimation of Non-equilibrium Demography), a flexible two-locus method to infer the age and strength of founder events. This method uses the correlation in allele sharing across the genome between pairs of individuals to recover signatures of past bottlenecks. By performing coalescent simulations, we show that ASCEND can reliably estimate the parameters of founder events under a range of demographic scenarios, with genotype or sequence data. We apply ASCEND to ~5,000 worldwide human samples (~3,500 present-day and ~1,500 ancient individuals), and ~1,000 domesticated dog samples. In both species, we find pervasive evidence of founder events in the recent past. In humans, over half of the populations surveyed in our study had evidence for a founder events in the past 10,000 years, associated with geographic isolation, modes of sustenance, and historical invasions and epidemics. We document that island populations have historically maintained lower population sizes than continental groups, ancient hunter-gatherers had stronger founder events than Neolithic Farmers or Steppe Pastoralists, and periods of epidemics such as smallpox were accompanied by major population crashes. Many present-day groups–including Central & South Americans, Oceanians and South Asians–have experienced founder events stronger than estimated in Ashkenazi Jews who have high rates of recessive diseases due to their history of founder events. In dogs, we uncovered extreme founder events in most groups, more than ten times stronger than the median strength of founder events in humans. These founder events occurred during the last 25 generations and are likely related to the establishment of dog breeds during Victorian times. Our results highlight a widespread history of founder events in humans and dogs, and provide insights about the demographic and cultural processes underlying these events.
This method is pretty cool because it scales and works on non-phased data (good luck phasing a lot of low coverage of ancient DNA!). Through simulation and comparison to earlier results, the authors show that ASCEND does a good job estimating
1) the timing of a founder event
2) the intensity of a founding event
One of my hobby-horses is that Ashkenazi Jews aren’t really that inbred or bottlenecked a group. They’ve been extensively studied, so there’s a laser-like focus on their population and medical genetics. Importantly, they also have a recessive disease load, usually attributed to their endogamy and small effective population size. Studying Ashkenazi Jewish genetics is easy if you think of it in grant terms since there are diseases that are well known you can focus on.
But one of the results in this preprint, which aligns with other earlier published work, is that there are many groups far more homogeneous due to extreme founder events/endogamy than Ashkenazi Jews. Some of the outcomes are not surprising. Lots of South Asian groups seem to be extremely homogeneous due to endogamy and small founding populations, though today many of them number in the millions. The strong implication from these results is that they carry a lot of deleterious recessive allele load.
The other groups are not surprising. Islanders, hunter-gatherers in marginal habits. Basically, populations artificially prevented from gene flow, or, those subject to strong cultural barriers.
The method not only estimates the intensity of the founder events but also the period. Many of the results are totally explicable. Many Northern Europeans seem to have founding populations that go back to the Corded Ware expansion. The founding of the Basque dates to the Roman Empire. Why? I think a reasonable hypothesis that for whatever reason this is when the ancient Aquitani emerged as an exclusive ethnocultural group, as opposed to Romanizing like their Iberian and Celtiberian neighbors.
Probably the most interesting result for me is one that is obvious in much of the data, but hasn’t been analyzed as thoroughly before: ancient European hunter-gatherers had very small effective populations due to narrow founder events. The question is: is this true in general for pre-agricultural people? Many anthropologists have argued that large agglomerations of sedentary populations were more common before the Holocene than we might think, and modern hunter-gatherers are biased samples (they occupy marginal territory).
As we obtain more ancient DNA that question will be answered in the generality. Over ten years ago Hawks et al. argued that large populations resulted in faster adaptation. Whatever details one might quibble within their model, I think the results from ancient DNA raise the possibility of the greater relative efficacy of selection (due to weaker drift) and more population connectedness allowing for easier flow of beneficial alleles.
The software is already available. I’m going to take it for a test drive…