Reconstructing the history of founder events using genome-wide patterns of allele sha


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Founder events play a critical role in shaping genetic diversity, impacting the fitness of a species and disease risk in humans. Yet our understanding of the prevalence and distribution of founder events in humans and other species remains incomplete, as most existing methods for characterizing founder events require large sample sizes or phased genomes. 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.

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In Europe, many founder events date to ~3,500–5,000 years ago, coincident with the spread of Steppe Pastoralists and the appearance of Beaker and Corded Ware cultures in Eastern and Northern Europe. This period has been referred to as the “Neolithic decline” as it was accompanied by permanent abandonment of previously heavily-populated settlements. The causes are still disputed and could have involved warfare with invading Steppe Pastoralists, environmental overexploitation56, and/or the spread of infectious diseases like plague57. For instance, recent findings suggest there were multiple lineages of Yersinia pestis expanding through early trade networks across Eurasia during this period57.

We inferred strong founder events in the history of seven West Eurasian present-day populations, including in Western Europe (Basque country and Sardinia), Eastern and Northern Europe (Belarus, Estonia, Finland and Lithuania) and Anatolia (Turkey) (Figure 2). The timing of the founder events in Basque people (~1,700–2,500 years ago) overlaps with the Roman colonization of the Basque country. Strikingly, in Eastern and Northern Europe, the timing coincides with the spread of Steppe Pastoralists and the appearance of Beaker and Corded Ware cultures. The founder event in Sardinia occurred ~3,400-4,900 years ago and is coincident with the appearance of the Beaker culture on the island34. Similarly, in Eastern Europe (Lithuania, Estonia and Belarus) and Northern Europe (Finland), the estimated founder ages of ~4,500-5,000 years ago overlaps with the arrival of the Corded Ware culture35,36.

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