Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals

Abstract

Founder events play a critical role in shaping genetic diversity, fitness and disease risk in a population. Yet our understanding of the prevalence and distribution of founder events in humans and other species remains incomplete, as most existing methods require large sample sizes or phased genomes. Thus, we developed ASCEND that measures the correlation in allele sharing between pairs of individuals across the genome to infer the age and strength of founder events. We show that ASCEND can reliably estimate the parameters of founder events under a range of demographic scenarios. We then apply ASCEND to two species with contrasting evolutionary histories: ~460 worldwide human populations and ~40 modern dog breeds. In humans, we find that over half of the analyzed populations have evidence for recent founder events, associated with geographic isolation, modes of sustenance, or cultural practices such as endogamy. Notably, island populations have lower population sizes than continental groups and most hunter-gatherer, nomadic and indigenous groups have evidence of recent founder events. Many present-day groups––including Native Americans, Oceanians and South Asians––have experienced more extreme founder events than Ashkenazi Jews who have high rates of recessive diseases due their known history of founder events. Using ancient genomes, we show that the strength of founder events differs markedly across geographic regions and time––with three major founder events related to the peopling of Americas and a trend in decreasing strength of founder events in Europe following the Neolithic transition and steppe migrations. In dogs, we estimate extreme founder events in most breeds that occurred in the last 25 generations, concordant with the establishment of many dog breeds during the Victorian times. Our analysis highlights a widespread history of founder events in humans and dogs and elucidates some of the demographic and cultural practices related to these events.

Genomic signatures of bottleneck and founder effects in dingoes

“…The use of whole genome data also enables the measurement of lengths of long tracts of homozygous genotypes or runs of homozygosity (RoH) segments (Ceballos, et al 2018). A number of previous studies showed that bottleneck and founder effects increase the number of long RoHs (Bortoluzzi, et al 2020; Khan, et al 2021; Sánchez-Barreiro F 2021; Tournebize, et al 2022). Hence, estimating the lengths of RoH in dingoes and comparing them with those observed for other canines will potentially reveal whether the size of the founding dingo population was small.…”

The Newfoundland and Labrador mosaic founder population descends from an Irish and British diaspora from 300 years ago

“…Existing literature from historical 3 , clinical 1 , 10 – 14 , and population genetic studies 4 suggests evidence of a population bottleneck in the European settlement of NL. Furthermore, recent work has shown that island communities tend to experience stronger founder effects 40 . Therefore, we set out to characterise the magnitude of the NL founder effect using the NL 1,807 dataset and comparing this with European source populations.…”

Indigenous people from Amazon show genetic signatures of pathogen-driven selection

“…S3A) was built assuming a standstill in Beringia at 26,000 yr B.P., the settlement of America at 15,000 yr B.P., and divergence between Central and South American populations at 13,000 yr B.P. The effective population size and its changes over time were based on the Castro e Silva et al ( 60 ) dataset inferred through ASCEND ( 61 ) and IBDNe ( 62 ) softwares. We assume a mutation rate of 1 × 10 −8 and a generation time of 25 years.…”