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

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...

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Autores principales: Tournebize, Rémi, Chu, Gillian, Moorjani, Priya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9223333/
https://www.ncbi.nlm.nih.gov/pubmed/35737729
http://dx.doi.org/10.1371/journal.pgen.1010243
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author Tournebize, Rémi
Chu, Gillian
Moorjani, Priya
author_facet Tournebize, Rémi
Chu, Gillian
Moorjani, Priya
author_sort Tournebize, Rémi
collection PubMed
description 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.
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spelling pubmed-92233332022-06-24 Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals Tournebize, Rémi Chu, Gillian Moorjani, Priya PLoS Genet Research Article 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. Public Library of Science 2022-06-23 /pmc/articles/PMC9223333/ /pubmed/35737729 http://dx.doi.org/10.1371/journal.pgen.1010243 Text en © 2022 Tournebize et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Tournebize, Rémi
Chu, Gillian
Moorjani, Priya
Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals
title Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals
title_full Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals
title_fullStr Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals
title_full_unstemmed Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals
title_short Reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals
title_sort reconstructing the history of founder events using genome-wide patterns of allele sharing across individuals
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9223333/
https://www.ncbi.nlm.nih.gov/pubmed/35737729
http://dx.doi.org/10.1371/journal.pgen.1010243
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