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Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data

Whether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method...

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Autores principales: Garud, Nandita R., Messer, Philipp W., Petrov, Dmitri A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946363/
https://www.ncbi.nlm.nih.gov/pubmed/33635910
http://dx.doi.org/10.1371/journal.pgen.1009373
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author Garud, Nandita R.
Messer, Philipp W.
Petrov, Dmitri A.
author_facet Garud, Nandita R.
Messer, Philipp W.
Petrov, Dmitri A.
author_sort Garud, Nandita R.
collection PubMed
description Whether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population of Drosophila melanogaster (DGRP) allowed us to rediscover three known cases of adaptation at the loci Ace, Cyp6g1, and CHKov1 known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harris et al. 2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and that instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps in D. melanogaster are first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that most demographic models employed in such analyses are necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require a large number of free parameters.
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spelling pubmed-79463632021-03-22 Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data Garud, Nandita R. Messer, Philipp W. Petrov, Dmitri A. PLoS Genet Research Article Whether hard sweeps or soft sweeps dominate adaptation has been a matter of much debate. Recently, we developed haplotype homozygosity statistics that (i) can detect both hard and soft sweeps with similar power and (ii) can classify the detected sweeps as hard or soft. The application of our method to population genomic data from a natural population of Drosophila melanogaster (DGRP) allowed us to rediscover three known cases of adaptation at the loci Ace, Cyp6g1, and CHKov1 known to be driven by soft sweeps, and detected additional candidate loci for recent and strong sweeps. Surprisingly, all of the top 50 candidates showed patterns much more consistent with soft rather than hard sweeps. Recently, Harris et al. 2018 criticized this work, suggesting that all the candidate loci detected by our haplotype statistics, including the positive controls, are unlikely to be sweeps at all and that instead these haplotype patterns can be more easily explained by complex neutral demographic models. They also claim that these neutral non-sweeps are likely to be hard instead of soft sweeps. Here, we reanalyze the DGRP data using a range of complex admixture demographic models and reconfirm our original published results suggesting that the majority of recent and strong sweeps in D. melanogaster are first likely to be true sweeps, and second, that they do appear to be soft. Furthermore, we discuss ways to take this work forward given that most demographic models employed in such analyses are necessarily too simple to capture the full demographic complexity, while more realistic models are unlikely to be inferred correctly because they require a large number of free parameters. Public Library of Science 2021-02-26 /pmc/articles/PMC7946363/ /pubmed/33635910 http://dx.doi.org/10.1371/journal.pgen.1009373 Text en © 2021 Garud et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://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
Garud, Nandita R.
Messer, Philipp W.
Petrov, Dmitri A.
Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data
title Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data
title_full Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data
title_fullStr Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data
title_full_unstemmed Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data
title_short Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data
title_sort detection of hard and soft selective sweeps from drosophila melanogaster population genomic data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7946363/
https://www.ncbi.nlm.nih.gov/pubmed/33635910
http://dx.doi.org/10.1371/journal.pgen.1009373
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