Distinguishing between selective sweeps from standing variation and from a de novo mutation.

An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminat...

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Autores principales:	Benjamin M Peter, Emilia Huerta-Sanchez, Rasmus Nielsen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/40024da6128b4aaf8a77a605246f1bb8
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spelling	oai:doaj.org-article:40024da6128b4aaf8a77a605246f1bb82021-11-18T06:20:38ZDistinguishing between selective sweeps from standing variation and from a de novo mutation.1553-73901553-740410.1371/journal.pgen.1003011https://doaj.org/article/40024da6128b4aaf8a77a605246f1bb82012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23071458/pdf/?tool=EBIhttps://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminating between models of selection and providing estimates of the age of selected alleles and the selection coefficients acting on them. We use simulations to assess the power and accuracy of our method and apply it to seven of the strongest sweeps currently known in humans. We identify two genes, ASPM and PSCA, that are most likely affected by selection on standing variation; and we find three genes, ADH1B, LCT, and EDAR, in which the adaptive alleles seem to have swept from a new mutation. We also confirm evidence of selection for one further gene, TRPV6. In one gene, G6PD, neither neutral models nor models of selective sweeps fit the data, presumably because this locus has been subject to balancing selection.Benjamin M PeterEmilia Huerta-SanchezRasmus NielsenPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 8, Iss 10, p e1003011 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Benjamin M Peter Emilia Huerta-Sanchez Rasmus Nielsen Distinguishing between selective sweeps from standing variation and from a de novo mutation.
description	An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminating between models of selection and providing estimates of the age of selected alleles and the selection coefficients acting on them. We use simulations to assess the power and accuracy of our method and apply it to seven of the strongest sweeps currently known in humans. We identify two genes, ASPM and PSCA, that are most likely affected by selection on standing variation; and we find three genes, ADH1B, LCT, and EDAR, in which the adaptive alleles seem to have swept from a new mutation. We also confirm evidence of selection for one further gene, TRPV6. In one gene, G6PD, neither neutral models nor models of selective sweeps fit the data, presumably because this locus has been subject to balancing selection.
format	article
author	Benjamin M Peter Emilia Huerta-Sanchez Rasmus Nielsen
author_facet	Benjamin M Peter Emilia Huerta-Sanchez Rasmus Nielsen
author_sort	Benjamin M Peter
title	Distinguishing between selective sweeps from standing variation and from a de novo mutation.
title_short	Distinguishing between selective sweeps from standing variation and from a de novo mutation.
title_full	Distinguishing between selective sweeps from standing variation and from a de novo mutation.
title_fullStr	Distinguishing between selective sweeps from standing variation and from a de novo mutation.
title_full_unstemmed	Distinguishing between selective sweeps from standing variation and from a de novo mutation.
title_sort	distinguishing between selective sweeps from standing variation and from a de novo mutation.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/40024da6128b4aaf8a77a605246f1bb8
work_keys_str_mv	AT benjaminmpeter distinguishingbetweenselectivesweepsfromstandingvariationandfromadenovomutation AT emiliahuertasanchez distinguishingbetweenselectivesweepsfromstandingvariationandfromadenovomutation AT rasmusnielsen distinguishingbetweenselectivesweepsfromstandingvariationandfromadenovomutation
_version_	1718424473091178496

Distinguishing between selective sweeps from standing variation and from a de novo mutation.

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