A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.

The detection of footprints of natural selection in genetic polymorphism data is fundamental to understanding the genetic basis of adaptation, and has important implications for human health. The standard approach has been to reject neutrality in favor of selection if the pattern of variation at a c...

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Autores principales:	Christopher Toomajian, Tina T Hu, Maria José Aranzana, Clare Lister, Chunlao Tang, Honggang Zheng, Keyan Zhao, Peter Calabrese, Caroline Dean, Magnus Nordborg
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2006
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/d5f54adb435b4b8c87fedf65b3e7b4e1
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spelling	oai:doaj.org-article:d5f54adb435b4b8c87fedf65b3e7b4e12021-12-02T19:54:31ZA nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.1544-91731545-788510.1371/journal.pbio.0040137https://doaj.org/article/d5f54adb435b4b8c87fedf65b3e7b4e12006-05-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.0040137https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885The detection of footprints of natural selection in genetic polymorphism data is fundamental to understanding the genetic basis of adaptation, and has important implications for human health. The standard approach has been to reject neutrality in favor of selection if the pattern of variation at a candidate locus was significantly different from the predictions of the standard neutral model. The problem is that the standard neutral model assumes more than just neutrality, and it is almost always possible to explain the data using an alternative neutral model with more complex demography. Today's wealth of genomic polymorphism data, however, makes it possible to dispense with models altogether by simply comparing the pattern observed at a candidate locus to the genomic pattern, and rejecting neutrality if the pattern is extreme. Here, we utilize this approach on a truly genomic scale, comparing a candidate locus to thousands of alleles throughout the Arabidopsis thaliana genome. We demonstrate that selection has acted to increase the frequency of early-flowering alleles at the vernalization requirement locus FRIGIDA. Selection seems to have occurred during the last several thousand years, possibly in response to the spread of agriculture. We introduce a novel test statistic based on haplotype sharing that embraces the problem of population structure, and so should be widely applicable.Christopher ToomajianTina T HuMaria José AranzanaClare ListerChunlao TangHonggang ZhengKeyan ZhaoPeter CalabreseCaroline DeanMagnus NordborgPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 4, Iss 5, p e137 (2006)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Christopher Toomajian Tina T Hu Maria José Aranzana Clare Lister Chunlao Tang Honggang Zheng Keyan Zhao Peter Calabrese Caroline Dean Magnus Nordborg A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.
description	The detection of footprints of natural selection in genetic polymorphism data is fundamental to understanding the genetic basis of adaptation, and has important implications for human health. The standard approach has been to reject neutrality in favor of selection if the pattern of variation at a candidate locus was significantly different from the predictions of the standard neutral model. The problem is that the standard neutral model assumes more than just neutrality, and it is almost always possible to explain the data using an alternative neutral model with more complex demography. Today's wealth of genomic polymorphism data, however, makes it possible to dispense with models altogether by simply comparing the pattern observed at a candidate locus to the genomic pattern, and rejecting neutrality if the pattern is extreme. Here, we utilize this approach on a truly genomic scale, comparing a candidate locus to thousands of alleles throughout the Arabidopsis thaliana genome. We demonstrate that selection has acted to increase the frequency of early-flowering alleles at the vernalization requirement locus FRIGIDA. Selection seems to have occurred during the last several thousand years, possibly in response to the spread of agriculture. We introduce a novel test statistic based on haplotype sharing that embraces the problem of population structure, and so should be widely applicable.
format	article
author	Christopher Toomajian Tina T Hu Maria José Aranzana Clare Lister Chunlao Tang Honggang Zheng Keyan Zhao Peter Calabrese Caroline Dean Magnus Nordborg
author_facet	Christopher Toomajian Tina T Hu Maria José Aranzana Clare Lister Chunlao Tang Honggang Zheng Keyan Zhao Peter Calabrese Caroline Dean Magnus Nordborg
author_sort	Christopher Toomajian
title	A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.
title_short	A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.
title_full	A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.
title_fullStr	A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.
title_full_unstemmed	A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.
title_sort	nonparametric test reveals selection for rapid flowering in the arabidopsis genome.
publisher	Public Library of Science (PLoS)
publishDate	2006
url	https://doaj.org/article/d5f54adb435b4b8c87fedf65b3e7b4e1
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A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.

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