Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.

<h4>Background</h4>Many of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local ada...

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Autores principales:	Jeffrey Ross-Ibarra, Stephen I Wright, John Paul Foxe, Akira Kawabe, Leah DeRose-Wilson, Gesseca Gos, Deborah Charlesworth, Brandon S Gaut
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/793e0d193f4d4bdfaed92100d5d0a9a2
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spelling	oai:doaj.org-article:793e0d193f4d4bdfaed92100d5d0a9a22021-11-25T06:12:03ZPatterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.1932-620310.1371/journal.pone.0002411https://doaj.org/article/793e0d193f4d4bdfaed92100d5d0a9a22008-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18545707/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Many of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local adaptation. Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation.<h4>Principal findings</h4>We studied nucleotide diversity in six natural populations of Arabidopsis lyrata, using 77 loci sampled from 140 chromosomes. The six populations were highly differentiated, with a median FST of 0.52, and structure analysis revealed no evidence of admixed individuals. Average within-population diversity varied among populations, with the highest diversity found in a German population; this population harbors 3-fold higher levels of silent diversity than worldwide samples of A. thaliana. All A. lyrata populations also yielded positive values of Tajima's D. We estimated a demographic model for these populations, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations. Finally, we used the inferred demographic model to perform an initial test for local adaptation and identified several genes, including the flowering time gene FCA and a disease resistance locus, as candidates for local adaptation events.<h4>Conclusions</h4>Our results underscore the importance of population-specific, non-equilibrium demographic processes in patterning diversity within A. lyrata. Moreover, our extensive dataset provides an important resource for future molecular population genetic studies of local adaptation in A. lyrata.Jeffrey Ross-IbarraStephen I WrightJohn Paul FoxeAkira KawabeLeah DeRose-WilsonGesseca GosDeborah CharlesworthBrandon S GautPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 3, Iss 6, p e2411 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jeffrey Ross-Ibarra Stephen I Wright John Paul Foxe Akira Kawabe Leah DeRose-Wilson Gesseca Gos Deborah Charlesworth Brandon S Gaut Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.
description	<h4>Background</h4>Many of the processes affecting genetic diversity act on local populations. However, studies of plant nucleotide diversity have largely ignored local sampling, making it difficult to infer the demographic history of populations and to assess the importance of local adaptation. Arabidopsis lyrata, a self-incompatible, perennial species with a circumpolar distribution, is an excellent model system in which to study the roles of demographic history and local adaptation in patterning genetic variation.<h4>Principal findings</h4>We studied nucleotide diversity in six natural populations of Arabidopsis lyrata, using 77 loci sampled from 140 chromosomes. The six populations were highly differentiated, with a median FST of 0.52, and structure analysis revealed no evidence of admixed individuals. Average within-population diversity varied among populations, with the highest diversity found in a German population; this population harbors 3-fold higher levels of silent diversity than worldwide samples of A. thaliana. All A. lyrata populations also yielded positive values of Tajima's D. We estimated a demographic model for these populations, finding evidence of population divergence over the past 19,000 to 47,000 years involving non-equilibrium demographic events that reduced the effective size of most populations. Finally, we used the inferred demographic model to perform an initial test for local adaptation and identified several genes, including the flowering time gene FCA and a disease resistance locus, as candidates for local adaptation events.<h4>Conclusions</h4>Our results underscore the importance of population-specific, non-equilibrium demographic processes in patterning diversity within A. lyrata. Moreover, our extensive dataset provides an important resource for future molecular population genetic studies of local adaptation in A. lyrata.
format	article
author	Jeffrey Ross-Ibarra Stephen I Wright John Paul Foxe Akira Kawabe Leah DeRose-Wilson Gesseca Gos Deborah Charlesworth Brandon S Gaut
author_facet	Jeffrey Ross-Ibarra Stephen I Wright John Paul Foxe Akira Kawabe Leah DeRose-Wilson Gesseca Gos Deborah Charlesworth Brandon S Gaut
author_sort	Jeffrey Ross-Ibarra
title	Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.
title_short	Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.
title_full	Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.
title_fullStr	Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.
title_full_unstemmed	Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.
title_sort	patterns of polymorphism and demographic history in natural populations of arabidopsis lyrata.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/793e0d193f4d4bdfaed92100d5d0a9a2
work_keys_str_mv	AT jeffreyrossibarra patternsofpolymorphismanddemographichistoryinnaturalpopulationsofarabidopsislyrata AT stepheniwright patternsofpolymorphismanddemographichistoryinnaturalpopulationsofarabidopsislyrata AT johnpaulfoxe patternsofpolymorphismanddemographichistoryinnaturalpopulationsofarabidopsislyrata AT akirakawabe patternsofpolymorphismanddemographichistoryinnaturalpopulationsofarabidopsislyrata AT leahderosewilson patternsofpolymorphismanddemographichistoryinnaturalpopulationsofarabidopsislyrata AT gessecagos patternsofpolymorphismanddemographichistoryinnaturalpopulationsofarabidopsislyrata AT deborahcharlesworth patternsofpolymorphismanddemographichistoryinnaturalpopulationsofarabidopsislyrata AT brandonsgaut patternsofpolymorphismanddemographichistoryinnaturalpopulationsofarabidopsislyrata
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Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata.

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