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PMID: 15654111 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism.

Genetics ·Vol. 169 ·No. 3 ·2005-03-00 ·Pages 1601-15

Schmid KJ, Ramos-Onsins S, Ringys-Beckstein H, Weisshaar B, Mitchell-Olds T

Abstract

The simultaneous analysis of multiple genomic loci is a powerful approach to studying the effects of population history and natural selection on patterns of genetic variation of a species. By surveying nucleotide sequence polymorphism at 334 randomly distributed genomic regions in 12 accessions of Arabidopsis thaliana, we examined whether a standard neutral model of nucleotide sequence polymorphism is consistent with observed data. The average nucleotide diversity was 0.0071 for total sites and 0.0083 for silent sites. Although levels of diversity are variable among loci, no correlation with local recombination rate was observed, but polymorphism levels were correlated for physically linked loci (<250 kb). We found that observed distributions of Tajima's D- and D/D(min)- and of Fu and Li's D-, D*- and F-, F*-statistics differed significantly from the expected distributions under a standard neutral model due to an excess of rare polymorphisms and high variances. Observed and expected distributions of Fay and Wu's H were not different, suggesting that demographic processes and not selection at multiple loci are responsible for the deviation from a neutral model. Maximum-likelihood comparisons of alternative demographic models like logistic population growth, glacial refugia, or past bottlenecks did not produce parameter estimates that were more consistent with observed patterns. However, exclusion of highly polymorphic "outlier loci" resulted in a fit to the logistic growth model. Various tests of neutrality revealed a set of candidate loci that may evolve under selection.

MeSH Terms
Arabidopsis/genetics Base Sequence DNA, Plant/chemistry,genetics Genetic Variation Genome, Plant Models, Genetic Molecular Sequence Data Polymorphism, Genetic Selection, Genetic
Chemicals
DNA, Plant
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Schmid Karl J
Department of Genetics and Evolution, Max-Planck Institute of Chemical Ecology, Jena, Germany. [email protected]
Ramos-Onsins Sebastian
Ringys-Beckstein Henriette
Weisshaar Bernd
Mitchell-Olds Thomas
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Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
DOI
10.1534/genetics.104.033795
Email
[email protected]
Published
2005-03-00
Epub
2005-00-16
Pages
1601-15
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC1449538
Subset
IM
Databases
GENBANK
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PubMed source DOI: 10.1534/genetics.104.033795 PMC Full Text View journal details
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