Format

Send to

Choose Destination
Genetics. 2005 Mar;169(3):1601-15. Epub 2005 Jan 16.

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

Author information

1
Department of Genetics and Evolution, Max-Planck Institute of Chemical Ecology, Jena, Germany. schmid@ice.mpg.de

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.

PMID:
15654111
PMCID:
PMC1449538
DOI:
10.1534/genetics.104.033795
[Indexed for MEDLINE]
Free PMC Article

Publication type, MeSH terms, Substance, Secondary source ID

Publication type

MeSH terms

Substance

Secondary source ID

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center