Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species
Open Access
- 1 January 2011
- journal article
- research article
- Published by Oxford University Press (OUP) in Genome Biology and Evolution
- Vol. 3, 868-880
- https://doi.org/10.1093/gbe/evr085
Abstract
Population genetic theory predicts that the efficacy of natural selection in a self-fertilizing species should be lower than its outcrossing relatives because of the reduction in the effective population size (Ne) in the former brought about by inbreeding. However, previous analyses comparing Arabidopsis thaliana (selfer) with A. lyrata (outcrosser) have not found conclusive support for this prediction. In this study, we addressed this issue by examining silent site polymorphisms (synonymous and intronic), which are expected to be informative about changes in Ne. Two comparisons were made: A. thaliana versus A. lyrata and Capsella rubella (selfer) versus C. grandiflora (outcrosser). Extensive polymorphism data sets were obtained by compiling published data from the literature and by sequencing 354 exon loci in C. rubella and 89 additional loci in C. grandiflora. To extract information from the data effectively for studying these questions, we extended two recently developed models in order to investigate detailed selective differences between synonymous codons, mutational biases, and biased gene conversion (BGC), taking into account the effects of recent changes in population size. We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC.Keywords
This publication has 86 references indexed in Scilit:
- Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thalianaProceedings of the National Academy of Sciences, 2010
- Establishing, maintaining and modifying DNA methylation patterns in plants and animalsNature Reviews Genetics, 2010
- Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation linesGenome Research, 2009
- Recent speciation ofCapsella rubellafromCapsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneckProceedings of the National Academy of Sciences of the United States of America, 2009
- Recent speciation associated with the evolution of selfing inCapsellaProceedings of the National Academy of Sciences of the United States of America, 2009
- Estimating Translational Selection in Eukaryotic GenomesMolecular Biology and Evolution, 2008
- The effects of deleterious mutations on evolution in non-recombining genomesTrends in Genetics, 2008
- Selection on Amino Acid Substitutions in ArabidopsisMolecular Biology and Evolution, 2008
- Native range genetic variation in Arabidopsis thaliana is strongly geographically structured and reflects Pleistocene glacial dynamicsMolecular Ecology, 2007
- Adaptive genic evolution in the Drosophila genomesProceedings of the National Academy of Sciences of the United States of America, 2007