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MBE Advance Access published online on October 13, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp249
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Indel-associated mutation rate varies with mating system in flowering plants

Jesse D. Hollister1,3, Jeffrey Ross-Ibarra2 and Brandon S. Gaut1

1 University of California, Irvine, Irvine, CA 92697-2525
2 University of California, Davis, Davis, CA 95616

3 Address for Correspondence: Jesse D. Hollister, Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave, Cambridge, MA 02138, jhollist{at}uci.edu, Phone: 617 496-3890

Received for publication August 13, 2009. Revision received October 6, 2009. Accepted for publication October 9, 2009.

A recently proposed mutational mechanism, indel-associated mutation (IDAM), posits that heterozygous insertions/deletions (indels) increase the point mutation rate at nearby nucleotides due to errors during meiosis. This mechanism could have especially dynamic consequences for the evolution of plant genomes, because the high degree of variation in the rate of self-fertilization among plant species causes differences in the heterozygosity of alleles, including indel alleles, segregating in plant species. In this study, we investigated the consequences of IDAM for species differing in mating system using both forward population genetic simulations and genome-wide DNA re-sequencing data from Arabidopsis thaliana, Oryza sativa, and Oryza rufipogon. Simulations of different levels of selfing suggest that the effect of IDAM on surrounding nucleotide diversity should decrease with increasing selfing rate. Further simulations incorporating selfing rates and the time of onset of selfing suggest that the time since the switch to selfing also affects patterns of nucleotide diversity due to IDAM. Population genetic analyses of A. thaliana and Oryza DNA sequence datasets empirically confirmed our simulation results, revealing the strongest effect of IDAM in the out-crossing O. rufipogon, a weaker effect in the recently evolved selfer O. sativa, and the weakest effect in the relatively ancient selfer A. thaliana. These results support the novel idea that differences in life-history, such as the level of selfing, can affect the per-individual mutation rate among species.

Key Words: mutation rate • insertions/deletions • mating system • angiosperms


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