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Originally published as Genetics Published Articles Ahead of Print on September 1, 2006.
Genetics, Vol. 174, 1421-1430, November 2006, Copyright © 2006
doi:10.1534/genetics.106.062588
Testing for Effects of Recombination Rate on Nucleotide Diversity in Natural Populations of Arabidopsis lyrata
Stephen I. Wright*,1,
John Paul Foxe*,
Leah DeRose-Wilson
,
Akira Kawabe
,
Mark Looseley,2,
Brandon S. Gaut and
Deborah Charlesworth
* Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada, Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697 and Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
1 Corresponding author: Department of Biology, York University, 4700 Keele St., Toronto, ON M3J 1P3, Canada.
E-mail: stephenw{at}yorku.ca
We investigated DNA sequence diversity for loci on chromosomes 1 and 2 in six natural populations of Arabidopsis lyrata and tested for the role of natural selection in structuring genomewide patterns of variability, specifically examining the effects of recombination rate on levels of silent polymorphism. In contrast with theoretical predictions from models of genetic hitchhiking, maximum-likelihood-based analyses of diversity and divergence do not suggest reduction of diversity in the region of suppressed recombination near the centromere of chromosome 1, except in a single population from Russia, in which the pericentromeric region may have undergone a local selective sweep or demographic process that reduced variability. We discuss various possibilities that might explain why nucleotide diversity in most A. lyrata populations is not related to recombination rate, including genic recombination hotspots, and low gene density in the low recombination rate region.
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