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doi:10.1534/genetics.106.062588
A more recent version of this article appeared on November 1, 2006.
REGULAR RESEARCH PAPERS |
Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata
Stephen I. Wright 1*, John Paul Foxe 1, Leah DeRose Wilson 2, Akira Kawabe 3, Mark Looseley 4, Brandon Gaut 5 and Deborah Charlesworth 6
1 York University
2 University of California Irvine
3 Institute of Evolutionary Biology
4 St. Andrew's University
5 University of California
6 University of Edinburgh
* To whom correspondence should be addressed. E-mail: stephenw{at}yorku.ca.
Submitted on June 26, 2006
Revised on August 1, 2006
Accepted on 11 August 2006
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 genome-wide patterns of variability, specifically examining the effects of recombination rate on levels of silent polymorphism. In contrast with theoretical predictions from models of genetic hitch-hiking, 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 regions.
Key Words: Arabidopsis, background selection, nucleotide polymorphism, recombination, selective sweep
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