Originally published as Genetics Published Articles Ahead of Print on May 27, 2008.

Genetics, Vol. 179, 985-995, June 2008, Copyright © 2008
doi:10.1534/genetics.107.085282

High DNA Sequence Diversity in Pericentromeric Genes of the Plant Arabidopsis lyrata

Akira Kawabe*,1, Alan Forrest*, Stephen I. Wright{dagger} and Deborah Charlesworth*,2

* Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom and {dagger} Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada

2 Corresponding author: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, King's Bldgs., W. Mains Rd., Edinburgh EH9 3JT, United Kingdom.
E-mail: deborah.charlesworth{at}ed.ac.uk

Differences in neutral diversity at different loci are predicted to arise due to differences in mutation rates and from the "hitchhiking" effects of natural selection. Consistent with hitchhiking models, Drosophila melanogaster chromosome regions with very low recombination have unusually low nucleotide diversity. We compared levels of diversity from five pericentromeric regions with regions of normal recombination in Arabidopsis lyrata, an outcrossing close relative of the highly selfing A. thaliana. In contrast with the accepted theoretical prediction, and the pattern in Drosophila, we found generally high diversity in pericentromeric genes, which is consistent with the observation in A. thaliana. Our data rule out balancing selection in the pericentromeric regions, suggesting that hitchhiking is more strongly reducing diversity in the chromosome arms than the pericentromere regions.