Testing for effects of recombination rate on nucleotide diversity in natural populations of Arabidopsis lyrata

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. yrata populations is not related to recombination rate, including genic recombination hotspots, and low gene density in the low recombination rate region.