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.