Interference among loci subject to selection (the Hill-Robertson effect) may considerably reduce levels of adaptation and variability in genomic regions that lack recombination. Y- or W chromosomes are particularly vulnerable to such effects, since they represent large, non-recombining blocks of genetic material. In birds, the W chromosome and mitochondrial genomes are both maternally transmitted, and hence fail to recombine with each other, whereas in mammals the Y chromosome is paternally transmitted. We show here that mitochondrial DNA sequence diversity is reduced in non-ratite birds compared with mammals. After considering possible confounding factors, such as differences in generation times, mutation rates and demography, we conclude that Hill-Robertson effects associated with the W chromosome provide the most likely explanation for this difference.
