Intron size and natural selection

Intron sizes vary widely among different genes and among homologous genes of different species. The distribution of intron sizes may be maintained in a steady state, reflecting the processes of insertion and deletion of gene sequences, or it may be that the distribution is constrained by natural selection1,2,3. If intron size is governed by natural selection, there should be a statistical association between this size and the rate of recombination per map unit of the genome, assuming that natural selection is less effective in genomic regions of low recombination4,5,6. Here we show that larger introns of Drosophila melanogaster occur preferentially in regions of low recombination, which is consistent with large introns having a deleterious effect. The association is significant (P=40.001, linear regression), despite the fact that no effort was made to stratify the data by other factors that affect intron size, such as the size of the associated coding region7 or the presence of regulatory sequences inside the intron.