Dynamic molecular evolution of a supergene with suppressed recombination in white-throated sparrows

In the white throated sparrow two alternative morphs differing in plumage and behavior segregate with a large chromosomal rearrangement. As with sex chromosomes, the rearranged version of chromosome two (ZAL2m), is maintained in a near-constant state of heterozygosity, offering an opportunity to investigate how both degenerative and selective processes act during the early evolutionary stages of supergenes. Here we generated whole genome sequencing data to better understand the evolutionary forces shaping the evolution of ZAL2m and the standard version of the chromosome, ZAL2.