Phylogenomic analysis of pigeons and doves (Columbiformes) informs molecular evolution of a potential magnetoreceptor

ABSTRACT Pigeons and doves began to diversify shortly after the Cretaceous–Paleogene (K–Pg) boundary, subsequently colonizing new land masses via long-distance dispersal. Extant pigeon and dove species occupy a range of habitats and exhibit both migratory and homing behaviors. Here, we used whole-genome sequencing to infer the phylogenetic relationships of 108 pigeon and dove species; a significant expansion of taxa compared to prior phylogenomic studies. Phylogenetic analysis using different methods produced trees that were largely consistent, except with regard to the placement of the genus Macropygia, and generally follows subfamily and genus classification, with two exceptions. Given the similarities between trees, one of the resulting trees was used to examine molecular evolution in a candidate magnetoreceptor in birds, cryptochrome 4. A radical-pair within the cryptochrome 4 protein may allow birds to detect the Earth’s magnetic field. Phylogenetic studies have the potential to identify evolutionary changes within the cryptochrome 4 gene and protein sequences that are associated with behavioral changes, and may inform subsequent functional studies. By examining cryptochrome 4 guided by a phylogenomic reconstruction of pigeon and dove species, we find that three amino acid changes in cryptochrome 4 are under positive selection in some species. The three changes occur within two different functional regions within cryptochrome 4, but are not statistically significantly associated with changes in dispersal and foraging behaviors.