Mito-nuclear discordance in the phenotypically variable Andean hummingbirds Coeligena bonapartei and Coeligena helianthea (Trochilidae)

Abstract The interplay among evolutionary mechanisms like gene flow and selection may result in discordant signals between mitochondrial DNA, nuclear markers and phenotypes. The Andean hummingbirds Coeligena bonapartei and Coeligena helianthea showed differentiation in the gene ND2 which is discordant with plumage coloration but consistent with geography. We analysed complete mitochondrial genomes of individuals from Coeligena bonapartei bonapartei, Coeligena bonapartei consita, Coeligena helianthea helianthea, and Coeligena helianthea tamai to inform their evolutionary history. We found genetic structure despite low genetic differentiation among these populations. Phylogenetic and network analyses based on mitogenomes showed a northern vs. southern differentiation pattern which is discordant with the relationships based on nuclear markers and the coloration phenotypes (serving as a basis for taxonomy). Mitogenomes of the two nominate subspecies are indistinguishable, suggesting incomplete lineage sorting or introgression, while those of C. b. consita and C. h. tamai are more similar to each other than they are to their respective nominate subspecies. Our results indicate that various evolutionary mechanisms drove the divergence in phenotypes, and nuclear and mitochondrial genomes of Coeligena hummingbirds, playing out over a complex biogeographic scenario likely involving periods of isolation and secondary contact. We outline hypotheses to be tested with future analyses of genome-wide variation.