Making two andean hummingbird species: genome divergence and structural coloration

Instances of low genetic differentiation combined with clear phenotypic differences between closely related and recent diverged taxa are ideal scenarios to search for drivers of speciation. The two hummingbirds Coeligena bonapartei and Coeligena helianthea are sister species distributed parapatrically in the high Andes in the north of South America. These hummingbirds show strikingly different plumage coloration but low genetic divergence in mitochondrial DNA and Ultra Conserved Elements (UCEs). In this study, we used whole genome sequencing and low coverage (population-level) genome re-sequencing to search for candidate genes related to plumage coloration differences. In total we obtained 45 genomic sequences from both species at a coverage of ~3x. We identified highly differentiated genomic regions (i.e., differentiation peaks) and ~1.7 million single nucleotide polymorphisms (SNPs) between these hummingbirds. We found significant genetic differentiation among subspecies, which was moderate for C. b. bonapartei, C. h. helianthea and C. h. tamai, and strong between the subspecies C. b. consita and all others. Currently, C. b. consita is geographically isolated from the remaining subspecies in the Serranía del Perijá, and thus could have differentiated mainly in allopatry under divergent ecological pressures. However, C. b. bonapartei and C. helianthea remain in contact in the south of their distribution facing similar ecological pressures, and may have diverged in the face of gene flow. It is possible that in this context sexual selection drove divergence among species through the coloration differences. We discuss association between genetic variants and structural coloration differences in this system.