Complete mitochondrial genomes do not distinguish phenotypically distinct lineages of Andean Coeligena hummingbirds

Lack of divergence in mitochondrial DNA between species with clear phenotypic differences may be the result of low resolution of markers, incomplete lineage sorting, introgression, or the interplay of various evolutionary mechanisms acting on different traits and genomic regions through time. Previous work revealed that the Andean hummingbirds Coeligena bonapartei and C. helianthea lack genetic divergence in the mitochondrial ND2 gene, which shows variation discordant with coloration phenotype but consistent with geography. We sequenced and analyzed complete mitochondrial genomes for C. b. bonapartei, C. b. consita, C. h. helianthea and C. h. tamai to assess whether patterns revealed by ND2 analyses hold when considering the entire mitogenome, and to shed light into the evolutionary history of these hummingbirds. We found very low genetic differentiation in mitogenomes among the four lineages of Coeligena, confirming patterns based on ND2 data. Estimates of genetic differentiation, phylogenies and haplotype network analyses of complete mitogenomes did not separate phenotypically distinct taxa, but were consistent with a previously described pattern of northern vs. southern divergence along the Cordillera Oriental of Colombia. Mitogenomes of C. b. bonapartei and C. h. helianthea are indistinguishable, suggesting incomplete lineage sorting or strong introgression. Mitogenomes of C. b. consita and C. h. tamai are slightly differentiated, but they are more similar to each other than either is to that of its respective nominate subspecies, a result also suggestive of mtDNA introgression despite distinct phenotypic differences. Our results indicate that various evolutionary mechanisms playing out over a complex biogeographic scenario in the Colombian Andes drove divergence in phenotypes and mitochondrial genomes of Coeligena hummingbirds, and lead to alternative hypotheses to be tested with whole-genome analyses.