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Background The Mesoamerican dominion is a biogeographic area of great interest due to its complex topography and distinctive climatic history. This area has a large diversity of habitats, including tropical deciduous forests, which house a large number of endemic species. Here, we assess phylogeographic pattern, genetic and morphometric variation in the Cinnamon Hummingbird complex Amazilia rutila, which prefers habitats in this region. This resident species is distributed along the Pacific coast from Sinaloa—including the Tres Marías Islands in Mexico to Costa Rica, and from the coastal plain of the Yucatán Peninsula of Mexico south to Belize. Methods We obtained genetic data from 85 samples of A. rutila, using 4 different molecular markers (mtDNA: ND2, COI; nDNA: ODC, MUSK) on which we performed analyses of population structure (median-joining network, STRUCTURE, FST, AMOVA), Bayesian and Maximum Likelihood phylogenetic analyses, and divergence time estimates. In order to evaluate the historic suitability of environmental conditions, we constructed projection models using past scenarios (Pleistocene periods), and conducted Bayesian Skyline Plots (BSP) to visualize changes in population sizes over time. To analyze morphometric variation, we took measurements of 5 morphological traits from 210 study skins. We tested for differences between sexes, differences among geographic groups (defined based on genetic results), and used PCA to examine the variation in multivariate space. Results Using mtDNA, we recovered four main geographic groups: the Pacific coast, the Tres Marías Islands, the Chiapas region, and the Yucatán Peninsula together with Central America. These same groups were recovered by the phylogenetic results based on the multilocus dataset. Demography based on BSP results showed constant population size over time throughout the A. rutila complex and within each geographic group. Ecological niche model projections onto past scenarios revealed no drastic changes in suitable conditions, but revealed some possible refuges. Morphometric results showed minor sexual dimorphism in this species and statistically significant differences between geographic groups. The Tres Marías Islands population was the most differentiated, having larger body size than the remaining groups. Conclusions The best supported evolutionary hypothesis of diversification within this group corresponds to geographic isolation (limited gene flow), differences in current environmental conditions, and historical habitat fragmentation promoted by past events (Pleistocene refugia). Four well-defined clades comprise the A. rutila complex, and we assess the importance of a taxonomic reevaluation. Our data suggest that both of A. r. graysoni (Tres Marías Islands) and A. r. rutila (Pacific coast) should be considered full species. The other two strongly supported clades are: (a) the Chiapas group (southern Mexico), and (b) the populations from Yucatán Peninsula and Central America. These clades belong to the corallirostris taxon, which needs to be split and properly named.

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Many avian species from the temperate zone show low levels of genetic diversity when compared with species from the tropics, although there are some interesting exceptions, and species whose ranges occur across the temperate-tropical boundary could have characteristics of either or both zones. The distribution of the Streak-backed Oriole (Icterus pustulatus) extends from northwestern Sonora in Mexico south along the Pacific coast to Costa Rica. In addition, there is a population on the Tres Marías Islands. Northern populations are migratory and dichromatic (sexes different), whereas southern populations are nonmigratory and monochromatic (sexes alike). We sequenced mtDNA (control region domain I) from 102 individuals across the range of this species. Maximum parsimony and maximum likelihood analyses did not support the existence of multiple species within Icterus pustulatus based on mtDNA. However, populations from the Tres Marías Islands seem to have been isolated long enough to have fixed differences from populations on the mainland. The species complex shows an uncommon phylogeographic pattern, with shallow haplotype trees and weak geographic structure, suggesting that it has undergone recent population expansion. We recommend that the insular populations be considered a separate species, Icterus graysonii, given the fixed differences from mainland birds in multiple characteristics, including mtDNA and plumage patterns.