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.

The integration of genetic, morphological, behavioral, and ecological information in the analysis of species boundaries has increased, allowing integrative systematics that better reflect the evolutionary history of biological groups. In this context, the goal of this study was to recognize independent evolutionary lineages within Euphonia affinis at the genetic, morphological, and ecological levels. Three subspecies have been described: E. affinis godmani, distributed in the Pacific slope from southern Sonora to Guerrero; E. affinis affinis, from Oaxaca, Chiapas and the Yucatan Peninsula to Costa Rica; and E. affinis olmecorum from Tamaulipas and San Luis Potosi east to northern Chiapas (not recognized by some authors). A multilocus analysis was performed using mitochondrial and nuclear genes. These analyses suggest two genetic lineages: E. godmani and E. affinis, which diverged between 1.34 and 4.3 My, a period in which the ice ages and global cooling fragmented the tropical forests throughout the Neotropics. To analyze morphometric variations, six morphometric measurements were taken, and the Wilcoxon Test was applied to look for sexual dimorphism and differences between the lineages. Behavioral information was included, by performing vocalization analysis which showed significant differences in the temporal characteristics of calls. Finally, Ecological Niche Models were estimated with MaxEnt, and then compared using the method of Broennimann. These analyses showed that the lineage distributed in western Mexico (E. godmani) has a more restricted niche than the eastern lineage (E. affinis) and thus we rejected the hypotheses of niche equivalence and similarity. Based on the combined evidence from genetic, morphological, behavioral, and ecological data, it is concluded that E. affinis (with E. olmecorum as its synonym) and E. godmani represent two independent evolutionary lineages.

Animals derive their coloration from a variety of pigments as well as non-pigmentary structural features. One of the most widespread types of pigments are carotenoids, which are used by all invertebrate taxa and most vertebrate orders to generate red, pink, orange and yellow coloration. Despite their widespread use by diverse animal groups, animals obligately obtain carotenoid pigments from diet. Carotenoid-based coloration is therefore modulated by evolutionary and ecological processes that affect the acquisition and deposition of these pigments into tegumentary structures. The Flame-colored Tanager (Piranga bidentata) is a highland songbird in the cardinal family (Cardinalidae) that is distributed from Mexican sierras through Central America up to western Panama. While female plumage throughout its entire range is predominantly yellow, males exhibit a noticeable split in ventral plumage color, which is bright orange on the West slope and the Tres Marias Islands and blood red in Eastern Mexico and Central America. We used Multiple Regression on Matrices (MRM) to evaluate the relative contributions of geographic distance, climate and genetic distance on color divergence and body differences between geographically disjunct populations. We found that differentiation in carotenoid plumage coloration was mainly explained by rainfall differences between disjunct populations, whereas body size differences was best explained by variation in the annual mean temperature and temperature of coldest quarter. These results indicate that climate is a strong driver of phenotypic divergence in Piranga bidentata.