Data from: Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue-throated populations (Sierra Madre del Sur); two groups of amethyst-throated populations (Trans-Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39–0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue- and amethyst-throated populations does not correspond to the 2-MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species' suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest-interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.Ornelas_et al_IMa_AMETvsBLUE_mt+microsAmethyst-throated (Sierra Madre Oriental and Trans-Mexican Volcanic Belt) versus blue-throated (Sierra Madre del Sur) populations of Lampornis amethystinus for mitochondrial markers (ND2 and cytochrome b) and microsatellites.Ornelas_et al_IMa_SMOSvsTMVB_mt+microsAmethyst-throated populations from the Sierra Madre Oriental versus amethyst-throated populations along the Trans-Mexican Volcanic Belt of Lampornis amethystinus for mitochondrial markers (ND2 and cytochrome b) and microsatellites.Ornelas_et al_IMa_WESTvsEAST_mt+microsAmethyst-throated (incl. blue-throated) populations west of the Istmus of Tehuantepec versus amethyst-throated populations east of the Isthmus of Tehuantepec of Lampornis amethystinus for mitochondrial markers (ND2 and cytochrome b) and microsatellites.Ornelas_et al_DIYABC_Genotypes_mitoOrnelas_et al_DIYABC_Genotypes_mito text-formatted DIYABC data file containing microsatellite genotypes and mitochondrial ND2 and cytochrome b concatenated sequences of populations of Lampornis amethystinus.Ornelas_et al_DIYABC_Genotypes_mt.txtOrnelas_et al_DIYABC_models_headerOrnelas_et al_DIYABC_models_header text-formatted DIYABC reftableHeader file containing scenarios, priors and summary statistics used in the DIYABC analysis.Ornelas_et al_microsatellites_infoMicrosatellite sizing for 126 samples of Lampornis amethystinus hummingbirds genotyped at eigth autosomal microsatellite loci previously designed for Campylopterus curvipennis (Cacu16-1 and Cacu17-2; Molecular Ecology Resources Primer Development Consortium et al. 2010; GenBank accession nos. GQ294539–GQ294550) and Selasphorus platycercus (HUMB2, HUMB3, HUMB9, HUMB10, HUMBB11 and HUMB15Oyler-McCance et al. 2011; HQ316946–HQ316955). Microsatellite sizing for each loci consists in 3 digits (e.g. 216 for L32 Malinche, Tlax. at loci Cacu 16-1).Ornelas_et al_MAXENT_Lampornis_amethystinusLampornis amethystinus_MAXENT_File: coordinates longitude and latitude of Lampornis amethystinus