DOI: 10.5061/dryad.88589
title: Data from: Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

description: 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.
description: 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.