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.