Data from: Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

The influence of geologic and Pleistocene glacial cycles might result in
morphological and genetic complex scenarios in the biota of the
Mesoamerican region. We tested whether berylline, blue-tailed and
steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and
Amazilia saucerottei, show evidence of historical or current introgression
as their plumage colour variation might suggest. We also analysed the role
of past and present climatic events in promoting genetic introgression and
species diversification. We collected mitochondrial DNA (mtDNA) sequence
data and microsatellite loci scores for populations throughout the range
of the three Amazilia species, as well as morphological and ecological
data. Haplotype network, Bayesian phylogenetic and divergence time
inference, historical demography, palaeodistribution modelling, and niche
divergence tests were used to reconstruct the evolutionary history of this
Amazilia species complex. An isolation-with-migration coalescent model and
Bayesian assignment analysis were assessed to determine historical
introgression and current genetic admixture. mtDNA haplotypes were
geographically unstructured, with haplotypes from disparate areas
interdispersed on a shallow tree and an unresolved haplotype network.
Assignment analysis of the nuclear genome (nuDNA) supported three genetic
groups with signs of genetic admixture, corresponding to: (1) A. beryllina
populations located west of the Isthmus of Tehuantepec; (2) A. cyanura
populations between the Isthmus of Tehuantepec and the Nicaraguan
Depression (Nuclear Central America); and (3) A. saucerottei populations
southeast of the Nicaraguan Depression. Gene flow and divergence time
estimates, and demographic and palaeodistribution patterns suggest an
evolutionary history of introgression mediated by Quaternary climatic
fluctuations. High levels of gene flow were indicated by mtDNA and
asymmetrical isolation-with-migration, whereas the microsatellite analyses
found evidence for three genetic clusters with distributions corresponding
to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression
and signs of admixture. Historical levels of migration between genetically
distinct groups estimated using microsatellites were higher than
contemporary levels of migration. These results support the scenario of
secondary contact and range contact during the glacial periods of the
Pleistocene and strongly imply that the high levels of structure currently
observed are a consequence of the limited dispersal of these hummingbirds
across the isthmus and depression barriers.