DOI: 10.5061/dryad.2c088
title: Data from: Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective

description: 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.
description: Jiménez&Ornelas_IMa_BERYvsHYB_mtBERY (Amazilia beryllina) populations west of the Isthmus of Tehuantepec versus HYBRID populations east of the IT (Amazilia beryllina and Amazilia cyanura), combining mitochondrial markers (ND2 and ATPase 6-8).Jiménez&Ornelas_IMa_SAUCvsHIB_mtSAUC (Amazilia saucerottei) populations south of the Nicaraguan Depression versus HYBRID populations between the Nicaraguan Depression and the Isthmus of Tehuantepec (Amazilia saucerottei and Amazilia cyanura), combining mitochondrial markers (ND2 and ATPase 6-8).Jiménez&Ornelas_IMa_BERYvsSAUC_mtBERY (Amazilia beryllina) populations west of the Isthmus of Tehuantepec versus SAUC (Amazilia saucerottei) populations south of the Nicaraguan Depression, combining mitochondrial markers (ND2 and ATPase 6-8).Jiménez&Ornelas_Microsatellites_infoMicrosatellite sizing for 145 hummingbirds samples genotyped at twelve autosomal microsatellite loci previously designed for Amazilia cyanocephala (A1-3-5, A1-4-1, A2-1-2 and A2-5-3; Molecular Ecology Resources Primer Development Consortium et al., 2013), Campylopterus curvipennis (Cacu1-10, Cacu4-8, Cacu13-1, Cacu13-7; Molecular Ecology Resources Primer Development Consortium et al., 2010) and Selasphorus platycercus (HumB1, HumB2, HumB3, HumB9; Oyler-McCance et al., 2011). Microsatellite sizing for each loci consists in 3 digits (e.g. 222 for 82442 at loci A1-3-5). Numbers of POP correspond to sampling localities. Refer Table S4 for sampling locality information. ID corresponds to individual identifiers of the samples worked in this study. Genbank accession numbers for mitochondrial information is available for each sample; samples with no Genbank accession number were not sequenced for mitochondria. Missing data code= 0Jiménez&Ornelas_Morphology_infoPlumage color variation of 145 adult hummingbirds assessed using a qualitative index created by summing up the scores of 10 morphological characters (rufous patch on secondary feathers, rufous patch on primary feathers, undertail feathers, belly color, throat and chest color, wings, upper tail feathers, back color, tail color, rachis color on tail feathers). Sex: male; female. Collection number corresponds to individual identifiers of the samples worked in this study. Sex: male; female. Collection number corresponds to individual identifiers of the samples worked in this study.