DOI: 10.5061/dryad.89kq4
title: Data from: At the passing gate: past introgression in the process of species formation between Amazilia violiceps and A. viridifrons hummingbirds along the Mexican Transition Zone

description: Aim: We tested whether populations of violet-crowned and green-fronted
 hummingbirds, Amazilia violiceps and Amazilia viridifrons, are genetically
 and environmentally differentiated, and examined the role of past
 geological and climatic changes in driving their diversification.
 Location: Trans-Mexican Volcanic Belt. Methods: Mitochondrial and nuclear
 DNA of individuals collected throughout the species' ranges were
 sequenced and then analysed using maximum-likelihood and Bayesian
 approaches. Species tree analysis, Bayesian species delimitation,
 divergence time inference, historical demography, palaeodistribution
 modelling, and niche divergence tests were used to reconstruct the
 evolutionary history of the Amazilia species, and the
 isolation-with-migration coalescent model was assessed to determine
 whether genetic divergence between Amazilia species occurred in the
 presence of gene flow. Results: Genetic divergence between A. violiceps
 and A. viridifrons was shallow, with incomplete lineage sorting and
 introgression. Species delimitation supported three independent lineages:
 A. violiceps populations located north of the Trans-Mexican Volcanic Belt;
 a mixture of A. violiceps south of the volcanic belt and A. viridifrons
 populations; and A. villadai populations east of the Isthmus of
 Tehuantepec. Gene flow and divergence time estimates, and demographic and
 palaeodistribution patterns support the model of species diversification
 by isolation with migration and habitat shifting in response to
 Pleistocene climatic fluctuations. Main conclusions: The process of
 speciation in the Amazilia species complex may be explained by the
 combined effects of isolation resulting from the Trans-Mexican Volcanic
 Belt and the lowlands at the Isthmus of Tehuantepec and habitat shifting
 in response to Quaternary climatic changes.
description: ND2
 SequencesND2_File: Amazilia
 viridifrons and Amazilia violiceps nicotinamide adenine dinucleotide
 dehydrogenase (NADH) subunit 2 mitochondial sequences.ND2.fasND5 SequencesND5_File: Amazilia viridifrons and Amazilia violiceps nicotinamide adenine dinucleotide dehydrogenase (NADH) subunit 5 mitochondial sequences.ND5.fasARCO SequencesARCO_File: Amazilia viridifrons and Amazilia violiceps hypervariable domain I of the noncoding control region mitochondial sequences.ARCO.fasATPASE SequencesATPase_File: Amazilia viridifrons and Amazilia violiceps ATPase 6 and ATPase 8 mitochondial sequences.ATPASE.fas20454 Sequences20454_File: Amazilia viridifrons and Amazilia violiceps 20454 locus nuclear sequences.20454.fasRodríguez-Gómez&Ornelas_IMa_VIOLICvsVIRIDI_combRodríguez-Gómez&Ornelas_IMa_VIOLICvsVIRIDI_comb: VIOLIC populations from North of the TMVB versus VIRIDI populations from South of the TMVB of Amazilia violiceps and Amazilia viridifrons, combining mitochondrial and nuclear markers.Amazilia violiceps_MAXENT_FileAmazilia violiceps_MAXENT_File: coordinates longitude and latitude of Amazilia violicepsAmazilia viridifrons_MAXENT_FileAmazilia viridifrons_MAXENT_File: coordinates longitude and latitude of Amazilia viridifrons.