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

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.

研究目的：本研究旨在检测紫冠蜂鸟（violet-crowned hummingbird, Amazilia violiceps）与绿额蜂鸟（green-fronted hummingbird, Amazilia viridifrons）的种群是否存在遗传与环境分化，并探究过往地质与气候变迁对其物种分化的驱动作用。
研究区域：跨墨西哥火山带（Trans-Mexican Volcanic Belt）。
研究方法：我们对覆盖两个物种种群全分布范围的个体样本的线粒体DNA（mitochondrial DNA）与核DNA（nuclear DNA）进行测序，随后采用最大似然法（maximum-likelihood）与贝叶斯分析方法开展数据分析。通过物种树分析、贝叶斯物种界定、分化时间推断、历史种群动态分析、古分布区建模以及生态位分化检验，重构该Amazilia属蜂鸟的演化历史；同时评估隔离-迁移溯祖模型（isolation-with-migration coalescent model），以明确两物种间的遗传分化是否伴随基因交流发生。
研究结果：Amazilia violiceps与Amazilia viridifrons之间的遗传分化程度较浅，存在不完全谱系分选（incomplete lineage sorting）与基因渐渗（introgression）现象。物种界定结果支持三个独立演化支系：跨墨西哥火山带以北的A. violiceps种群；火山带以南的A. violiceps种群与A. viridifrons种群的混合类群；以及特万特佩克地峡（Isthmus of Tehuantepec）以东的A. villadai种群。基因流与分化时间估算结果，结合种群动态与古分布格局，支持隔离-迁移的物种分化模型，即该类群在更新世（Pleistocene）气候波动下发生栖息地变迁并伴随物种分化。
主要结论：该Amazilia属蜂鸟复合类群的物种形成过程，可由跨墨西哥火山带、特万特佩克地峡低地带来的隔离效应，与第四纪（Quaternary）气候变化驱动的栖息地变迁共同解释。