Data from: Genetic structuring and secondary contact in the white-chested Amazilia hummingbird species complex

Pleistocene climate cycles have been recognized to be a major driver of postglacial northward range expansion of North American bird populations. During glacial maxima, allopatric lineages that were reproductively isolated might have come into secondary contact with one another during expansion periods and the genetic signatures of past hybridization as a result of secondary contact events should produce detectable hybrid zones. The white-chested hummingbirds, Amazilia violiceps and A. viridifrons, constitute a species complex showing phenotypic similarity across its range. One exception is the subspecies found in the Central Depression of Chiapas (A. viridifrons villadai), which shares some plumage traits with the endemic but allopatric green-fronted populations in Oaxaca. Phylogenetic relationships, taxonomy and species limits among violiceps, viridifrons and villadai have been controversial for decades. We assessed genetic structure of populations and introgression in this species complex by analysing 95 individuals at ten nuclear microsatellites and morphology. Bayesian analysis yielded four clusters. However, only two clusters generally match previously described mtDNA haplogroups, one parental taxon in the south (villadai) and a cluster with two admixed taxa (viridifrons and violiceps) that cannot be attributed to any pure parental population. High genetic admixture was recorded in the violiceps/viridifrons range, probably as a consequence of a postglacial northern expansion of violiceps. Signs of admixture and gene flow between violiceps/viridifrons and villadai were low. Historical and contemporary migration rates and Approximate Bayesian computations support a scenario of divergence with gene flow: a Pleistocene basal split separating A. violiceps and the other two clades are derived from a second split (villadai and viridifrons) or from a merger of violiceps and villadai into viridifrons due to gene flow.

更新世（Pleistocene）气候周期被认为是驱动北美鸟类种群冰期后向北分布扩张的核心驱动因素。在冰期极盛期，经历生殖隔离的异域支系（allopatric lineage）在种群扩张阶段可能发生二次接触（secondary contact），由这类二次接触事件引发的古杂交所遗留的遗传印记，应当能够形成可被检测到的杂交带（hybrid zone）。白胸蜂鸟类群包含紫顶蜂鸟（Amazilia violiceps）与绿额蜂鸟（Amazilia viridifrons），二者构成一个在整个分布区内表现出高度表型相似性的物种复合群（species complex），唯一的例外是分布于墨西哥恰帕斯中央洼地的亚种维拉代绿额蜂鸟（A. viridifrons villadai），该类群与瓦哈卡州的特有异域绿额种群共享部分羽色特征。数十年来，关于violiceps、viridifrons与villadai三者间的系统发育关系（phylogenetic relationships）、分类学（taxonomy）及物种界定（species limits）始终存在争议。本研究通过对95个个体的10个核微卫星（nuclear microsatellite）位点进行分析，并结合形态学数据，评估了该物种复合群的种群遗传结构（genetic structure）与基因渐渗（introgression）情况。贝叶斯分析（Bayesian analysis）共识别出四个聚类簇，但其中仅有两个聚类簇大致匹配此前已报道的线粒体DNA单倍群（mtDNA haplogroup）：一类为分布于南部的亲本类群villadai，另一类则包含两个混合类群viridifrons与violiceps，二者均无法归属于任何纯合亲本种群。在violiceps与viridifrons的分布区内检测到了高水平的遗传混合，这一现象大概率源于violiceps冰期后的向北种群扩张。而violiceps/viridifrons类群与villadai之间的遗传混合与基因流（gene flow）信号则相对较弱。历史与当代迁移率估算结果以及近似贝叶斯计算（Approximate Bayesian computation）均支持"伴基因流的分化（divergence with gene flow）"这一演化场景：一次更新世的基部分化事件将紫顶蜂鸟（A. violiceps）与另外两个演化支（clade）分隔开来，而后者可进一步溯源至第二次分化事件（villadai与viridifrons），或是由于基因流作用使得violiceps与villadai融合为viridifrons。