Data from: Diversification in wild populations of the model organism Anolis carolinensis: a genome-wide phylogeographic investigation

The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito-nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long-term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.

绿安乐蜥（Anolis carolinensis）是广泛分布于美国东南部的蜥蜴物种，同时也是开展繁殖行为、生理学、神经生物学与基因组学研究的模式生物（model organism）。此前针对A. carolinensis的系统地理学研究多采用线粒体DNA与少量核基因座进行分析，得到的地理演化支间的演化关系既相互矛盾，又缺乏足够的统计支持；这类不一致性导致在结合采样地点的形态学、生理学或繁殖生物学研究中，无法可靠地援引A. carolinensis的演化历史，因此亟需投入更多研究以厘清其自然种群间的演化关系。本研究通过锚定杂交富集（anchored hybrid enrichment）技术，获取了A. carolinensis全基因组范围内的数百个遗传标记，并鉴定出五个支持度极高的系统地理学类群。通过多种分析方法，我们构建了完全解析的物种树，探究了所有基因树中各谱系的相对支持度，并将本研究结果与既往研究对比后，发现了线粒体-核基因演化不协调（mito-nuclear discordance）现象。本研究仅在一个演化支中发现了固定遗传差异——即仅分布于大沼泽地区的佛罗里达南部类群——而多数多态性位点在不同谱系间共享。佛罗里达南部类群大概率在上新世时期与其他种群发生分化，其余类群的物种分化事件均发生于更新世。多项证据——包括系统发育关系、遗传多样性的纬度梯度分布特征，以及南部系统地理学类群相对更稳定的长期种群规模——均表明，A. carolinensis的物种分化是从佛罗里达南部向北扩张完成的。