Data from: Lineage diversification of fringe-toed lizards (Phrynosomatidae: Uma notata complex) in the Colorado Desert: Delimiting species in the presence of gene flow

Multi-locus nuclear DNA data were used to delimit species of fringe-toed lizards of the Uma notata complex, which are specialized for living in wind-blown sand habitats in the deserts of southwestern North America, and to infer whether Quaternary glacial cycles or Tertiary geological events were important in shaping the historical biogeography of this group. We analyzed ten nuclear loci collected using Sanger sequencing and genome-wide sequence and single-nucleotide polymorphism (SNP) data collected using restriction-associated DNA (RAD) sequencing. A combination of species discovery methods (concatenated phylogenies, parametric and non-parametric clustering algorithms) and species validation approaches (coalescent-based species tree/isolation-with-migration models) were used to delimit species, infer phylogenetic relationships, and to estimate effective population sizes, migration rates, and speciation times. Uma notata, U. inornata, U. cowlesi, and an undescribed species from Mohawk Dunes, Arizona (U. sp.) were supported as distinct in the concatenated analyses and by clustering algorithms, and all operational taxonomic units were decisively supported as distinct species by ranking hierarchical nested speciation models with Bayes factors based on coalescent-based species tree methods. However, significant unidirectional gene flow (2NM >1) from U. cowlesi and U. notata into U. rufopunctata was detected under the isolation-with-migration model. Therefore, we conservatively delimit four species-level lineages within this complex (U. inornata, U. notata, U. cowlesi, and U. sp.), treating U. rufopunctata as a hybrid population (U. notata x cowlesi). Both concatenated and coalescent-based estimates of speciation times support the hypotheses that speciation within the complex occurred during the late Pleistocene, and that the geological evolution of the Colorado River delta during this period was an important process shaping the observed phylogeographic patterns.

本研究采用多位点核DNA数据，对北美西南部沙漠中特化于风积沙生境的缘趾蜥——乌玛趾蜥（Uma notata）复合群的物种进行界定，并旨在推断第四纪冰期旋回与第三纪地质事件何者对该类群的历史生物地理学格局塑造起到关键作用。本研究分析了通过桑格测序（Sanger sequencing）获得的10个核基因位点数据，以及通过限制性酶切位点相关DNA测序（RAD sequencing）获得的全基因组序列与单核苷酸多态性（SNP）数据。本研究结合物种发现方法（串联系统发育分析、参数与非参数聚类算法）与物种验证策略（基于溯祖的物种树/隔离-迁移模型（isolation-with-migration models）），完成物种界定、系统发育关系推断，并估算有效种群大小、迁移速率与物种形成时间。串联分析与聚类算法均支持乌玛趾蜥（U. notata）、无斑趾蜥（U. inornata）、考尔斯趾蜥（U. cowlesi）以及来自亚利桑那州莫霍克沙丘的未描述物种（U. sp.）为独立物种；基于溯祖物种树方法的贝叶斯因子（Bayes factors）分级嵌套物种模型排序分析，则确凿支持所有操作分类单元（operational taxonomic units）均为独立物种。但基于隔离-迁移模型的分析显示，存在从考尔斯趾蜥与乌玛趾蜥向红斑点趾蜥（U. rufopunctata）的显著单向基因流（2NM>1）。因此，本研究审慎地将该复合群划分为4个物种级支系（无斑趾蜥、乌玛趾蜥、考尔斯趾蜥与U. sp.），将红斑点趾蜥视为乌玛趾蜥与考尔斯趾蜥的杂交种群。串联分析与溯祖分析得到的物种形成时间估算结果均支持以下假说：该复合群的物种形成事件发生于更新世晚期（late Pleistocene），且同期科罗拉多河三角洲（Colorado River delta）的地质演化是塑造当前观测到的系统地理格局（phylogeographic patterns）的关键过程。