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风积沙生境特化的乌玛趾缘蜥（Uma notata）复合种开展物种界定，并探究第四纪冰期旋回与第三纪地质事件是否为塑造该类群历史生物地理格局的关键驱动因素。本研究分析了通过桑格测序（Sanger sequencing）获取的10个核基因座数据，以及通过限制性酶切关联DNA（restriction-associated DNA, RAD）测序获得的全基因组序列与单核苷酸多态性（single-nucleotide polymorphism, 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）与物种验证手段（基于溯祖理论的物种树（coalescent-based species tree）/隔离与迁移模型（isolation-with-migration models）），实现物种界定、系统发育关系推断，以及有效种群大小、基因流速率与物种分化时间的估算。串联分析与聚类算法结果均支持乌玛趾缘蜥、无斑趾缘蜥（U. inornata）、考尔斯趾缘蜥（U. cowlesi）以及采自亚利桑那州莫霍克沙丘的未描述物种（U. sp.）为独立类群；基于溯祖物种树方法的贝叶斯因子（Bayes factors）层级嵌套物种分化模型排序分析，则确凿支持所有操作分类单元（operational taxonomic unit, OTU）均为独立物种。然而，基于隔离与迁移模型分析，本研究检测到从考尔斯趾缘蜥与乌玛趾缘蜥向红斑点趾缘蜥（U. rufopunctata）存在显著的单向基因流（2NM >1）。因此，本研究审慎地将该复合种划分为4个物种级支系（无斑趾缘蜥、乌玛趾缘蜥、考尔斯趾缘蜥与U. sp.），将红斑点趾缘蜥视为乌玛趾缘蜥与考尔斯趾缘蜥的杂交种群。串联分析与溯祖方法得到的物种分化时间估算结果均支持以下假说：该复合种的物种分化发生于晚更新世，且同期科罗拉多河三角洲的地质演化是塑造当前观测到的系统地理格局的关键过程。