Data from: Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing

Sequence capture and restriction site associated DNA sequencing (RADseq) are popular methods for obtaining large numbers of loci for phylogenetic analysis. These methods are typically used to collect data at different evolutionary timescales; sequence capture is primarily used for obtaining conserved loci, whereas RADseq is designed for discovering single nucleotide polymorphisms (SNPs) suitable for population genetic or phylogeographic analyses. Phylogenetic questions that span both “recent” and “deep” timescales could benefit from either type of data, but studies that directly compare the two approaches are lacking. We compared phylogenies estimated from sequence capture and double digest RADseq (ddRADseq) data for North American phrynosomatid lizards, a species-rich and diverse group containing nine genera that began diversifying approximately 55 million years ago. Sequence capture resulted in 584 loci that provided a consistent and strong phylogeny using concatenation and species tree inference. However, the phylogeny estimated from the ddRADseq data was sensitive to the bioinformatics steps used for determining homology, detecting paralogs, and filtering missing data. The topological conflicts among the SNP trees were not restricted to any particular timescale, but instead were associated with short internal branches. Species tree analysis of the largest SNP assembly, which also included the most missing data, supported a topology that matched the sequence capture tree. This preferred phylogeny provides strong support for the paraphyly of the earless lizard genera Holbrookia and Cophosaurus, suggesting that the earless morphology either evolved twice, or that it evolved once and was subsequently lost in Callisaurus.

序列捕获（Sequence capture）与限制性酶切位点相关DNA测序（restriction site associated DNA sequencing, RADseq）是当前获取大量基因座用于系统发育分析的主流实验方法。这类方法通常被应用于不同进化时间尺度的数据采集：序列捕获主要用于获取保守基因座，而RADseq则旨在发掘适用于群体遗传学或系统地理学分析的单核苷酸多态性（single nucleotide polymorphisms, SNPs）。跨越“近期”与“深层”进化时间尺度的系统发育研究问题，可从这两类数据中获益，但目前尚缺乏直接对比两种实验策略的相关研究。本研究针对北美角蜥科蜥蜴（phrynosomatid lizards）展开对比分析，该类群物种丰富、多样性极高，包含9个属，其分化起始于约5500万年前。序列捕获实验共得到584个基因座，通过串联拼接法与物种树推断均可获得一致且支持度优异的系统发育树。然而，基于双酶切RADseq（double digest RADseq, ddRADseq）数据构建的系统发育树，对用于判定同源性、检测旁系同源基因以及过滤缺失数据的生物信息学处理步骤极为敏感。SNP树间存在的拓扑冲突并非局限于某一特定时间尺度，而是与较短的内部分支密切相关。对包含最多缺失数据的最大规模SNP数据集进行物种树分析后，其得到的拓扑结构与序列捕获法获得的系统发育树完全一致。这一最优系统发育树为无耳蜥蜴属Holbrookia与Cophosaurus的并系群属性提供了强力支持，表明无耳形态要么独立演化了两次，要么仅演化一次后在Callisaurus属中发生了次生丢失。