Data from: Delimiting Species Using DNA and Morphological Variation and Discordant Species Limits in Spiny Lizards (Sceloporus)

Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies based on morphology. However, few studies have critically compared species limits based on morphological and DNA data, and the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches for species delimitation (tree-based with DNA data and tree-based and character-based with morphological data) and propose explicit protocols for each. We then compare species limits inferred from these approaches, using morphological and mtDNA data for the Yarrow's spiny lizard (Sceloporus jarrovii), a traditionally polytypic species from the southwestern United States and Mexico. All three approaches support division of S. jarrovii into five species, but only two species are the same among the three approaches. We find the greatest support for the five species that are delimited based on mtDNA data, and we argue that mtDNA data may have important (and previously unappreciated) advantages for species delimitation. Because different data and approaches can disagree so extensively, our results demonstrate that the methodology of species delimitation is a critical issue in systematics.基于DNA序列数据的单倍型系统发育树（haplotype phylogenies）正愈发广泛地被用于验证基于形态学特征建立的传统物种级分类系统。然而，鲜有研究对基于形态学与DNA数据的物种界限开展严谨比对，且针对两类数据分别划定物种的方法也极少得到清晰阐释。本研究综述了三种物种界定策略：分别为基于DNA数据的树构分析法，以及基于形态学数据的树构分析法与特征分析法，并为每种策略提出了明确的操作规范。随后，我们以美国西南部与墨西哥境内的传统多型物种——亚罗刺蜥（Sceloporus jarrovii）的形态学数据与线粒体DNA（mtDNA）数据为案例，对比了上述策略推导的物种界限。三种策略均支持将S. jarrovii划分为五个物种，但三种策略间仅有两个物种的界定结果完全一致。我们发现，基于线粒体DNA数据界定的五个物种得到了最高的支持度，且我们认为线粒体DNA数据在物种界定中可能具备重要且此前未被重视的优势。由于不同的数据类型与分析策略可能存在如此显著的分歧，我们的研究结果表明，物种界定的方法论是系统分类学中的关键议题。