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）正日益被用于检验传统上基于形态学构建的物种级分类系统。然而，鲜有研究对基于形态学与DNA数据的物种界定界限进行严谨对比，且针对两类数据所采用的物种界定（species delimitation）方法也极少得到清晰阐释。本文针对三类物种界定方法——基于DNA数据的树构法、以及基于形态学数据的树构法与性状界定法——进行综述，并为每种方法提出明确的操作规范。随后，我们以分布于美国西南部与墨西哥的传统多型种亚罗棘蜥（Sceloporus jarrovii）的形态学与线粒体DNA（mtDNA）数据为研究实例，对比不同方法推导得到的物种界定结果。三类方法均支持将亚罗棘蜥划分为5个物种，但三类方法中仅有2个物种的界定结果一致。我们针对基于线粒体DNA数据界定的5个物种得到了最强的支持证据，并认为线粒体DNA数据在物种界定中可能具备重要且此前未被认知的优势。由于不同数据类型与研究方法可能存在显著分歧，本研究结果表明，物种界定的方法论是系统分类学（systematics）领域的关键议题。