Data from: A genomic evaluation of taxonomic trends through time in coast horned lizards (genus Phrynosoma)

Determining the boundaries between species and deciding when to describe new species are challenging practices that are particularly difficult in groups with high levels of geographic variation. The coast horned lizards (Phrynosoma blainvillii, P. cerroense, and P. coronatum) have an extensive geographic distribution spanning many distinctive ecological regions ranging from northern California to the Cape Region of Baja California, Mexico, and populations differ substantially with respect to external morphology across much of this range. The number of taxa recognized in the group has been re-evaluated by herpetologists over 20 times during the last 180 years, and typically without the aid of explicit species delimitation methods, resulting in a turbulent taxonomy containing anywhere from one to seven taxa. In this study, we evaluate taxonomic trends through time by ranking 15 of these species delimitation models (SDMs) using coalescent analyses of nuclear loci and SNPs in a Bayesian model comparison framework. SDMs containing more species were generally favored by Bayesian model selection; however, several three-species models outperformed some four and five species SDMs, and the top-ranked model, which contained five species, outperformed all SDMs containing six species. Model performance peaked in the 1950s based on marginal likelihoods estimated from nuclear loci and SNPs. Not surprisingly, SDMs based on genetic data outperformed morphological taxonomies when using genetic data alone to evaluate models. The de novo estimation of population structure favors a three-population model that matches the currently recognized integrative taxonomy containing three species. We discuss why Bayesian model selection might favor models containing more species, and why recognizing more than three species might be warranted.

界定物种边界与判定新物种的描述时机本就是极具挑战性的科研工作，在地理变异程度较高的类群中，这一难度尤甚。海岸角蜥（Phrynosoma blainvillii、P. cerroense及P. coronatum）的地理分布范围极广，涵盖从美国加利福尼亚州北部至墨西哥下加利福尼亚半岛开普地区的诸多特色生态区域；在该分布范围的绝大多数区域内，不同种群的外部形态均存在显著差异。在过去180年间，两栖爬行动物学家已对该类群的公认分类单元数量进行了20余次重新评估，且此类评估通常未借助明确的物种界定方法，最终形成了包含1至7个分类单元不等的混乱分类体系。本研究采用贝叶斯模型比较框架，借助核基因座与单核苷酸多态性（single nucleotide polymorphism，SNPs）的溯祖分析，对该类群的15种物种界定模型（species delimitation models，SDMs）进行排序，以此剖析分类学趋势随时间的演变规律。贝叶斯模型选择通常更青睐包含更多物种的SDMs；不过，部分包含3个物种的模型性能优于部分4物种及5物种的SDMs，而排名最高的5物种模型性能则优于所有包含6个物种的SDMs。基于核基因座与SNPs估算的边际似然值可知，模型性能在20世纪50年代达到峰值。不出所料，若仅使用遗传数据对模型进行评估，基于遗传数据构建的SDMs性能优于形态分类学框架下的模型。种群结构的从头估算结果支持3种群模型，该模型与当前公认的包含3个物种的整合分类学体系相符。本研究还探讨了贝叶斯模型选择更青睐包含更多物种类群的原因，以及为何有必要承认3个以上的物种分类单元。