Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington.
Mol Ecol. 2018 Jul;27(13):2884-2895. doi: 10.1111/mec.14715. Epub 2018 May 28.
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, Phrynosoma 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 reevaluated 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. Species delimitation models containing more species were generally favoured 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 favours a three-population model that matches the currently recognized integrative taxonomy containing three species. We discuss why Bayesian model selection might favour models containing more species, and why recognizing more than three species might be warranted.
确定物种的界限并决定何时描述新物种是具有挑战性的实践，在具有高水平地理变异的群体中尤其困难。海岸角响尾蜥（Phrynosoma blainvillii、Phrynosoma cerroense 和 P. coronatum）的地理分布范围很广，从加利福尼亚北部到墨西哥下加利福尼亚半岛的海角地区都有分布，而且在很大程度上，不同生态区域的种群在外貌上存在显著差异。在过去的 180 年里，两栖动物学家已经对该物种群进行了 20 多次重新评估，而且通常没有明确的物种划分方法，导致其分类学非常混乱，包含一到七个分类单元。在这项研究中，我们通过在贝叶斯模型比较框架中使用核基因座和 SNP 的合并分析，对这 15 种物种划分模型（SDM）进行排名，从而评估随时间推移的分类趋势。包含更多物种的物种划分模型通常受到贝叶斯模型选择的青睐；然而，一些三物种模型的表现优于一些四物种和五物种 SDM，排名最高的模型，包含五个物种，表现优于所有包含六个物种的 SDM。基于核基因座和 SNP 估计的边缘似然率，模型性能在 20 世纪 50 年代达到顶峰。毫不奇怪，当仅使用遗传数据评估模型时，基于遗传数据的 SDM 优于形态分类学。种群结构的从头估计支持三种群模型，该模型与目前公认的包含三个物种的综合分类学相匹配。我们讨论了为什么贝叶斯模型选择可能偏向于包含更多物种的模型，以及为什么识别超过三个物种可能是合理的。
