Data from: Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae) endemic to the Brazilian Atlantic Forest

Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing “Terrarana” frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree) uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP), and Genealogical Sorting Index (GSI), providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

形态相似性结合受限的分布范围与低下的扩散能力，使得帕克蛙属（Euparkerella）“Terrarana”类群的直接发育蛙类成为研究物种分化过程的优良模型。本研究利用1个线粒体基因与4个核基因的DNA序列数据，结合传统贝叶斯系统发育重建方法与近年兴起的物种树溯祖推断方法，对该属内的系统发育关系进行了推断。我们还采用贝叶斯聚类分析，以及专门用于物种界定的贝叶斯溯祖方法开展相关分析。对4个已知帕克蛙属物种的39个个体开展的分析显示，该属存在高水平的遗传多样性，尤其是在此前基于形态定义的柯氏帕克蛙（E. cochranae）与巴西帕克蛙（E. brasiliensis）两个类群中。在这两个类群内，5个独立基因座的基因树以及联合数据构建的系统发育树（串联数据集与物种树）均揭示出6个深度分化、地理分布格局清晰的进化单元，这些单元的分化时间大致介于中新世与更新世之间。贝叶斯聚类分析同样识别出这6个进化单元，且贝叶斯溯祖物种界定法（BPP）与谱系分选指数（GSI）也为其提供了支持，这为帕克蛙属当前多样性水平被低估提供了强有力的证据。本次研究揭示的隐存多样性，为在空间异质性与/或受人类活动严重干扰的巴西大西洋森林生物多样性热点区域的生境破碎化背景下，探究微特有现象的起源与维持机制提供了新的研究契机。