Data from: A phylogeny and evolutionary natural history of Mesoamerican toads (Anura: Bufonidae: Incilius) based on morphology, life history, and molecular data

We combine mitochondrial and nuclear DNA sequence data with non-molecular (morphological and natural history) data to conduct phylogenetic analyses and generate an evolutionary hypothesis for the relationships among nearly every species of Mesoamerican bufonid in the genus Incilius. We collected a total of 5,898 aligned base-pairs (bp) of sequence data from mitochondrial (mtDNA: 12S–16S, cyt b, ND2–CO1, including tRNAsTRP–TYR and the origin of light strand replication; total 4,317 bp) and nuclear (CXCR4 and RAG1; total 1,581 bp) loci from 52 individuals representing 37 species. For the non-molecular data, we collected 44 characters from 29 species. We also include Crepidophryne, a genus that has not previously been included in molecular analyses. We present results of parsimony and Bayesian analyses for these data separately and combined. Relationships based on the non-molecular data were poorly supported and did not resolve a monophyletic Incilius (Rhinella marina was nested within). Our molecular data provide significant support to most of the relationships. Our combined analyses demonstrate that inclusion of a considerably smaller dataset (44 vs. 5,898 characters) of non-molecular characters can provide significant support where the molecular relationships were lacking support. Our combined results indicate that Crepidophryne is nested within Incilius; therefore, we place the former in the synonymy of the latter taxon. Our study provides the most comprehensive evolutionary framework for Mesoamerican bufonids (Incilius), which we use as a starting point to invoke discussion on the evolution of their unique natural history traits.本研究整合线粒体DNA（mitochondrial DNA, mtDNA）、核DNA（nuclear DNA）序列数据与非分子数据（形态学与自然历史数据），开展系统发育分析，构建几乎所有中美洲蟾蜍科真蟾属（Incilius）物种间的演化关系假说。本研究共收集了5898个经比对的碱基对（base-pair, bp）序列数据，其中线粒体DNA位点数据总长4317 bp，涵盖12S–16S、cyt b、ND2–CO1区域（包含tRN^A^TRP–TYR及轻链复制起点）；核DNA位点数据总长1581 bp，涵盖CXCR4与RAG1基因，上述序列数据来自代表37个物种的52个个体。非分子数据方面，我们从29个物种中收集了44个性状。本研究还纳入了此前从未被纳入分子分析的Crepidophryne属。我们分别及联合上述数据开展了简约法与贝叶斯分析，并展示了对应结果。基于非分子数据得到的系统发育关系支持度极低，且未能恢复单系的真蟾属（Incilius）——海蟾蜍（Rhinella marina）嵌套于该属内。本研究的分子数据为多数系统发育关系提供了显著支持。联合数据分析表明，尽管非分子性状数据集的规模远小于分子数据（44对5898个性状），却能为分子分析中缺乏支持的分支关系提供显著支持。联合分析结果显示，Crepidophryne属嵌套于真蟾属（Incilius）内部；因此，我们将前者归为后者的同物异名。本研究为中美洲蟾蜍科真蟾属（Incilius）物种提供了迄今最为全面的演化框架，并以此为起点，探讨其独特自然历史性状的演化历程。