Data from: A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

The extant amphibians are one of the most diverse radiations of terrestrial vertebrates (>6800 species). Despite much recent focus on their conservation, diversification, and systematics, no previous phylogeny for the group has contained more than 522 species. However, numerous studies with limited taxon sampling have generated large amounts of partially overlapping sequence data for many species. Here, we combine these data and produce a novel estimate of extant amphibian phylogeny, containing 2871 species (40% of the known extant species) from 432 genera (85% of the 500 currently recognized extant genera). Each sampled species contains up to 12,712 bp from 12 genes (three mitochondrial, nine nuclear), with an average of 2563 bp per species. This data set provides strong support for many groups recognized in previous studies, but it also suggests non-monophyly for several currently recognized families, particularly in hyloid frogs (e.g., Ceratophryidae, Cycloramphidae, Leptodactylidae, Strabomantidae). To correct these and other problems, we provide a revised classification of extant amphibians for taxa traditionally delimited at the family and subfamily levels. This new taxonomy includes several families not recognized in current classifications (e.g., Alsodidae, Batrachylidae, Rhinodermatidae, Odontophrynidae, Telmatobiidae), but which are strongly supported and important for avoiding non-monophyly of current families. Finally, this study provides further evidence that the supermatrix approach provides an effective strategy for inferring large-scale phylogenies using the combined results of previous studies, despite many taxa having extensive missing data.

现存两栖类（extant amphibians）是陆生脊椎动物中多样性最为丰富的类群之一，已知物种数逾6800种。尽管近年来学界对其保护生物学、物种多样化进程与分类系统的研究持续受到关注，但此前针对该类群的系统发育（phylogeny）研究中，涵盖的物种数量均未超过522种。不过，诸多分类采样范围有限的研究已为众多物种积累了大量部分重叠的序列数据。本研究整合上述数据，构建了全新的现存两栖类系统发育估计框架，共包含2871个物种（占已知现存两栖类物种总数的40%），涉及432个属（占当前已确认的500个现存属的85%）。每个采样物种均可获得来自12个基因（3个线粒体基因、9个核基因）的最长12712 bp序列，单物种平均序列长度为2563 bp。本数据集为既往研究中已确认的诸多类群提供了强有力的支持，但同时也揭示多个当前被认可的科存在非单系（non-monophyly）现象，其中尤以蛙超科类蛙（hyloid frogs）为甚，例如角花蟾科（Ceratophryidae）、短头蟾科（Cycloramphidae）、细趾蟾科（Leptodactylidae）与暴蛙科（Strabomantidae）。为修正此类及其他分类学问题，我们针对传统上以科、亚科级别界定的现存两栖类类群，提出了修订后的分类方案。这一新分类体系纳入了多个当前主流分类系统尚未认可的科，如阿尔多蟾科（Alsodidae）、巴塔克蟾科（Batrachylidae）、鼻角蟾科（Rhinodermatidae）、齿蟾科（Odontophrynidae）以及泽蟾科（Telmatobiidae），这些类群均得到强有力的系统发育支持，且可有效规避当前科级分类单元的非单系问题。最后，本研究进一步验证了超级矩阵法（supermatrix approach）作为整合既往研究结果以推断大规模系统发育的有效策略的可行性，即便诸多类群存在大量缺失数据。