Data from: Biogeography and evolution of body size and life history of African frogs: phylogeny of squeakers (Arthroleptis) and long-fingered frogs (Cardioglossa) estimated from mitochondrial data

The evolutionary history of living African amphibians remains poorly understood. This study estimates the phylogeny within the frog genera Arthroleptis and Cardioglossa using approximately 2400 bases of mtDNA sequence data (12S, tRNA-Valine, and 16S genes) from half of the described species. Analyses are conducted using parsimony, maximum likelihood, and Bayesian methods. The effect of alignment on phylogeny estimation is explored by separately analyzing alignments generated with different gap costs and a consensus alignment. The consensus alignment results in species paraphyly, low nodal support, and incongruence with the results based on other alignments, which produced largely similar results. Most nodes in the phylogeny are highly supported, yet several topologies are inconsistent with previous hypotheses. The monophyly of Cardioglossa and of miniature species previously assigned to Schoutedenella was further examined using Templeton and Shimodaira–Hasegawa tests. Cardioglossa monophyly is rejected and C. aureoli is transferred to Arthroleptis. These tests do not reject Schoutedenella monophyly, but this hypothesis receives no support from non-parametric bootstrapping or Bayesian posterior probabilities. This phylogeny provides a framework for reconstructing historical biogeography and analyzing the evolution of body size and life history. Direct development and miniaturization appear at the base of Arthroleptis phylogeny concomitant with a range expansion from Central Africa to throughout most of sub-Saharan Africa.现存非洲两栖动物的演化历史迄今仍未得到充分阐明。本研究基于已描述物种中半数类群的线粒体DNA（mtDNA）序列数据（包含12S、缬氨酸转运RNA（tRNA-Valine）以及16S基因）约2400个碱基对，对节蛙属（Arthroleptis）和心舌蛙属（Cardioglossa）内的系统发育关系进行推断。本研究采用简约法、最大似然法以及贝叶斯方法开展分析。本研究通过分别分析不同空位代价下生成的序列比对结果以及一致性比对结果，探究序列比对对系统发育推断的影响。一致性比对结果会导致物种并系现象、节点支持度偏低，且与其他比对方法得到的结果存在冲突；而其他比对方法的分析结果整体较为一致。该系统发育树的绝大多数节点均具有较高支持度，但部分拓扑结构与此前提出的演化假说存在不一致。本研究进一步采用特普莱顿检验（Templeton test）与岛田-长谷川检验（Shimodaira–Hasegawa test），对心舌蛙属以及此前划归至舒特蛙属（Schoutedenella）的小型物种的单系性进行验证。心舌蛙属的单系性被推翻，且金心舌蛙（Cardioglossa aureoli）被划归至节蛙属。上述检验未否定舒特蛙属的单系性，但该假说并未得到非参数自举法或贝叶斯后验概率的支持。本研究构建的系统发育树为历史生物地理学重建以及体型大小与生活史演化分析提供了研究框架。直接发育与体型小型化现象起源于节蛙属系统发育树的基部类群，且伴随着从中非向撒哈拉以南非洲绝大多数区域的分布范围扩张。