Data from: Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as “Tilapia”

African cichlids formerly referred to as ”Tilapia” represent a paraphyletic species assemblage belonging to the so called haplotilapiine lineage which gave rise to the spectacular East African cichlid radiations (EARs) as well as to globally important aquaculture species. We present a comprehensive molecular phylogeny of representative haplotilapiine cichlids, combining in one data set four mitochondrial and five nuclear loci for 76 species, and compare it with phylogenetic information of a second data set of 378 mitochondrial ND2 haplotypes representing almost all important “Tilapia” or Tilapia-related lineages as well as most EAR lineages. The monophyly of haplotilapiines is supported, as is the nested sister group relationship of Etia and mouthbrooding tilapiines with the remaining haplotilapiines. The latter are consistently placed in eight monophyletic clades over all datasets and analyses, but several dichotomous phylogenetic relationships appear compromised by cytonuclear discordant phylogenetic signal. Based on these results as well as on extensive morphological evidence we propose a novel generic and suprageneric classification including a (re-)diagnosis of 20 haplotilapiine cichlid genera and nine tribes. New tribes are provided for the former subgenera Coptodon Gervais, 1853, HeterotilapiaRegan, 1920 and PelmatolapiaThys van den Audenaerde, 1969, in addition for “Tilapia” joka, Tilapia sensu stricto and Chilochromis, Etia, Steatocranus sensu stricto, the mouthbrooding tilapiines and for a clade of West African tilapiines.曾被归类为"罗非鱼（Tilapia）"的非洲慈鲷，是隶属于所谓的褶唇丽鱼支系（haplotilapiine lineage）的并系物种集合，该支系不仅催生了极具物种多样性的东非慈鲷适应性辐射（East African cichlid radiations, EARs），同时也演化出了全球具有重要经济价值的水产养殖物种。本研究针对具有代表性的褶唇丽鱼支系慈鲷构建了综合分子系统发育树，整合了涵盖76个物种的4个线粒体基因座与5个核基因座的数据集，并将其与另一组数据集的系统发育信息进行对比：第二组数据集包含378个线粒体ND2单倍型，覆盖了几乎所有重要的"罗非鱼"或罗非鱼相关支系，以及绝大多数东非慈鲷适应性辐射支系。褶唇丽鱼支系的单系性得到了支持，伊提丽鱼属（Etia）与口育型罗非鱼和其余褶唇丽鱼支系之间的嵌套姐妹群关系，同样得到了支持。其余褶唇丽鱼支系在所有数据集与分析中均被划分为8个单系演化支，但部分两两分支的系统发育关系因核质系统发育信号冲突而缺乏可靠支持。基于上述研究结果与大量形态学证据，本研究提出了一套全新的属级与超属级分类体系，其中包含对20个褶唇丽鱼支系慈鲷属与9个族的（重新）鉴别特征描述。本研究为以下类群设立了新族：原亚属包括1853年Gervais命名的非鲫亚属（Coptodon）、1920年Regan命名的异非鲫亚属（Heterotilapia）与1969年Thys van den Audenaerde命名的瓣非鲫亚属（Pelmatolapia），此外还包括"Tilapia" joka、严格意义罗非鱼（Tilapia sensu stricto）、色丽鱼属（Chilochromis）、伊提丽鱼属（Etia）、严格意义壮头丽鱼属（Steatocranus sensu stricto）、口育型罗非鱼，以及西非罗非鱼演化支。