A robust phylogeny among major lineages of the East African cichlids
A robust phylogeny among major lineages of the East African cichlids
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东非慈鲷主要谱系中强大的系统发育
DOI：
10.1016/j.ympev.2016.04.012
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发表时间：
2016
影响因子：
4.1
通讯作者：
Sota T
中科院分区：
文献类型：
--
作者：
Takahashi T;Sota T
东非丽鱼科鱼 (EAR) 庞大的单系类群由属于 12-14 个部落的数千种物种组成；不同研究中的部落数量有所不同。许多研究利用各种遗传标记推断了 EAR 部落的系统发育。然而，这些系统发育在一定程度上相互矛盾，并且统计支持很弱。在这项研究中，我们使用限制性位点相关 DNA (RAD) 序列进行了最大似然 (ML) 系统发育分析，并在覆盖大多数 EAR 部落的坦噶尼喀湖慈鲷鱼中提出了一种新的稳健的系统发育假说。数据矩阵的大小和内容可能会有所不同，具体取决于用于处理 RAD 序列的策略。因此，我们准备了23个具有不同处理策略的数据矩阵。从 15 个大型矩阵（2.0 × 106 到 1.1 × 107 碱基对）推断出的 ML 系统发育将每个部落解析为具有 100% bootstrap 支持的单系群，并且在部落之间的关系方面共享相同的拓扑。部落中的大多数节点都受到 100% bootstrap 值的支持，而其他节点的 bootstrap 支持在 15 个 ML 树中从 70% 到 100% 不等。这些强大的 ML 树在拓扑结构上与早期研究中的树有部分不同，这些系统发育关系对 EAR 的部落分类具有重要意义。
The huge monophyletic group of the East African cichlid radiations (EAR) consists of thousands of species belonging to 12–14 tribes; the number of tribes differs among studies. Many studies have inferred phylogenies of EAR tribes using various genetic markers. However, these phylogenies partly contradict one another and can have weak statistic support. In this study, we conducted maximum-likelihood (ML) phylogenetic analyses using restriction site-associated DNA (RAD) sequences and propose a new robust phylogenetic hypothesis among Lake Tanganyika cichlid fishes, which cover most EAR tribes. Data matrices can vary in size and contents depending on the strategies used to process RAD sequences. Therefore, we prepared 23 data matrices with various processing strategies. The ML phylogenies inferred from 15 large matrices (2.0 × 106to 1.1 × 107base pairs) resolved every tribe as a monophyletic group with 100% bootstrap support and shared the same topology regarding relationships among the tribes. Most nodes among the tribes were supported by 100% bootstrap values, and the bootstrap support for the other node varied among the 15 ML trees from 70% to 100%. These robust ML trees differ partly in topology from those in earlier studies, and these phylogenetic relationships have important implications for the tribal classification of EAR.