Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA; Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA.
Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA.
Mol Phylogenet Evol. 2018 Dec;129:268-279. doi: 10.1016/j.ympev.2018.09.001. Epub 2018 Sep 6.
Notothenioids are a clade of ∼120 species of marine fishes distributed in extreme southern hemisphere temperate near-shore habitats and in the Southern Ocean surrounding Antarctica. Over the past 25 years, molecular and morphological approaches have redefined hypotheses of relationships among notothenioid lineages as well as their relationships among major lineages of percomorph teleosts. These phylogenies provide a basis for investigation of mechanisms of evolutionary diversification within the clade and have enhanced our understanding of the notothenioid adaptive radiation. Despite extensive efforts, there remain several questions concerning the phylogeny of notothenioids. In this study, we deploy DNA sequences of ∼100,000 loci obtained using RADseq to investigate the phylogenetic relationships of notothenioids and to assess the utility of RADseq loci for lineages that exhibit divergence times ranging from the Paleogene to the Quaternary. The notothenioid phylogenies inferred from the RADseq loci provide unparalleled resolution and node support for several long-standing problems including, (1) relationships among species of Trematomus, (2) resolution of Indonotothenia cyanobrancha as the sister lineage of Trematomus, (3) the deep paraphyly of Nototheniidae, (4) the paraphyly of Lepidonotothen s.l., (5) paraphyly of Artedidraco, and 6) the monophyly of the Bathydraconidae. Assessment of site rates demonstrates that RADseq loci are similar to mtDNA protein coding genes and exhibit peak phylogenetic informativeness at the time interval during which the major Antarctic notothenioid lineages originated and diversified. In addition to providing a well-resolved phylogenetic hypothesis for notothenioids, our analyses quantify the predicted utility of RADseq loci for Cenozoic phylogenetic inferences.
南极鱼是一个约有 120 个物种的分支，分布在南半球温带近岸栖息地和环绕南极洲的南大洋。在过去的 25 年里，分子和形态学方法重新定义了南极鱼谱系之间以及它们与后生动物鲈形目主要谱系之间的关系假设。这些系统发育为研究该分支内进化多样化的机制提供了基础，并增强了我们对南极鱼辐射适应的理解。尽管进行了广泛的努力，但关于南极鱼的系统发育仍存在一些问题。在这项研究中，我们使用 RADseq 获得的约 100000 个基因座的 DNA 序列来研究南极鱼的系统发育关系，并评估 RADseq 基因座在从古近纪到第四纪分化时间范围的谱系中的有效性。从 RADseq 基因座推断的南极鱼系统发育为几个长期存在的问题提供了无与伦比的分辨率和节点支持，包括：（1） Trematomus 种间的关系；（2）将 Indonotothenia cyanobrancha 确定为 Trematomus 的姐妹谱系；（3）Nototheniidae 的深并系性；（4）Lepidonotothen s.l. 的并系性；（5）Artedidraco 的并系性；以及（6）Bathydraconidae 的单系性。位点速率评估表明，RADseq 基因座与 mtDNA 蛋白编码基因相似，在主要南极南极鱼谱系起源和多样化的时间间隔内表现出最高的系统发育信息量。除了为南极鱼提供一个分辨率较高的系统发育假设外，我们的分析还量化了 RADseq 基因座对新生代系统发育推断的预测效用。
