Linchangco Gregorio V, Foltz David W, Reid Rob, Williams John, Nodzak Conor, Kerr Alexander M, Miller Allison K, Hunter Rebecca, Wilson Nerida G, Nielsen William J, Mah Christopher L, Rouse Greg W, Wray Gregory A, Janies Daniel A
Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA.
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
Mol Phylogenet Evol. 2017 Oct;115:161-170. doi: 10.1016/j.ympev.2017.07.022. Epub 2017 Jul 27.
Multi-locus phylogenetic studies of echinoderms based on Sanger and RNA-seq technologies and the fossil record have provided evidence for the Asterozoa-Echinozoa hypothesis. This hypothesis posits a sister relationship between asterozoan classes (Asteroidea and Ophiuroidea) and a similar relationship between echinozoan classes (Echinoidea and Holothuroidea). Despite this consensus around Asterozoa-Echinozoa, phylogenetic relationships within the class Asteroidea (sea stars or starfish) have been controversial for over a century. Open questions include relationships within asteroids and the status of the enigmatic taxon Xyloplax. Xyloplax is thought by some to represent a newly discovered sixth class of echinoderms - and by others to be an asteroid. To address these questions, we applied a novel workflow to a large RNA-seq dataset that encompassed a broad taxonomic and genomic sample. This study included 15 species sampled from all extant orders and 13 families, plus four ophiuroid species as an outgroup. To expand the taxonomic coverage, the study also incorporated five previously published transcriptomes and one previously published expressed sequence tags (EST) dataset. We developed and applied methods that used a range of alignment parameters with increasing permissiveness in terms of gap characters present within an alignment. This procedure facilitated the selection of phylogenomic data subsets from large amounts of transcriptome data. The results included 19 nested data subsets that ranged from 37 to 4,281loci. Tree searches on all data subsets reconstructed Xyloplax as a velatid asteroid rather than a new class. This result implies that asteroid morphology remains labile well beyond the establishment of the body plan of the group. In the phylogenetic tree with the highest average asteroid nodal support several monophyletic groups were recovered. In this tree, Forcipulatida and Velatida are monophyletic and form a clade that includes Brisingida as sister to Forcipulatida. Xyloplax is consistently recovered as sister to Pteraster. Paxillosida and Spinulosida are each monophyletic, with Notomyotida as sister to the Paxillosida. Valvatida is recovered as paraphyletic. The results from other data subsets are largely consistent with these results. Our results support the hypothesis that the earliest divergence event among extant asteroids separated Velatida and Forcipulatacea from Valvatacea and Spinulosida.
基于桑格测序技术、RNA测序技术以及化石记录开展的棘皮动物多位点系统发育研究，为海星动物-海胆动物假说提供了证据。该假说认为海星动物纲（海星纲和蛇尾纲）之间存在姐妹关系，海胆动物纲（海胆纲和海参纲）之间也存在类似关系。尽管围绕海星动物-海胆动物假说已达成共识，但海星纲（海星或海盘车）内部的系统发育关系在一个多世纪以来一直存在争议。悬而未决的问题包括小行星类群内部的关系以及神秘分类单元木星海星的地位。一些人认为木星海星代表新发现的第六类棘皮动物，而另一些人则认为它是一种海星。为解决这些问题，我们将一种新颖的工作流程应用于一个大型RNA测序数据集，该数据集涵盖了广泛的分类学和基因组样本。这项研究包括从所有现存目和13个科中选取的15个物种，外加4种蛇尾类物种作为外类群。为扩大分类学覆盖范围，该研究还纳入了5个先前发表的转录组和1个先前发表的表达序列标签（EST）数据集。我们开发并应用了一些方法，这些方法使用了一系列比对参数，在比对中允许出现的间隙字符方面逐渐放宽限制。这一过程有助于从大量转录组数据中选择系统发育基因组数据子集。结果包括19个嵌套数据子集，范围从37个位点到4281个位点。对所有数据子集进行的树形搜索将木星海星重建为一种瓣海星类海星，而非一个新类别。这一结果意味着，在该类群身体结构确立之后很久，海星的形态仍然不稳定。在平均海星节点支持度最高的系统发育树中，恢复了几个单系类群。在这棵树中，钳棘目和瓣海星目是单系的，并形成一个分支，其中包含蛇海星目作为钳棘目的姐妹类群。木星海星始终被重建为翼海星的姐妹类群。栉海星目和刺冠海星目各自是单系的，其中无腕海星目是栉海星目的姐妹类群。冠海星目被重建为并系的。其他数据子集的结果在很大程度上与这些结果一致。我们的结果支持这样一种假说，即现存海星中最早的分化事件将瓣海星目和钳棘目与冠海星目和刺冠海星目分离开来。
