A revised taxonomy and phylogeny of opalinids (Stramenopiles, Opalinata) inferred from the analysis of complete nuclear ribosomal DNA (rDNA) genes - alignments and phylogenetic trees

The data include 1) the sequence alignments of the SSU rDNA gene and of the ITS-LSU rDNA gene of opalinids, proteromonads and related species, in fasta format and formatted for MEGA-X ('?' added). 2) the phylogenetic trees obtained in MEGA-X by using the sequence alignments (SSU and ITS-LSU) and the maximum likelihood and maximum parsimony methods, and the trees obtained in MrBayes by using the bayesian inference method. 3) The trees obtained in the timetree analysis made in MEGA-X with the SSU rDNA alignment. Three groups of time calibration points were used: A, "sequence evolution" group, included calibrations for the Apicomplexa-Dinoflagellata divergence, Ciliophora divergence, and Stramenopiles divergence nodes; B, "host Class constraints" include calibrations for the Karotomorpha and Proteromonas divergence nodes, based on the maximum estimated time of emergence of amphibians (for the Karotomorpha node) and sauria (for the Proteromonas node); and C, "host family constraints" include calibrations for the Protoopalina and Opalina-Zelleriella nodes based on the estimated time of emergence of the most ancient anuran family in which each genus has been cited. Four scenarios were considered (the timetree obtained in each scenario is provided): scenario 1, only calibration points of group A; scenario 2, groups A-B; scenario 3, groups A-C; scenario 4, groups A-B-C.

本数据集包含以下三类内容：1) 偏眼虫类（opalinids）、前滴虫类（proteromonads）及其近缘物种的SSU rDNA基因与ITS-LSU rDNA基因序列比对文件，格式为FASTA，且适配MEGA-X软件（已添加通配符“?”）。2) 基于上述SSU rDNA与ITS-LSU rDNA序列比对文件，通过MEGA-X采用最大似然法与最大简约法构建的系统发育树，以及通过MrBayes采用贝叶斯推断法构建的系统发育树。3) 基于SSU rDNA序列比对文件，在MEGA-X中开展时间树（timetree）分析得到的系统发育树。本次分析采用三类时间校准点：A组为"序列演化校准组"，涵盖顶复门（Apicomplexa）-双鞭毛虫门（Dinoflagellata）分歧节点、纤毛虫门（Ciliophora）分歧节点以及不等鞭毛类（Stramenopiles）分歧节点的校准信息；B组为"宿主纲约束校准组"，基于两栖动物最大估计出现时间校准Karotomorpha分歧节点、基于蜥类（sauria）最大估计出现时间校准前滴虫属（Proteromonas）分歧节点的校准信息；C组为"宿主科约束校准组"，基于各属首次被报道所在的最古老无尾目科的估计出现时间，校准原纤毛虫属（Protoopalina）以及Opalina-Zelleriella分歧节点的校准信息。本次分析共设置四种场景（各场景下得到的时间树均已提供）：场景1仅使用A组校准点；场景2使用A、B两组校准点；场景3使用A、C两组校准点；场景4使用A、B、C三组校准点。