Lack of reproducibility of molecular phylogenetic analysis of Copepoda orders

Supplementary figures and additional material for: Mikhailov KV, Ivanenko VN. (2019a) Low support values and lack of reproducibility of molecular phylogenetic analysis of Copepoda orders. BioRxiv: e650507. 10.1101/650507 Figure S1. Maximum likelihood reconstruction with the concatenated alignment of the four genes (18S and 28S rRNA, COI mtDNA and H3 histone) from the study by Khodami et al., 2017. The tree was reconstructed with RAxML using the GTRGAMMAI model optimized separately for the four gene partitions; tree node support values are bootstrap percentages evaluated with 10,000 replicates. Figure S2. Bayesian inference with the concatenated alignment of the four genes (18S and 28S rRNA, COI mtDNA and H3 histone) from the study by Khodami et al., 2017. The tree was reconstructed by MrBayes using the GTR model for the rDNA partitions and the codon models in conjunction with GTR for the protein coding gene partitions; tree node support values are posterior probabilities given as percentage values. Funding: The reanalysis of the dataset was conducted with support of the Russian Foundation for Basic Research (grants #18-04-01192).配套补充图及附加材料引自：米哈伊洛夫（Mikhailov KV）、伊万连科（Ivanenko VN）（2019a）《桡足纲（Copepoda）目级分子系统发育分析的低支持度与可重复性缺失》，预印本平台BioRxiv：e650507，DOI:10.1101/650507。 补充图S1：基于Khodami等（2017）研究中4个基因（18S、28S核糖体RNA（rRNA）、线粒体细胞色素氧化酶I（COI mtDNA）及组蛋白H3（H3 histone））的串联比对序列构建的最大似然（Maximum likelihood）系统发育树。该树采用RAxML软件，基于针对4个基因分区分别优化的GTRGAMMAI模型完成构建；树节点支持度为经10000次重复计算得到的自展百分比（bootstrap percentages）。 补充图S2：基于Khodami等（2017）研究中上述4个基因的串联比对序列构建的贝叶斯推断（Bayesian inference）系统发育树。该树通过MrBayes软件构建，其中核糖体DNA（rDNA）分区采用GTR模型，蛋白质编码基因分区则采用结合GTR模型的密码子替换模型；树节点支持度为以百分比形式呈现的后验概率（posterior probabilities）。 资助说明：本数据集的重新分析工作获得俄罗斯基础研究基金会（Russian Foundation for Basic Research）资助，项目编号为#18-04-01192。