Data from: Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda—Highlighting the strength of taxon-specific matrices in phylogenomics

Understanding the evolution of Tetraconata or Pancrustacea —the clade that includes crustaceans and insects—requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Herein, we assembled a taxon-rich phylogenomic data set focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81 to 684 orthogroups and 17,690 to 242,530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e., Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda, Hexapoda) were monophyletic and well supported. Within Branchiopoda Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly depending on the analysis for the complete matrix but were consistently recovered monophyletic in the malacostracan-specific matrix. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.

理解四神经类（Tetraconata）或称泛甲壳动物（Pancrustacea）——这一类群涵盖甲壳类与昆虫类——的演化历程，需要建立其内部及各组成类群间系统发育关系的明确假说。本研究中，我们仅依托基因组数据与新一代Illumina测序获得的转录组数据，构建了聚焦甲壳类支系的类群丰富型系统发育组学数据集，共纳入89个四神经类类群代表样本。本研究是首个专门针对软甲纲（含26个物种）与鳃足纲（含36个物种）内部系统发育关系的系统发育组学研究。我们共构建并分析了7套矩阵，其涵盖的直系同源基因簇（orthogroup）数量为81至684个，氨基酸位点数量为17690至242530个，并采用5种不同的分析策略进行推演。为最大化基因占比并提升系统发育分辨率，我们针对软甲纲与鳃足纲分别设计了类群专属矩阵。关键四神经类类群，即寡甲总纲（Oligostraca）、多甲壳类（Multicrustacea）、鳃足纲、软甲纲、鞘甲亚纲（Thecostraca）、桡足类（Copepoda）以及六足亚门（Hexapoda），均为单系群且得到了良好的统计支持。在鳃足纲内部，叶足亚纲（Phyllopoda）、双甲目（Diplostraca）、枝角类总群（Cladoceromorpha）以及枝角目（Cladocera）均为单系群。在软甲纲内部，真软甲亚纲（Eumalacostraca）、十足目（Decapoda）以及爬行亚目（Reptantia）均得到了良好的统计支持。在全矩阵的系统发育重建中，糠虾总目（Caridoida）与囊虾总目（Peracarida）的单系性结果高度依赖于所采用的分析方法，但在软甲纲专属矩阵中，二者均被稳定重建为单系群。基于上述结果，我们证明：类群专属矩阵、特定演化模型（即CAT-GTR模型）以及分析方法（即Dayhoff重编码技术），在解决系统发育组学分析中部分顽固节点的问题上，优于其他分析策略。