Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics
Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics
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DOI：
10.1098/rspb.2018.1524
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发表时间：
2018-08-29
影响因子：
4.7
通讯作者：
Giribet, Gonzalo
中科院分区：
文献类型：
--
作者：
Schwentner, Martin;Richter, Stefan;Giribet, Gonzalo
了解Tetraconata或Pancrustacea（包括甲壳类和昆虫的进化枝）的进化需要对其组成分类群内部和之间的关系提出一个很好的假设。在这里，我们组装了一个分类丰富的基因组数据集，专注于甲壳类动物谱系，仅基于基因组和新一代Illumina生成的转录组，包括89个Tetraconata的代表。据我们所知，这是第一个专门针对软甲纲（包括26种）和鳃足纲（36种）内部关系的基因组研究。7矩阵，包括81-684正交群和17 690-242 530个氨基酸的位置组装和分析下五种不同的分析方法。为了最大限度地提高基因占有率和分辨率，分类特异性矩阵的软甲纲和鳃足目的设计。关键的四角动物分类群（即寡甲纲、多甲壳纲、鳃足纲、软甲纲、介甲纲、桡足纲和六足纲）是单系的，并得到了很好的支持。在鳃足类中，叶足类、双甲类、枝角类和枝角类是单系的。在软甲纲中，Eumalacostraca，十足目和Reptantia的分支得到了很好的支持。恢复Caridoida或Peracarida是高度依赖于完整的矩阵的分析，但它始终是单系的软甲介属特定的矩阵。从这样的例子中，我们表明，分类特异性矩阵和特定的进化模型和分析方法，即CAT-GTR和Dayhoff重新编码，优于其他方法，在解决某些cancercitrant节点的cancergenomic分析。
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. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81-684 orthogroups and 17 690-242 530 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 and 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 dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. 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.