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.