DOI: 10.5061/dryad.p8cz8w9th
title: Data from: Arthropod phylotranscriptomics with a special focus on the basal phylogeny of the Myriapoda

description: Arthropoda are the most diverse animal phylum, but the phylogenetic
 relationships of arthropods are difficult to determine because many
 arthropod lineages diverged in a short period of time. In order to solve
 the controversial problems in the deep phylogeny of arthropods with a
 focus on Myriapoda, we conducted phylogenetic analyses based on ten
 supermatrices, which contain 751-1,233 orthologous genes from
 transcriptome data of 64 representative arthropod species, of which 28
 transcriptomes are newly generated in this study. The results
 unambiguously support monophyly of the higher arthropod taxa, Chelicerata,
 Mandibulata, Myriapoda, Pancrustacea, and Hexapoda. The Crustacea are
 paraphyletic, with the class Remipedia supported as the lineage most
 closely related to hexapods. Within Hexapoda, our results basically
 support the phylogenetic relationships among the deep hexapod lineages
 proposed to date, except that the Paraneoptera (Hemiptera, Thysanoptera,
 and Psocodea) was recovered as a monophyletic lineage in some analyses.
 The results also strongly support the recently proposed phylogenetic
 framework of the four myriapod classes, in which the Symphyla and
 Pauropoda, and the Chilopoda and Diplopoda are sister relationship,
 respectively. These findings provide important insights into understanding
 the phylogeny and evolution of arthropods.
description: A total of 64 species representing all arthropod classes (three
 chelicerate classes: Pycnogonida, Merostomata, and Arachnida; four
 myriapod classes: Chilopoda, Diplopoda, Pauropoda, and Symphyla; six
 crustacean classes: Ostracoda, Hexanauplia, Malacostraca, Branchiopoda,
 Cephalocarida, and Remipedia; two hexapod classes: Entognatha and
 Ectognatha) were analyzed in this study. Of which 28 species (10
 crustaceans, 13 myriapods, and 5 chelecerates), which were collected from
 the Ryukyu Islands and the Kansai region of Japan, were used for
 transcriptome sequencing. The transcriptome sequences of other arthropod
 species and five outgroup species were retrieved from NCBI (National
 Center for Biotechnology Information) sequence database. For construction
 of the datasets, tree files, etc., refer to the paper.
description: # Data from: Arthropod phylotranscriptomics with a special focus on the
 basal phylogeny of the Myriapoda Amino acid sequence alignments of
 orthologous genes and tree files ## Description of the Data and file
 structure HaMStR was used to search the assembled transcriptome data to
 find protein sequences that matched two different gene sets referred to as
 arthropod core orthologs: the Coreset insecta_hmmer3_2 (Coreset A) and
 Coreset arthropoda_hmmer3 (Coreset B). Datasets (A1-A5 and B1-B5) were
 constructed based on the sequence data of orthologs with different samples
 as follows. Dataset_A1 is constructed based on the Coreset A with all
 samples. Dataset_A2 is constructed based on the Coreset A with
 representative samples for the phylogenetic analysis among the four
 arthropod subphyla. Dataset_A3 is constructed based on the Coreset A with
 all myriapod samples and other representative arthropods as outgroups.
 Dataset_A4 is constructed based on the Coreset A with all samples of
 Diplopoda and Chilopoda, and each one sample of Symphyla and Pauropoda as
 outgroups. Dataset_A5 is constructed based on the Coreset A with all
 pancrustacean samples and several representative species of myriapods and
 chelicerates as outgroups. Dataset_B1 is constructed based on the Coreset
 B with all samples. Dataset_B2 is constructed based on the Coreset B with
 representative samples for the phylogenetic analysis among the four
 arthropod subphyla. Dataset_B3 is constructed based on the Coreset B with
 all myriapod samples and other representative arthropods as outgroups.
 Dataset_B4 is constructed based on the Coreset B with all samples of
 Diplopoda and Chilopoda, and each one sample of Symphyla and Pauropoda as
 outgroups. Dataset_B5 is constructed based on the Coreset B with all
 pancrustacean samples and several representative species of myriapods and
 chelicerates as outgroups. Mafft and Gblocks were used to align sequences
 and eliminate poorly aligned positions and divergent regions for each
 dataset. Each dataset was used for phylogenetic analyses with RAxML and
 MrBayes except for Dataset A1 and B1, which were only used for inferring
 tree by RAxML.