DOI: 10.5061/dryad.tb40v
title: Data from: Phylotranscriptomics to bring the understudied into the fold: monophyletic Ostracoda, fossil placement and pancrustacean phylogeny

description: An ambitious, yet fundamental goal for comparative biology is to
 understand the evolutionary relationships for all of life. Yet many
 important taxonomic groups have remained recalcitrant to inclusion into
 broader scale studies. Here, we focus on collection of 9 new 454
 transcriptome data sets from Ostracoda, an ancient and diverse group with
 a dense fossil record, which is often under-sampled in broader studies. We
 combine the new transcriptomes with a new morphological matrix (including
 fossils) and existing Expressed Sequence Tag (EST), mitochondrial genome,
 nuclear genome and rDNA data. Our analyses lead to new insights into
 ostracod and pancrustacean phylogeny. We obtained support for three epic
 pancrustacean clades that likely originated in the Cambrian: Oligostraca
 (Ostracoda, Mystacocarida, Branchiura, Pentastomida); Multicrustacea
 (Copepoda, Malacostraca, Thecostraca); and a clade we refer to as
 Allotriocarida (Hexapoda, Remipedia, Cephalocarida, Branchiopoda). Within
 the Oligostraca clade, our results support the unresolved question of
 ostracod monophyly. Within Multicrustacea, we find support for Thecostraca
 plus Copepoda, for which we suggest the name Hexanauplia. Within
 Allotriocarida, some analyses support the hypothesis that Remipedia is the
 sister taxon to Hexapoda, but others support Brachiopoda+Cephalocarida as
 the sister group of hexapods. In multiple different analyses, we see
 better support for equivocal nodes using slow-evolving genes or when
 excluding distant outgroups, highlighting the increased importance of
 conditional data combination in this age of abundant, often anonymous
 data. Yet, when we analyze the same set of species and ignore rate of gene
 evolution, we find higher support when including all data, more in line
 with a ‘total evidence’ philosophy. By concatenating molecular and
 morphological data, we place pancrustacean fossils in the phylogeny, which
 can be used for studies of divergence times in Pancrustacea, Arthropoda,
 or Metazoa. Our results and new data will allow for attributes of
 Ostracoda, such as its amazing fossil record and diverse biology, to be
 leveraged in broader scale comparative studies. Further, we illustrate how
 adding extensive next-generation sequence data from understudied groups
 can yield important new phylogenetic insights into long-standing
 questions, especially when carefully analyzed in combination with other
 data.
description: Conchoecissa sequence
 dataAssembled 454
 transcriptome data, otherwise unpublished. Only sequences used in
 MBE-published phylogenetic analysis are provided here. Collection
 information: Trawl Lower Sur Canyon on R/V Western Flyer Trawl on Western
 Flyer 36.06° N 122.29 W December 10th, 2009Conchoecissa_sp.fastaMorphological matrix for phylogeneticsMorhpological data matrix, including extant and fossil taxa. Stored in Morphobank, project ID 689 Raw 454: Vestalenula_spRaw Transcriptome sequence from full bodies. Adapter sequences included. Pooled together multiple individuals. Adapter = AAGCAGTGGTATCAACGCAGAGTACTTTTTTCTTTTTT. Collection Information: Freshwater Puddle, Isla Colon, Bocas del Toro, Panama. Net collecting 9º21.17'N 82º15.45'W July 29th, 2009 10cmVestalenula_sp.fastaRaw 454: Vestalenula_sp quality fileQuality associated with fasta file.Vestalenula_sp.fasta.qualRaw 454: Euphilomedes_morini_Compound_EyesEuphilomedes morini. 454 transcriptome data. from compound eyes. Pooled ~50 animals together (100 eyes). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Stern’s Wharf Pier, Santa Barbara, CA Eckman grab 34º24.4'N 119º40.5'W Oct., Nov., 2008 10 m depth.Euphilomedes_morini_Compound_Eyes.fastaRaw 454: Euphilomedes_morini_Compound_Eyes.fastaQuality file associated with fasta sequence fileEuphilomedes_morini_Compound_Eyes.fasta.qualRaw 454: Euphilomedes_morini median eye transcriptomeEuphilomedes morini. 454 transcriptome data from median eyes. Pooled ~50 animals together (50 eyes). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Stern’s Wharf Pier, Santa Barbara, CA Eckman grab 34º24.4'N 119º40.5'W Oct., Nov., 2008 10 m depth.Euphilomedes_morini_Median_Eyes.fastaRaw 454: Euphilomedes_morini_Median_Eyes qualityQuality file associated with fasta sequence fileEuphilomedes_morini_Median_Eyes.fasta.qualRaw 454: Cytherelloidea_californicaCytherelloidea californica. 454 transcriptome data. from full bodies. Pooled 26 animals together (50 eyes). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Camino de la Costa Beach Access, La Jolla, San Diego algae collecting 24º46.9'N 80º54.58'W May 14th, 2010 intertidal only on very low tideCytherelloidea_californica.fastaRaw 454: Cytherelloidea_californica quality fileQuality file associated with fasta sequence fileCytherelloidea_californica.fasta.qualRaw 454: Puriana_sp_BodiesPuriana sp. 454 transcriptome data. from Bodies minus median eyes. Pooled multiple animals together. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Isla Colon, Bocas del Toro, Panama net collecting 9º21'N 82º15.45'W July 23rd, 2009 1m depthPuriana_sp_Bodies.fastaRaw 454: Puriana_sp_Median_Eyes quality fileQuality file associated with fasta sequence filePuriana_sp_Median_Eyes.fasta.qualRaw 454: Puriana_sp_Median_EyesPuriana sp. 454 transcriptome data. from Median Eyes. Pooled multiple animals together. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Isla Colon, Bocas del Toro, Panama net collecting 9º21'N 82º15.45'W July 23rd, 2009 1m depthPuriana_sp_Median_Eyes.fastaRaw 454: Puriana_sp_Bodies quality fileQuality file associated with fasta sequence filePuriana_sp_Bodies.fasta.qualRaw 454: Heterocypris_sp_BodiesHeterocypris sp. 454 transcriptome data. bodies minus eyes. Pooled 30 animals together. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Temporary Freshwater Pool, More Mesa, Santa Barbara, CA net collecting 34º25.23'N 119º47.29'W 10cm depthHeterocypris_sp_Bodies.fastaRaw 454: Heterocypris_sp_Bodies Quality fileQuality file associated with fasta sequence fileHeterocypris_sp_Bodies.fasta.qualRaw 454: Heterocypris_sp_Median_EyesHeterocypris sp. 454 transcriptome data median eyes. Pooled 100 eyes together Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Temporary Freshwater Pool, More Mesa, Santa Barbara, CA net collecting 34º25.23'N 119º47.29'W 10cm depthHeterocypris_sp_Median_Eyes.fastaRaw 454: Heterocypris_sp_Median_Eyes quality fileQuality file associated with fasta sequence fileHeterocypris_sp_Median_Eyes.fasta.qualRaw 454: Skogsbergia_lerneri_Compound_EyesSkogsbergia lerneri. 454 transcriptome data. compound eyes (more than 50 pooled together). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Duck Key Viaduct, FL. bait trap. 24º46.9'N 80º54.58'W. July 16th thru July 18th, 2009. 2-3m depth.Skogsbergia_lerneri_Compound_Eyes.fastaRaw 454: Skogsbergia_lerneri_Compound_Eyes quality fileSkogsbergia_lerneri_Compound_Eyes.fasta.qualRaw 454: Skogsbergia_lerneri_Median_EyesSkogsbergia lerneri. 454 transcriptome data. median eyes (more than 50 pooled together). Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Duck Key Viaduct, FL. bait trap. 24º46.9'N 80º54.58'W. July 16th thru July 18th, 2009. 2-3m depth.Skogsbergia_lerneri_Median_Eyes.fastaRaw 454: Skogsbergia_lerneri_Median_Eyes quality fileQuality file associated with fasta sequence fileSkogsbergia_lerneri_Median_Eyes.fasta.qualRaw 454: Vargula_tsujii_Body1Vargula tsujii. 454 transcriptome data. 33 Bodies minus eyes. Two separate runs of 454 from same RNA. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Fishermen’s Cove, Twin Harbors, Catalina Island, CA bait trap 33º26.66'N 118º29.34'W July 10th and 11th, 2009 Depth: 5-10mVargula_tsujii_Body1.fastaRaw 454: Vargula_tsujii_Body1 quality fileQuality file associated with fasta sequence fileVargula_tsujii_Body1.fasta.qualRaw 454: Vargula_tsujii_Body2Vargula tsujii 454 transcriptome data. 33 Bodies minus eyes. Two separate runs of 454 from same RNA. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Fishermen’s Cove, Twin Harbors, Catalina Island, CA bait trap 33º26.66'N 118º29.34'W July 10th and 11th, 2009 Depth: 5-10mVargula_tsujii_Body2.fastaRaw 454: Vargula_tsujii_Body2.fastaQuality file associated with fasta sequence fileVargula_tsujii_Body2.fasta.qualRaw 454: Actinoseta_jonesiActinoseta jonesi 454 transcriptome data. Full bodies including eyes. Multiple pooled individuals. Raw sequence reads, including adaptors. Adaptor: AAGCAGTGGTATCAACGCAGAGT. Collection information: Cayo Enrique, La Parguera, Puerto Rico net collecting 17°57.335’N 67°03.185’W September 12th, 2010 2-3m depth.Actinoseta_jonesi.fastaRaw 454: Actinoseta_jonesi quality filesQuality file associated with fasta sequence fileActinoseta_jonesi.fasta.qualData used in phylogenetic analysesData used in phylogenetic analyses, in column separated text format. First column is species name, second column is name of data partition, third column is a unique id for the species/partition data (ie GenBank GI number), fourth column is sequence or morphological data. The sequence data are derived from the raw 454 data, or from other sources. Raw 454 data was assembled using Newbler. We pulled genes from transcriptomes using Hamstr. We then aligned sequences with MUSCLE, and cut out ambiguously aligned regions with AliScore/AliCut. Unique identifiers with "Voucher" in the name are previously unpublished, and will be placed in GenBank. This 4-column data format can be used with many tools developed in the Osiris package for conducting phylogenetics in Galaxy.FullData.csv