DOI: 10.5061/dryad.nb2f7
title: Data from: Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal

description: Chelicerata represents one of the oldest groups of arthropods, with a
 fossil record extending to the Cambrian, and is sister group to the
 remaining extant arthropods, the mandibulates. Attempts to resolve the
 internal phylogeny of chelicerates have achieved little consensus, due to
 marked discord in both morphological and molecular hypotheses of
 chelicerate phylogeny. The monophyly of Arachnida, the terrestrial
 chelicerates, is generally accepted, but has garnered little support from
 molecular data, which have been limited either in breadth of taxonomic
 sampling or in depth of sequencing. To address the internal phylogeny of
 this group, we employed a phylogenomic approach, generating transcriptomic
 data for 17 species in combination with existing data, including two
 complete genomes. We analyzed multiple data sets containing up to
 1,235,912 sites across 3,644 loci, using alternative approaches to
 optimization of matrix composition. Here, we show that phylogenetic signal
 for the monophyly of Arachnida is restricted to the 500 slowest-evolving
 genes in the data set. Accelerated evolutionary rates in Acariformes,
 Pseudoscorpiones, and Parasitiformes potentially engender long-branch
 attraction artifacts, yielding nonmonophyly of Arachnida with increasing
 support upon incrementing the number of concatenated genes. Mutually
 exclusive hypotheses are supported by locus groups of variable
 evolutionary rate, revealing significant conflicts in phylogenetic signal.
 Analyses of gene-tree discordance indicate marked incongruence in
 relationships among chelicerate orders, whereas derived relationships are
 demonstrably robust. Consistently recovered and supported relationships
 include the monophyly of Chelicerata, Euchelicerata, Tetrapulmonata, and
 all orders represented by multiple terminals. Relationships supported by
 subsets of slow-evolving genes include Ricinulei + Solifugae; a clade
 comprised of Ricinulei, Opiliones, and Solifugae; and a clade comprised of
 Tetrapulmonata, Scorpiones, and Pseudoscorpiones. We demonstrate that
 outgroup selection without regard for branch length distribution
 exacerbates long-branch attraction artifacts and does not mitigate
 gene-tree discordance, regardless of high gene representation for
 outgroups that are model organisms. Arachnopulmonata (new name) is
 proposed for the clade comprising Scorpiones + Tetrapulmonata (previously
 named Pulmonata).
description: 3644-ortholog
 alignment3644-ortholog alignment
 of Arachnida, with 47 taxaAL13_47.phyGene partitions file for 3644-ortholog alignmentGene partitions file for 3644-ortholog alignmentAlignmentAL13.txt2806-ortholog alignment2806-ortholog alignment of Arachnida, with at least 15 taxa represented for each gene.AL15.phyGene partitions file for 2806-ortholog alignmentGene partitions file for 2806-ortholog alignmentAlignmentAL15.txt1152-ortholog alignment1152-ortholog alignment of Arachnida, with at least 20 taxa represented for each gene.AL20.phyGene partitions file for 1152-ortholog alignmentGene partitions file for 1152-ortholog alignmentAlignmentAL20.txt352-ortholog alignment352-ortholog alignment of Arachnida, with at least 25 taxa represented for each gene.AL25.phyGene partitions file for 352-ortholog alignmentGene partitions file for 352-ortholog alignmentAlignmentAL25.txt98-ortholog alignment98-ortholog alignment of Arachnida, with at least 30 taxa represented for each geneAL30.phyGene partitions file for 98-ortholog alignmentGene partitions file for 98-ortholog alignmentAlignmentAL30.txt23-ortholog alignment23-ortholog alignment of Arachnida, with at least 35 taxa represented for each gene.AL35.phyGene partitions file for 23-ortholog alignmentGene partitions file for 23-ortholog alignmentAlignmentAL35.txt516-ortholog alignment from MAtrix REduction (MARE)516-ortholog alignment from MAtrix REduction (MARE), retaining all 47 taxaAL13MARE.phyGene partitions file for 516-ortholog MARE alignmentGene partitions file for 516-ortholog MARE alignmentAlignmentMARE.txt1237-ortholog alignment from MAtrix REduction (MARE)1237-ortholog alignment with MAtrix REduction (MARE), retaining taxa with full genomes or Illumina libraries onlyAL13MARE2.phyGene partitions file for 1237-ortholog MARE alignmentGene partitions file for 1237-ortholog MARE alignmentAlignmentMARE2.txt3644-ortholog alignment with data-rich terminals only3644-ortholog alignment, retaining only terminals with full genomes or Illumina librariesAL13_NGS.phy100 slowest-evolving orthologs alignment100-slowest-evolving orthologs alignmentG100.phyGene partitions file for 100 slowest-evolving orthologsGene partitions file for 100 slowest-evolving orthologsAlignmentG100.txt200 slowest-evolving orthologs alignment200 slowest-evolving orthologs alignmentG200.phyGene partitions file for 200 slowest-evolving orthologsGene partitions file for 200 slowest-evolving orthologsAlignmentG200.txt300 slowest-evolving orthologs alignment300 slowest-evolving orthologs alignmentG300.phyGene partitions file for 300 slowest-evolving orthologsGene partitions file for 300 slowest-evolving orthologsAlignmentG300.txt400 slowest-evolving orthologs alignment400 slowest-evolving orthologs alignmentG400.phyGene partitions file for 400 slowest-evolving orthologsGene partitions file for 400 slowest-evolving orthologsAlignmentG400.txt500 slowest-evolving orthologs alignment500 slowest-evolving orthologs alignmentG500.phyGene partitions file for 500 slowest-evolving orthologsGene partitions file for 500 slowest-evolving orthologsAlignmentG500.txt600 slowest-evolving orthologs alignment600 slowest-evolving orthologs alignmentG600.phyGene partitions file for 600 slowest-evolving orthologsGene partitions file for 600 slowest-evolving orthologsAlignmentG600.txt700 slowest-evolving orthologs alignment700 slowest-evolving orthologs alignmentG700.phyGene partitions file for 700 slowest-evolving orthologsGene partitions file for 700 slowest-evolving orthologsAlignmentG700.txt800 slowest-evolving orthologs alignment800 slowest-evolving orthologs alignmentG800.phyGene partitions file for 800 slowest-evolving orthologsGene partitions file for 800 slowest-evolving orthologsAlignmentG800.txt900 slowest-evolving orthologs alignment900 slowest-evolving orthologs alignmentG900.phyGene partitions file for 900 slowest-evolving orthologsGene partitions file for 900 slowest-evolving orthologsAlignmentG900.txt1000 slowest-evolving orthologs alignment1000 slowest-evolving orthologs alignmentG1000.phyGene partitions file for 1000 slowest-evolving orthologsAlignmentG1000.txt1500 slowest-evolving orthologs alignment1500 slowest-evolving orthologs alignmentG1500.phyGene partitions file for 1500 slowest-evolving orthologsGene partitions file for 1500 slowest-evolving orthologsAlignmentG1500.txt2000 slowest-evolving orthologs alignment2000 slowest-evolving orthologs alignmentG2000.phyGene partitions file for 2000 slowest-evolving orthologsGene partitions file for 2000 slowest-evolving orthologsAlignmentG2000.txt2500 slowest-evolving orthologs alignment2500 slowest-evolving orthologs alignmentG2500.phy3000 slowest-evolving orthologs alignment3000 slowest-evolving orthologs alignmentG3000.phyGene partitions file for 2500 slowest-evolving orthologsGene partitions file for 2500 slowest-evolving orthologsAlignmentG2500.txtGene partitions file for 3000 slowest-evolving orthologsGene partitions file for 3000 slowest-evolving orthologsAlignmentG3000.txt3500 slowest-evolving orthologs alignment3500 slowest-evolving orthologs alignmentG3500.phyGene partitions file for 3500 slowest-evolving orthologsGene partitions file for 3500 slowest-evolving orthologsAlignmentG3500.txtAlipes grandidieri Trinity assemblyAlipes grandidieri (Chilopoda: Scolopendromorpha) Trinity assemblyAlipes.fastaCentruroides vittatus Trinity assemblyCentruroides vittatus (Chelicerata: Scorpiones) Trinity assemblyCentruroides.fastaDamon variegatus Trinity assemblyDamon variegatus (Chelicerata: Amblypygi) Trinity assemblyDamon.fastaEremobates sp. Trinity assemblyEremobates sp. (Chelicerata: Solifugae) Trinity assemblyEremobates.fastaFrontinella communis Trinity assemblyFrontinella communes (Chelicerata: Araneae) Trinity assemblyFrontinella.fastaHesperonemastoma modestum Trinity assemblyHesperonemastoma modestum (Chelicerata: Opiliones) Trinity assemblyHesperonemastoma.fastaLarifuga capensis Trinity assemblyLarifuga capensis (Chelicerata: Opiliones) Trinity assemblyLarifuga.fastaLeiobunum verrucosum Trinity assemblyLeiobunum verrucosum (Chelicerata: Opiliones) Trinity assemblyLeiobunum.fastaLeucage venusta Trinity assemblyLeucage venusta (Chelicerata: Opiliones) Trinity assemblyLeucage.fastaLimulus polyphemus Trinity assemblyLimulus polyphemus (Chelicerata: Xiphosura) Trinity assemblyLimulus.fastaLiphistius malayanus Trinity assemblyLiphistius malayanus (Chelicerata: Araneae) Trinity assemblyLiphistius.fastaMastigoproctus giganteus Trinity assemblyMastigoproctus giantess (Chelicerata: Uropygi) Trinity assemblyMastigoproctus.fastaMetabiantes sp. Trinity assemblyMetabiantes sp. (Chelicerata: Opiliones) Trinity assemblyMetabiantes.fastaMetasiro americanus Trinity assemblyMetasiro americanus (Chelicerata: Opiliones) Trinity assemblyMetasiro.fastaNeoscona arabesca Trinity assemblyNeoscona arabesca (Chelicerata: Araneae) Trinity assemblyNeoscona.fastaOrtholasma coronadense Trinity assemblyOrtholasma corona dense (Chelicerata: Opiliones) Trinity assemblyOrtho.fastaPachylicus acutus Trinity assemblyPachylicus acutus (Chelicerata: Opiliones) Trinity assemblyPachylicus.fastaPeripatopsis capensis Trinity assemblyPeripatopsis capensis (Onychophora: Peripatopsidae) Trinity assemblyPeripatopsis2.fastaPhalangium opilio Trinity assemblyPhalangium opilio (Chelicerata: Opiliones) Trinity assemblyPhalangium.fastaProtolophus singularis Trinity assemblyProtolophus singulars (Chelicerata: Opiliones) Trinity assemblyProtolophus.fastaPseudocellus sp. Trinity assemblyPseudocellus sp. (Chelicerata: Ricinulei) Trinity assemblyPseudocellus.fastaSclerobunus nondimorphicus Trinity assemblySclerobunus nondimorphicus (Chelicerata: Opiliones) Trinity assemblySclerobunus.fastaRicinoides atewa Trinity assemblyRicinoides atewa (Chelicerata: Ricinulei) Trinity assemblyRicinoides.fastaSiro boyerae Trinity assemblySiro boyerae (Chelicerata: Opiliones) Trinity assemblySiro.fastaSitalcina lobata Trinity assemblySitalcina lobata (Chelicerata: Opiliones) Trinity assemblySitalcina.fastaSynsphyronus apimelus Trinity assemblySynsphyronus apimelus (Chelicerata: Pseudoscorpiones) Trinity assemblySynsphyronus.fastaTrogulus martensi Trinity assemblyTrogulus martensi (Chelicerata: Opiliones) Trinity assemblyTrogulus.fastaVonones ornata Trinity assemblyVonones ornate (Chelicerata: Opiliones) Trinity assemblyVonones.fasta