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).
3644-ortholog alignment
3644-ortholog alignment of Arachnida, with 47 taxa
AL13_47.phy
Gene partitions file for 3644-ortholog alignment
Gene partitions file for 3644-ortholog alignment
AlignmentAL13.txt
2806-ortholog alignment
2806-ortholog alignment of Arachnida, with at least 15 taxa represented for each gene.
AL15.phy
Gene partitions file for 2806-ortholog alignment
Gene partitions file for 2806-ortholog alignment
AlignmentAL15.txt
1152-ortholog alignment
1152-ortholog alignment of Arachnida, with at least 20 taxa represented for each gene.
AL20.phy
Gene partitions file for 1152-ortholog alignment
Gene partitions file for 1152-ortholog alignment
AlignmentAL20.txt
352-ortholog alignment
352-ortholog alignment of Arachnida, with at least 25 taxa represented for each gene.
AL25.phy
Gene partitions file for 352-ortholog alignment
Gene partitions file for 352-ortholog alignment
AlignmentAL25.txt
98-ortholog alignment
98-ortholog alignment of Arachnida, with at least 30 taxa represented for each gene
AL30.phy
Gene partitions file for 98-ortholog alignment
Gene partitions file for 98-ortholog alignment
AlignmentAL30.txt
23-ortholog alignment
23-ortholog alignment of Arachnida, with at least 35 taxa represented for each gene.
AL35.phy
Gene partitions file for 23-ortholog alignment
Gene partitions file for 23-ortholog alignment
AlignmentAL35.txt
516-ortholog alignment from MAtrix REduction (MARE)
516-ortholog alignment from MAtrix REduction (MARE), retaining all 47 taxa
AL13MARE.phy
Gene partitions file for 516-ortholog MARE alignment
Gene partitions file for 516-ortholog MARE alignment
AlignmentMARE.txt
1237-ortholog alignment from MAtrix REduction (MARE)
1237-ortholog alignment with MAtrix REduction (MARE), retaining taxa with full genomes or Illumina libraries only
AL13MARE2.phy
Gene partitions file for 1237-ortholog MARE alignment
Gene partitions file for 1237-ortholog MARE alignment
AlignmentMARE2.txt
3644-ortholog alignment with data-rich terminals only
3644-ortholog alignment, retaining only terminals with full genomes or Illumina libraries
AL13_NGS.phy
100 slowest-evolving orthologs alignment
100-slowest-evolving orthologs alignment
G100.phy
Gene partitions file for 100 slowest-evolving orthologs
Gene partitions file for 100 slowest-evolving orthologs
AlignmentG100.txt
200 slowest-evolving orthologs alignment
200 slowest-evolving orthologs alignment
G200.phy
Gene partitions file for 200 slowest-evolving orthologs
Gene partitions file for 200 slowest-evolving orthologs
AlignmentG200.txt
300 slowest-evolving orthologs alignment
300 slowest-evolving orthologs alignment
G300.phy
Gene partitions file for 300 slowest-evolving orthologs
Gene partitions file for 300 slowest-evolving orthologs
AlignmentG300.txt
400 slowest-evolving orthologs alignment
400 slowest-evolving orthologs alignment
G400.phy
Gene partitions file for 400 slowest-evolving orthologs
Gene partitions file for 400 slowest-evolving orthologs
AlignmentG400.txt
500 slowest-evolving orthologs alignment
500 slowest-evolving orthologs alignment
G500.phy
Gene partitions file for 500 slowest-evolving orthologs
Gene partitions file for 500 slowest-evolving orthologs
AlignmentG500.txt
600 slowest-evolving orthologs alignment
600 slowest-evolving orthologs alignment
G600.phy
Gene partitions file for 600 slowest-evolving orthologs
Gene partitions file for 600 slowest-evolving orthologs
AlignmentG600.txt
700 slowest-evolving orthologs alignment
700 slowest-evolving orthologs alignment
G700.phy
Gene partitions file for 700 slowest-evolving orthologs
Gene partitions file for 700 slowest-evolving orthologs
AlignmentG700.txt
800 slowest-evolving orthologs alignment
800 slowest-evolving orthologs alignment
G800.phy
Gene partitions file for 800 slowest-evolving orthologs
Gene partitions file for 800 slowest-evolving orthologs
AlignmentG800.txt
900 slowest-evolving orthologs alignment
900 slowest-evolving orthologs alignment
G900.phy
Gene partitions file for 900 slowest-evolving orthologs
Gene partitions file for 900 slowest-evolving orthologs
AlignmentG900.txt
1000 slowest-evolving orthologs alignment
1000 slowest-evolving orthologs alignment
G1000.phy
Gene partitions file for 1000 slowest-evolving orthologs
AlignmentG1000.txt
1500 slowest-evolving orthologs alignment
1500 slowest-evolving orthologs alignment
G1500.phy
Gene partitions file for 1500 slowest-evolving orthologs
Gene partitions file for 1500 slowest-evolving orthologs
AlignmentG1500.txt
2000 slowest-evolving orthologs alignment
2000 slowest-evolving orthologs alignment
G2000.phy
Gene partitions file for 2000 slowest-evolving orthologs
Gene partitions file for 2000 slowest-evolving orthologs
AlignmentG2000.txt
2500 slowest-evolving orthologs alignment
2500 slowest-evolving orthologs alignment
G2500.phy
3000 slowest-evolving orthologs alignment
3000 slowest-evolving orthologs alignment
G3000.phy
Gene partitions file for 2500 slowest-evolving orthologs
Gene partitions file for 2500 slowest-evolving orthologs
AlignmentG2500.txt
Gene partitions file for 3000 slowest-evolving orthologs
Gene partitions file for 3000 slowest-evolving orthologs
AlignmentG3000.txt
3500 slowest-evolving orthologs alignment
3500 slowest-evolving orthologs alignment
G3500.phy
Gene partitions file for 3500 slowest-evolving orthologs
Gene partitions file for 3500 slowest-evolving orthologs
AlignmentG3500.txt
Alipes grandidieri Trinity assembly
Alipes grandidieri (Chilopoda: Scolopendromorpha) Trinity assembly
Alipes.fasta
Centruroides vittatus Trinity assembly
Centruroides vittatus (Chelicerata: Scorpiones) Trinity assembly
Centruroides.fasta
Damon variegatus Trinity assembly
Damon variegatus (Chelicerata: Amblypygi) Trinity assembly
Damon.fasta
Eremobates sp. Trinity assembly
Eremobates sp. (Chelicerata: Solifugae) Trinity assembly
Eremobates.fasta
Frontinella communis Trinity assembly
Frontinella communes (Chelicerata: Araneae) Trinity assembly
Frontinella.fasta
Hesperonemastoma modestum Trinity assembly
Hesperonemastoma modestum (Chelicerata: Opiliones) Trinity assembly
Hesperonemastoma.fasta
Larifuga capensis Trinity assembly
Larifuga capensis (Chelicerata: Opiliones) Trinity assembly
Larifuga.fasta
Leiobunum verrucosum Trinity assembly
Leiobunum verrucosum (Chelicerata: Opiliones) Trinity assembly
Leiobunum.fasta
Leucage venusta Trinity assembly
Leucage venusta (Chelicerata: Opiliones) Trinity assembly
Leucage.fasta
Limulus polyphemus Trinity assembly
Limulus polyphemus (Chelicerata: Xiphosura) Trinity assembly
Limulus.fasta
Liphistius malayanus Trinity assembly
Liphistius malayanus (Chelicerata: Araneae) Trinity assembly
Liphistius.fasta
Mastigoproctus giganteus Trinity assembly
Mastigoproctus giantess (Chelicerata: Uropygi) Trinity assembly
Mastigoproctus.fasta
Metabiantes sp. Trinity assembly
Metabiantes sp. (Chelicerata: Opiliones) Trinity assembly
Metabiantes.fasta
Metasiro americanus Trinity assembly
Metasiro americanus (Chelicerata: Opiliones) Trinity assembly
Metasiro.fasta
Neoscona arabesca Trinity assembly
Neoscona arabesca (Chelicerata: Araneae) Trinity assembly
Neoscona.fasta
Ortholasma coronadense Trinity assembly
Ortholasma corona dense (Chelicerata: Opiliones) Trinity assembly
Ortho.fasta
Pachylicus acutus Trinity assembly
Pachylicus acutus (Chelicerata: Opiliones) Trinity assembly
Pachylicus.fasta
Peripatopsis capensis Trinity assembly
Peripatopsis capensis (Onychophora: Peripatopsidae) Trinity assembly
Peripatopsis2.fasta
Phalangium opilio Trinity assembly
Phalangium opilio (Chelicerata: Opiliones) Trinity assembly
Phalangium.fasta
Protolophus singularis Trinity assembly
Protolophus singulars (Chelicerata: Opiliones) Trinity assembly
Protolophus.fasta
Pseudocellus sp. Trinity assembly
Pseudocellus sp. (Chelicerata: Ricinulei) Trinity assembly
Pseudocellus.fasta
Sclerobunus nondimorphicus Trinity assembly
Sclerobunus nondimorphicus (Chelicerata: Opiliones) Trinity assembly
Sclerobunus.fasta
Ricinoides atewa Trinity assembly
Ricinoides atewa (Chelicerata: Ricinulei) Trinity assembly
Ricinoides.fasta
Siro boyerae Trinity assembly
Siro boyerae (Chelicerata: Opiliones) Trinity assembly
Siro.fasta
Sitalcina lobata Trinity assembly
Sitalcina lobata (Chelicerata: Opiliones) Trinity assembly
Sitalcina.fasta
Synsphyronus apimelus Trinity assembly
Synsphyronus apimelus (Chelicerata: Pseudoscorpiones) Trinity assembly
Synsphyronus.fasta
Trogulus martensi Trinity assembly
Trogulus martensi (Chelicerata: Opiliones) Trinity assembly
Trogulus.fasta
Vonones ornata Trinity assembly
Vonones ornate (Chelicerata: Opiliones) Trinity assembly
Vonones.fasta