Data from: Phylogenomic interrogation of Arachnida reveals systemic conflicts in phylogenetic signal
Data files
Nov 07, 2014 version files 3.01 GB
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AL13_47.phy
85.22 MB
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AL13_NGS.phy
51.93 MB
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AL13MARE.phy
9.21 MB
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AL13MARE2.phy
15.69 MB
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AL15.phy
67.41 MB
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AL20.phy
23.52 MB
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AL25.phy
3.80 MB
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AL30.phy
1.25 MB
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AL35.phy
303.88 KB
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AlignmentAL13.txt
129.31 KB
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AlignmentAL15.txt
98.16 KB
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AlignmentAL20.txt
39.84 KB
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AlignmentAL25.txt
12.08 KB
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AlignmentAL30.txt
3.19 KB
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AlignmentAL35.txt
717 B
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AlignmentG100.txt
3.25 KB
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AlignmentG1000.txt
34.50 KB
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AlignmentG1500.txt
52.09 KB
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AlignmentG200.txt
6.59 KB
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AlignmentG2000.txt
69.71 KB
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AlignmentG2500.txt
87.36 KB
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AlignmentG300.txt
9.91 KB
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AlignmentG3000.txt
105.41 KB
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AlignmentG3500.txt
124.15 KB
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AlignmentG400.txt
13.41 KB
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AlignmentG500.txt
16.93 KB
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AlignmentG600.txt
20.44 KB
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AlignmentG700.txt
23.96 KB
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AlignmentG800.txt
27.47 KB
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AlignmentG900.txt
30.99 KB
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AlignmentMARE.txt
14.23 KB
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AlignmentMARE2.txt
35.28 KB
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Alipes.fasta
87.74 MB
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Centruroides.fasta
6.16 MB
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Damon.fasta
38.05 MB
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Eremobates.fasta
60.61 MB
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Frontinella.fasta
125.76 MB
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G100.phy
2.14 MB
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G1000.phy
27.47 MB
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G1500.phy
41.60 MB
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G200.phy
4.51 MB
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G2000.phy
54.91 MB
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G2500.phy
67.42 MB
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G300.phy
7.28 MB
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G3000.phy
79.37 MB
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G3500.phy
90.19 MB
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G400.phy
10.03 MB
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G500.phy
12.93 MB
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G600.phy
15.94 MB
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G700.phy
18.70 MB
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G800.phy
21.84 MB
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G900.phy
24.65 MB
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Hesperonemastoma.fasta
73.50 MB
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Larifuga.fasta
74.22 MB
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Leiobunum.fasta
62.26 MB
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Leucage.fasta
171.65 MB
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Limulus.fasta
96.33 MB
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Liphistius.fasta
40.54 MB
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Mastigoproctus.fasta
80.19 MB
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Metabiantes.fasta
106.01 MB
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Metasiro.fasta
55.70 MB
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Neoscona.fasta
118 MB
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Ortho.fasta
76.14 MB
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Pachylicus.fasta
56.65 MB
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Peripatopsis2.fasta
46.68 MB
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Phalangium.fasta
97.71 MB
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Protolophus.fasta
239.84 MB
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Pseudocellus.fasta
14.53 MB
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Ricinoides.fasta
67.62 MB
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Sclerobunus.fasta
86.41 MB
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Siro.fasta
38.41 MB
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Sitalcina.fasta
80.13 MB
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Synsphyronus.fasta
80.61 MB
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Trogulus.fasta
67.56 MB
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Vonones.fasta
121.07 MB
Abstract
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).