DOI: 10.5061/dryad.n0qr5
title: Data from: Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

description: Scorpions represent an iconic lineage of arthropods, historically renowned
 for their unique bauplan, ancient fossil record and venom potency. Yet,
 higher level relationships of scorpions, based exclusively on morphology,
 remain virtually untested, and no multilocus molecular phylogeny has been
 deployed heretofore towards assessing the basal tree topology. We applied
 a phylogenomic assessment to resolve scorpion phylogeny, for the first
 time, to our knowledge, sampling extensive molecular sequence data from
 all superfamilies and examining basal relationships with up to 5025 genes.
 Analyses of supermatrices as well as species tree approaches converged
 upon a robust basal topology of scorpions that is entirely at odds with
 traditional systematics and controverts previous understanding of scorpion
 evolutionary history. All analyses unanimously support a single origin of
 katoikogenic development, a form of parental investment wherein embryos
 are nurtured by direct connections to the parent's digestive system.
 Based on the phylogeny obtained herein, we propose the following
 systematic emendations: Caraboctonidae is transferred to Chactoidea new
 superfamilial assignment; superfamily Bothriuroidea revalidated is
 resurrected and Bothriuridae transferred therein; and Chaerilida and
 Pseudochactida are synonymized with Buthida new parvordinal synonymies.
description: Matrix
 1Supermatrix of 136
 orthologs and 26,337 sites. Occupancy: 93.0%. Criterion: At least 36 taxa
 present for every ortholog.Scor.AL36.phyPartitions file for Matrix 1Partitions file for Matrix 1.Alignment.AL36.txtMatrix 2Supermatrix of 599 orthologs and 128,842 sites. Occupancy: 86.9%. Criterion: At least 33 taxa present for every ortholog.Scor.AL33.phyPartitions file for Matrix 2Partitions file for Matrix 2.AlignmentAL33.txtMatrix 3Supermatrix of 1,557 orthologs and 346,260 sites. Occupancy: 80.1%. Criterion: At least 29 taxa present for every ortholog.Scor.AL29.phyPartitions file for Matrix 3Partitions file for Matrix 3.AlignmentAL29.txtMatrix 4Supermatrix of 5,025 orthologs and 1,113,796 sites. Occupancy: 64.2%. Criterion: At least 19 taxa present for every ortholog.Scor.AL19.phyPartitions file for Matrix 4Partitions file for Matrix 4.AlignmentAL19.txtMatrix 5Supermatrix of 131 orthologs and 41,615 sites. Occupancy: 81.0%. Criterion: Minimal compositional heterogeneity.Scor.CH.phyPartitions file for Matrix 5Partitions file for Matrix 5.AlignmentCH.txtMatrix 6Supermatrix of 453 orthologs and 98,370 sites. Occupancy: 87.1%. Criterion: MAtrix REduction (MARE) of ortholog set in Matrix 2.Scor.MARE1.phyPartitions file for Matrix 6Partitions file for Matrix 6.AlignmentMARE1.txtMatrix 7Supermatrix of 2,580 orthologs and 565,648 sites. Occupancy: 72.0%. Criterion: MAtrix REduction (MARE) of ortholog set in Matrix 4.Scor.MARE2.phyPartitions file for Matrix 7Partitions file for Matrix 7.AlignmentMARE2.txtMatrix 8Supermatrix of 500 orthologs and 118,851 sites. Occupancy: 81.1%. Criterion: Slowest-evolving (as measured by percent pairwise identity) tertile of ortholog set in Matrix 3.Scor.Slow.phyPartitions file for Matrix 8Partitions file for Matrix 8.AlignmentSlow.txtMatrix 9Supermatrix of 500 orthologs and 118,260 sites. Occupancy: 80.1%. Criterion: Middle tertile of evolutionary rate (as measured by percent pairwise identity) of ortholog set in Matrix 3.Scor.Mid.phyPartitions file for Matrix 9Partitions file for Matrix 9.AlignmentMid.txtMatrix 10Supermatrix of 577 orthologs and 109,149 sites. Occupancy: 78.5%. Criterion: Fastest-evolving (as measured by percent pairwise identity) tertile of ortholog set in Matrix 3.Scor.Fast.phyPartitions file for Matrix 10Partitions file for Matrix 10.AlignmentFast.txtMatrix 11Supermatrix of 67 orthologs and 13,540 sites. Occupancy: 92.7%. Criterion: Intersection of Matrix 1 and BUSCO-Ar data set.SCO.AL36.phyPartitions file for Matrix 11Partitions file for Matrix 11.Alignment.SCO.AL36.txtMatrix 12Supermatrix of 280 orthologs and 63,274 sites. Occupancy: 86.9%. Criterion: Intersection of Matrix 2 and BUSCO-Ar data set.SCO.AL33.phyPartitions file for Matrix 12Partitions file for Matrix 12.Alignment.SCO.AL33.txtMatrix 13Supermatrix of 689 orthologs and 162,067 sites. Occupancy: 80.4%. Criterion: Intersection of Matrix 3 and BUSCO-Ar data set.SCO.AL29.phyPartitions file for Matrix 13Partitions file for Matrix 13.Alignment.SCO.AL29.txtMatrix 14Supermatrix of 1,725 orthologs and 421,446 sites. Occupancy: 66.4%. Criterion: Intersection of Matrix 4 and BUSCO-Ar data set.SCO.AL19.phyPartitions file for Matrix 14Partitions file for Matrix 14.Alignment.SCO.AL19.txt