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.
Matrix 1
Supermatrix of 136 orthologs and 26,337 sites. Occupancy: 93.0%. Criterion: At least 36 taxa present for every ortholog.
Scor.AL36.phy
Partitions file for Matrix 1
Partitions file for Matrix 1.
Alignment.AL36.txt
Matrix 2
Supermatrix of 599 orthologs and 128,842 sites. Occupancy: 86.9%. Criterion: At least 33 taxa present for every ortholog.
Scor.AL33.phy
Partitions file for Matrix 2
Partitions file for Matrix 2.
AlignmentAL33.txt
Matrix 3
Supermatrix of 1,557 orthologs and 346,260 sites. Occupancy: 80.1%. Criterion: At least 29 taxa present for every ortholog.
Scor.AL29.phy
Partitions file for Matrix 3
Partitions file for Matrix 3.
AlignmentAL29.txt
Matrix 4
Supermatrix of 5,025 orthologs and 1,113,796 sites. Occupancy: 64.2%. Criterion: At least 19 taxa present for every ortholog.
Scor.AL19.phy
Partitions file for Matrix 4
Partitions file for Matrix 4.
AlignmentAL19.txt
Matrix 5
Supermatrix of 131 orthologs and 41,615 sites. Occupancy: 81.0%. Criterion: Minimal compositional heterogeneity.
Scor.CH.phy
Partitions file for Matrix 5
Partitions file for Matrix 5.
AlignmentCH.txt
Matrix 6
Supermatrix of 453 orthologs and 98,370 sites. Occupancy: 87.1%. Criterion: MAtrix REduction (MARE) of ortholog set in Matrix 2.
Scor.MARE1.phy
Partitions file for Matrix 6
Partitions file for Matrix 6.
AlignmentMARE1.txt
Matrix 7
Supermatrix of 2,580 orthologs and 565,648 sites. Occupancy: 72.0%. Criterion: MAtrix REduction (MARE) of ortholog set in Matrix 4.
Scor.MARE2.phy
Partitions file for Matrix 7
Partitions file for Matrix 7.
AlignmentMARE2.txt
Matrix 8
Supermatrix 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.phy
Partitions file for Matrix 8
Partitions file for Matrix 8.
AlignmentSlow.txt
Matrix 9
Supermatrix 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.phy
Partitions file for Matrix 9
Partitions file for Matrix 9.
AlignmentMid.txt
Matrix 10
Supermatrix 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.phy
Partitions file for Matrix 10
Partitions file for Matrix 10.
AlignmentFast.txt
Matrix 11
Supermatrix of 67 orthologs and 13,540 sites. Occupancy: 92.7%. Criterion: Intersection of Matrix 1 and BUSCO-Ar data set.
SCO.AL36.phy
Partitions file for Matrix 11
Partitions file for Matrix 11.
Alignment.SCO.AL36.txt
Matrix 12
Supermatrix of 280 orthologs and 63,274 sites. Occupancy: 86.9%. Criterion: Intersection of Matrix 2 and BUSCO-Ar data set.
SCO.AL33.phy
Partitions file for Matrix 12
Partitions file for Matrix 12.
Alignment.SCO.AL33.txt
Matrix 13
Supermatrix of 689 orthologs and 162,067 sites. Occupancy: 80.4%. Criterion: Intersection of Matrix 3 and BUSCO-Ar data set.
SCO.AL29.phy
Partitions file for Matrix 13
Partitions file for Matrix 13.
Alignment.SCO.AL29.txt
Matrix 14
Supermatrix of 1,725 orthologs and 421,446 sites. Occupancy: 66.4%. Criterion: Intersection of Matrix 4 and BUSCO-Ar data set.
SCO.AL19.phy
Partitions file for Matrix 14
Partitions file for Matrix 14.
Alignment.SCO.AL19.txt