DOI: 10.5061/dryad.ns1rn8q0r
title: Phylogenomic analysis of brachyuran crabs using transcriptome data reveals possible sources of conflicting phylogenetic relationships within the group

description: Despite extensive morphological and molecular studies, the phylogenetic
 interrelationships within the infraorder Brachyura and the phylogenetic
 positions of many taxa remain uncertain. Studies that used a limited
 number of molecular markers have often failed to provide sufficient
 resolution and may be susceptible to stochastic errors and incomplete
 lineage sorting (ILS). Here we reconstructed the phylogenetic
 relationships within the Brachyura using transcriptome data of 56
 brachyuran species, including 14 newly sequenced taxa. Five supermatrices
 were constructed in order to exclude different sources of systematic
 error. The results of the phylogenetic analyses indicate that
 Heterotremata is non-monophyletic and that the two Old World primary
 freshwater crabs (Potamidae and Gecarcinucidae) and the Hymenosomatoidea
 form a clade that is sister to the Thoracotremata, and outside the
 Heterotremata. We also found that ILS is the main cause of the gene-tree
 discordance of these freshwater crabs. Divergence time estimations
 indicate that the Brachyura has an ancient origin, probably either in the
 Triassic or Jurassic, and that the majority of extant families and
 superfamilies first appeared during the Cretaceous, with a constant
 increase of diversity in Post-Cretaceous-Palaeogene times. The results
 support the hypothesis that the two Old World freshwater crab families
 included in this study (Potamidae and Gecarcinucidae) diverged from their
 marine ancestors around 120 Ma, in the Cretaceous. In addition, this work
 provides new insights that may aid in the reclassification of some of the
 more problematic brachyuran groups.
description: # Phylogenomic analysis of brachyuran crabs using transcriptome data
 reveals possible sources of conflicting phylogenetic relationships within
 the group
 [https://doi.org/10.5061/dryad.ns1rn8q0r](https://doi.org/10.5061/dryad.ns1rn8q0r) ## Description of the data and file structure Aligned phylotranscriptomic supermatrices for brachyuran crabs. supermatrix_1.fasta: supermatrix 30OC, OGs with a minimum of 30% species occupancy. supermatrix_2.fasta: supermatrix 50OC, OGs with a minimum of 50% species occupancy. supermatrix_3.fasta: supermatrix 50OC_CH, best 200 OGs selected with BaCoCa. supermatrix_4.fasta: supermatrix 50OC_BLH, best 200 OGs selected with TRESPEX. supermatrix_5.fasta: supermatrix 50OC_PI, best 200 OGs selected with PhyDesign. ## Supplementary material Supplementary Figure S1. The 200 OGs with the highest values of phylogenetic informativeness from PhyDesign. Supplementary Figure S2. Tree obtained by ML analysis in IQ-TREE2 of supermatrix 30OC (LG model). Supplementary Figure S3. Tree obtained by ML analysis in IQ-TREE2 of supermatrix 30OC (PMSF model). Supplementary Figure S4. Tree obtained by coalescent approach in ASTRAL-III of supermatrix 50OC. Supplementary Figure S5. Tree obtained by ML analysis with partitioned as implemented in IQ-TREE2 of supermatrix 50OC. Supplementary Figure S6. Tree obtained by ML analysis in IQ-TREE2 of supermatrix 50OC (PMSF model). Supplementary Figure S7. Tree obtained by BI analysis in Exabayes of supermatrix 50OC. Supplementary Figure S8. Tree obtained by coalescent approach in ASTRAL-III of supermatrix 50OC_CH. Supplementary Figure S9. Tree obtained by ML analysis with partitioned as implemented in IQ-TREE2 of supermatrix 50OC_CH. Supplementary Figure S10. Tree obtained by ML analysis in IQ-TREE2 of supermatrix 50OC_CH (PMSF model). Supplementary Figure S11. Tree obtained by BI analysis in Exabayes of supermatrix 50OC_CH. Supplementary Figure S12. Tree obtained by coalescent approach in ASTRAL-III of supermatrix 50OC_BLH. Supplementary Figure S13. Tree obtained by ML analysis with partitioned as implemented in IQ-TREE2 of supermatrix 50OC_BLH. Supplementary Figure S14. Tree obtained by ML analysis in IQ-TREE2 of supermatrix 50OC_BLH (PMSF model). Supplementary Figure S15. Tree obtained by BI analysis in Exabayes of supermatrix 50OC_BLH. Supplementary Figure S16. Tree obtained by coalescent approach in ASTRAL-III of supermatrix 50OC_PI. Supplementary Figure S17. Tree obtained by ML analysis with partitioned as implemented in IQ-TREE2 of supermatrix 50OC_PI. Supplementary Figure S18. Tree obtained by ML analysis in IQ-TREE2 of supermatrix 50OC_PI (PMSF model). Supplementary Figure S19. Tree obtained by BI analysis in Exabayes of supermatrix 50OC_PI. Supplementary Figure S20. Schematic diagrams showing phylogenetic relationships of superfamilies within Brachyura in all 18 phylogenetic trees reconstructed in this study. Supplementary Figure S21. The ancestral state reconstruction of Eubrachyura from RASP. Pie charts at nodes represent ancestral state estimations and node numbers are shown inside. Two types of gonopore positions are defined: thoracotreme-type gonopore position (red) and heterotreme-type gonopore position (blue). Supplementary Table S1. Details for all 56 transcriptomes. Supplementary Table S2. The number of OGs and minimum proportion occupancy species of ortholog inferences. Supplementary Table S3. RCFV value, maximum net phylogenetic informativeness, and long branch score heterogeneity of each OG. Supplementary Table S4. Detail of missingness in each supermatrix. Supplementary Table S5. Details of fossil calibrations across the outgroup and Brachyura.