DOI: 10.5061/dryad.870n1qj
title: Data from: Phylogenetic systematics and evolution of the spider infraorder Mygalomorphae using genomic scale data

description: The Infraorder Mygalomorphae is one of the three main lineages of spiders
 comprising over 3,000 nominal species. This ancient group has a world-wide
 distribution that includes among its ranks large and charismatic taxa such
 as tarantulas, trapdoor spiders, and highly venomous funnel web spiders.
 Based on past molecular studies using Sanger-sequencing approaches,
 numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae,
 Cyrtaucheniidae, Dipluridae and Nemesiidae) have been identified as
 non-monophyletic. However, these data were unable to sufficiently resolve
 the higher-level (intra- and interfamilial) relationships such that the
 necessary changes in classification could be made with confidence. Here we
 present a comprehensive phylogenomic treatment of the spider infraorder
 Mygalomorphae. We employ 472 loci obtained through anchored hybrid
 enrichment to reconstruct relationships among all the mygalomorph spider
 families and estimate the timeframe of their diversification. We sampled
 nearly all currently recognized families, which has allowed us to assess
 their status, and as a result, propose a new classification scheme. Our
 generic-level sampling has also provided an evolutionary framework for
 revisiting questions regarding silk use in mygalomorph spiders. The first
 such analysis for the group within a strict phylogenetic framework shows
 that a sheet web is likely the plesiomorphic condition for mygalomorphs,
 as well as providing insights to the ancestral foraging behavior for all
 spiders. Our divergence time estimates, concomitant with detailed
 biogeographic analysis, suggest that both ancient continental-level
 vicariance and more recent dispersal events have played an important role
 in shaping modern day distributional patterns. Based on our results, we
 relimit the generic composition of the Ctenizidae, Cyrtaucheniidae,
 Dipluridae and Nemesiidae. We also elevate five subfamilies to family
 rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW
 RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families
 Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae
 (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly
 proposed. Such a major rearrangement in classification, recognizing nine
 newly established family-level rank taxa, is the largest the group has
 seen in over three decades.
description: Opatova_et_at_2019_supplementary_materialTables Table S1: Specimen locality data Table S2: Specimens used in the combined analyses of genomic and transcriptomic data (DNAAA_matrix). Table S3: Character coding for web type ancestral state reconstruction Figures Supplemental Figure 1. Tree topology obtained in maximum likelihood (ML) analyses conducted in RAxML. Supplemental Figure 2. Tree topology obtained in Bayesian inference (BI) analyses conducted in ExaBayes. Supplemental Figure 3. Tree topology obtained in maximum likelihood (ML) analyses conducted in IQ-TREE. Supplemental Figure 4. Phylogenetic tree inferred after removal of Paratropididae terminals (“No_Paratropis” dataset). Supplemental Figure 5. Tree topology obtained in species tree analysis conducted in ASTRAL. Supplemental Figure 6. Comparison of resulting tree topologies obtained by concatenated analyses conducted in RAxML and ExaBayes and species tree approach conducted in ASTRAL. Supplemental Figure 7. Divergence time estimates of mygalomorph spiders inferred by treePL with placement of the calibrations. Supplemental Figure 8. Divergence time estimates of mygalomorph spiders inferred by treePL with the confidence intervals. Supplemental Figure 9. Phylogenetic tree of Mygalomorphae with current classification scheme (World Spider Catalog 2019). Data Matrices and Input Files RASP_ingroup.tre_dis.csv RAxML_DNAAA.nex RAxML_DNAAA_partitions.txt RAxML_ExaBayes_all_taxa.nex RAxML_ExaBayes_all_taxa_partitions.txt RAxML_No_Paratropis.nex RAxML_No_Paratropis_partitions.txt Tree Files ASTRAL_all_taxa.tre ASTRAL_all_taxa.trees ExaBayes_all_taxa.tre RAxML_DNAAA.tre RAxML_No_Paratropis.tre RAxML_all_taxa.tre treePL_boot_dated.tre Sequence Files Sequences per locus: L1 - L556 (472 loci), sequences before MAFFT alignment and ALISCORE/ALICUT treatment