DOI: 10.5061/dryad.387c58v
title: Data from: Next-generation museum genomics: phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea)

description: Historical museum specimens are invaluable for morphological and taxonomic
 research, but typically the DNA is degraded making traditional sequencing
 techniques difficult to impossible for many specimens. Recent advances in
 Next-Generation Sequencing, specifically target capture, makes use of
 short fragment sizes typical of degraded DNA, opening up the possibilities
 for gathering genomic data from museum specimens. This study uses museum
 specimens and recent target capture sequencing techniques to sequence both
 Ultra-Conserved Elements (UCE) and exonic regions for lineages that span
 the modern spiders, Araneomorphae, with a focus on Palpimanoidea. While
 many previous studies have used target capture techniques on dried museum
 specimens (for example, skins, pinned insects), this study includes
 specimens that were collected over the last two decades and stored in 70%
 ethanol at room temperature. Our findings support the utility of target
 capture methods for examining deep relationships within Araneomorphae:
 sequences from both UCE and exonic loci were important for resolving
 relationships; a monophyletic Palpimanoidea was recovered in many analyses
 and there was strong support for family and generic-level palpimanoid
 relationships. Ancestral character state reconstructions reveal that the
 highly modified carapace observed in mecysmaucheniids and archaeids has
 evolved independently.
description: RAxML, unpartitioned,
 combined data, 70% occupancyResulting phylogeny from
 the RAxML, unpartitioned, combined data, 70% occupancy
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UCE-only data, 70% occupancyResulting phylogeny from the RAxML, unpartitioned, UCE-only data, 70% occupancy analysis.RAxML_bipartitions_rename.treRAxML, unpartitioned, UCE-only data, 50% occupancyPhylip file for the RAxML, unpartitioned, UCE-only data, 50% occupancy analysis.mafft-nexus-min-50per-taxa.phylipRAxML, unpartitioned, UCE-only data, 50% occupancyResulting phylogeny from the RAxML, unpartitioned, UCE-only data, 50% occupancy analysis.RAxML_bipartitions_rename.treRAxML, unpartitioned, UCE-only data, 25% occupancyPhylip file for the RAxML, unpartitioned, UCE-only data, 25% occupancy analysis.mafft-nexus-min-25per-taxa.phylipRAxML, unpartitioned, UCE-only data, 25% occupancyResulting phylogeny from the RAxML, unpartitioned, UCE-only data, 25% occupancy analysis.RAxML_bipartitions_rename.treRAxML, unpartitioned, exon-only data, 70% occupancyPhylip file for the RAxML, unpartitioned, exon-only data, 70% occupancy analysis.mafft-nexus-min-70per-taxa.phylipRAxML, unpartitioned, exon-only data, 70% occupancyResulting phylogeny from the RAxML, unpartitioned, exon-only data, 70% occupancy analysis.RAxML_bipartitions_rename.treRAxML, unpartitioned, exon-only data, 50% occupancyPhylip file for the RAxML, unpartitioned, exon-only data, 50% occupancy analysis.mafft-nexus-min-50per-taxa.phylipRAxML, unpartitioned, exon-only data, 50% occupancyResulting phylogeny from the RAxML, unpartitioned, exon-only data, 50% occupancy analysis.RAxML_bipartitions_rename.treRAxML, unpartitioned, exon-only data, 25% occupancyPhylip file for the RAxML, unpartitioned, exon-only data, 25% occupancy analysis.mafft-nexus-min-25per-taxa.phylipRAxML, unpartitioned, exon-only data, 25% occupancyResulting phylogeny from the RAxML, unpartitioned, exon-only data, 25% occupancy analysis.RAxML_bipartitions_rename.treRAxML, partitioned, combined data, 70% occupancyPartition file for the RAxML, partitioned, combined data, 70% occupancy analysis.partition.txtRAxML, partitioned, combined data, 70% occupancyResulting phylogeny from the RAxML, partitioned, combined data, 70% occupancy analysis.RAxML_bipartitions.Combined_70_analysis.treRAxML, partitioned, combined data, 50% occupancyPartition file for the RAxML, partitioned, combined data, 50% occupancy analysis.partition.txtRAxML, partitioned, combined data, 50% occupancyResulting phylogeny from the RAxML, partitioned, combined data, 50% occupancy analysis.RAxML_bipartitions.Combined_50_analysis.treRAxML, partitioned, combined data, 25% occupancyPartition file for the RAxML, partitioned, combined data, 25% occupancy analysis.partition.txtRAxML, partitioned, combined data, 25% occupancyResulting phylogeny from the RAxML, partitioned, combined data, 25% occupancy analysis.RAxML_bipartitions.Combined_25_analysis.treRAxML, partitioned, UCE-only data, 70% occupancyPartition file for the RAxML, partitioned, UCE-only data, 70% occupancy analysis.partition.txtRAxML, partitioned, UCE-only data, 70% occupancyResulting phylogeny from the RAxML, partitioned, UCE-only data, 70% occupancy analysis.RAxML_bipartitions.UCE_70_analysis.treRAxML, partitioned, UCE-only data, 50% occupancyPartition file for the RAxML, partitioned, UCE-only data, 50% occupancy analysis.partition.txtRAxML, partitioned, UCE-only data, 50% occupancyResulting phylogeny from the RAxML, partitioned, UCE-only data, 50% occupancy analysis.RAxML_bipartitions.UCE_50_analysis.treRAxML, partitioned, UCE-only data, 25% occupancyPhylip file for the RAxML, partitioned, UCE-only data, 25% occupancy analysis.partition.txtRAxML, partitioned, UCE-only data, 25% occupancyResulting phylogeny from the RAxML, partitioned, UCE-only data, 25% occupancy analysis.RAxML_bipartitions.UCE_25_analysis.treRAxML, partitioned, exon-only data, 70% occupancyPartition file for the RAxML, partitioned, exon-only data, 70% occupancy analysis.partition.txtRAxML, partitioned, exon-only data, 70% occupancyResulting phylogeny from the RAxML, partitioned, exon-only data, 70% occupancy analysis.RAxML_bipartitions.Exon_70_analysis.treRAxML, partitioned, exon-only data, 50% occupancyPartition file for the RAxML, partitioned, exon-only data, 50% occupancy analysis.partition.txtRAxML, partitioned, exon-only data, 50% occupancyResulting phylogeny from the RAxML, partitioned, exon-only data, 50% occupancy analysis.RAxML_bipartitions.Exon_50_analysis.treRAxML, partitioned, exon-only data, 25% occupancyPartition file for the RAxML, partitioned, exon-only data, 25% occupancy analysis.partition.txtRAxML, partitioned, exon-only data, 25% occupancyResulting phylogeny from the RAxML, partitioned, exon-only data, 25% occupancy analysis.RAxML_bipartitions.Exon_25_analysis.treMrBayes, partitioned, combined data, 70% occupancyNexus file for the MrBayes, partitioned, combined data, 70% occupancy analysis.Combined_70per_nexus.nexMrBayes, partitioned, combined data, 70% occupancyResulting phylogeny from the MrBayes, partitioned, combined data, 70% occupancy analysis.Combined_70per_nexus.nex.con.treMrBayes, partitioned, combined data, 50% occupancyNexus file for the MrBayes, partitioned, combined data, 50% occupancy analysis.Combined_50per.nexMrBayes, partitioned, combined data, 50% occupancyResulting phylogeny from the MrBayes, partitioned, combined data, 50% occupancy analysis.Combined_50per.nex.con.treMrBayes, partitioned, combined data, 25% occupancyNexus file for the MrBayes, partitioned, combined data, 25% occupancy analysis.Combined_25per_X.nexMrBayes, partitioned, combined data, 25% occupancyResulting phylogeny from the MrBayes, partitioned, combined data, 25% occupancy analysis.Combined_25per.nex.con_correctBurnIn40000.treMrBayes, partitioned, UCE-only data, 70% occupancyNexus file for the MrBayes, partitioned, UCE-only data, 70% occupancy analysis.UCE_70per_taxa.nexMrBayes, partitioned, UCE-only data, 70% occupancyResulting phylogeny from the MrBayes, partitioned, UCE-only data, 70% occupancy analysis.UCE_70per_taxa.nex.con.treMrBayes, partitioned, UCE-only data, 50% occupancyNexus file for the MrBayes, partitioned, UCE-only data, 50% occupancy analysis.UCE_50per.nexMrBayes, partitioned, UCE-only data, 50% occupancyResulting phylogeny from the MrBayes, partitioned, UCE-only data, 50% occupancy analysis.UCE_50per.nex.con.treMrBayes, partitioned, UCE-only data, 25% occupancyNexus file for the MrBayes, partitioned, UCE-only data, 25% occupancy analysis.UCE_25per_X.nexMrBayes, partitioned, UCE-only data, 25% occupancyResulting phylogeny from the MrBayes, partitioned, UCE-only data, 25% occupancy analysis.UCE_25per.nex.con.treMrBayes, partitioned, exon-only data, 70% occupancyNexus file for the MrBayes, partitioned, exon-only data, 70% occupancy analysis.Exon_70per_taxa_X.nexMrBayes, partitioned, exon-only data, 70% occupancyResulting phylogeny from the MrBayes, partitioned, exon-only data, 70% occupancy analysis.Exon_70per_taxa.nex.con.treMrBayes, partitioned, exon-only data, 50% occupancyNexus file for the MrBayes, partitioned, exon-only data, 50% occupancy analysis.Exon_50per.nexMrBayes, partitioned, exon-only data, 50% occupancyResulting phylogeny from the MrBayes, partitioned, exon-only data, 50% occupancy analysis.Exon_50per.nex.con.treMrBayes, partitioned, exon-only data, 25% occupancyNexus file for the MrBayes, partitioned, exon-only data, 25% occupancy analysis.Exon_25per_X.nexMrBayes, partitioned, exon-only data, 25% occupancyResulting phylogeny from the MrBayes, partitioned, exon-only data, 25% occupancy analysis.Exon_25per.nex.con.treTable 1 from manuscriptUse this table to relate tip labels to genus and species names in the phylogeny files that were uploaded to Dryad. In all uploaded phylogeny files the tree needs to be rooted with the clade containing the Hypochilidae, Filistatidae, and Synspermiata specimens.Table 1_v5_NCBI_accession.xlsxASTRAL results, combined data, 70% occupancyASTRAL results, combined data, 70% occupancyASTRAL_results.treASTRAL results, combined data, 50% occupancyASTRAL results, combined data, 50% occupancyASTRAL_results.treASTRAL results, combined data, 25% occupancyASTRAL results, combined data, 25% occupancyASTRAL_results.treASTRAL results, UCE-only data, 70% occupancyASTRAL results, UCE-only data, 70% occupancyASTRAL_results.treASTRAL results, UCE-only data, 50% occupancyASTRAL results, UCE-only data, 50% occupancyASTRAL_results.treASTRAL results, UCE-only data, 25% occupancyASTRAL results, UCE-only data, 25% occupancyASTRAL_results.treASTRAL results, exon-only data, 70% occupancyASTRAL results, exon-only data, 70% occupancyASTRAL_results.treASTRAL results, exon-only data, 50% occupancyASTRAL results, exon-only data, 50% occupancyASTRAL_results.treASTRAL results, exon-only data, 25% occupancyASTRAL results, exon-only data, 25% occupancyASTRAL_results.tre