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.
RAxML, unpartitioned, combined data, 70% occupancy
Resulting phylogeny from the RAxML, unpartitioned, combined data, 70% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, unpartitioned, combined data, 70% occupancy
Phylip file for RAxML, unpartitioned, combined data, 70% occupancy analysis.
70per_nexus.phylip
RAxML, unpartitioned, combined data, 50% occupancy
Phylip file for the RAxML, unpartitioned, combined data, 50% occupancy analysis.
50per_nexus.phylip
RAxML, unpartitioned, combined data, 50% occupancy
Resulting phylogeny from the RAxML, unpartitioned, combined data, 50% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, unpartitioned, combined data, 25% occupancy
Phylip file for the RAxML, unpartitioned, combined data, 25% occupancy analysis.
25per_nexus.phylip
RAxML, unpartitioned, combined data, 25% occupancy
Resulting phylogeny from the RAxML, unpartitioned, combined data, 25% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, unpartitioned, UCE-only data, 70% occupancy
Phylip file for the RAxML, unpartitioned, UCE-only data, 70% occupancy analysis.
mafft-nexus-min-70per-taxa.phylip
RAxML, unpartitioned, UCE-only data, 70% occupancy
Resulting phylogeny from the RAxML, unpartitioned, UCE-only data, 70% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, unpartitioned, UCE-only data, 50% occupancy
Phylip file for the RAxML, unpartitioned, UCE-only data, 50% occupancy analysis.
mafft-nexus-min-50per-taxa.phylip
RAxML, unpartitioned, UCE-only data, 50% occupancy
Resulting phylogeny from the RAxML, unpartitioned, UCE-only data, 50% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, unpartitioned, UCE-only data, 25% occupancy
Phylip file for the RAxML, unpartitioned, UCE-only data, 25% occupancy analysis.
mafft-nexus-min-25per-taxa.phylip
RAxML, unpartitioned, UCE-only data, 25% occupancy
Resulting phylogeny from the RAxML, unpartitioned, UCE-only data, 25% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, unpartitioned, exon-only data, 70% occupancy
Phylip file for the RAxML, unpartitioned, exon-only data, 70% occupancy analysis.
mafft-nexus-min-70per-taxa.phylip
RAxML, unpartitioned, exon-only data, 70% occupancy
Resulting phylogeny from the RAxML, unpartitioned, exon-only data, 70% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, unpartitioned, exon-only data, 50% occupancy
Phylip file for the RAxML, unpartitioned, exon-only data, 50% occupancy analysis.
mafft-nexus-min-50per-taxa.phylip
RAxML, unpartitioned, exon-only data, 50% occupancy
Resulting phylogeny from the RAxML, unpartitioned, exon-only data, 50% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, unpartitioned, exon-only data, 25% occupancy
Phylip file for the RAxML, unpartitioned, exon-only data, 25% occupancy analysis.
mafft-nexus-min-25per-taxa.phylip
RAxML, unpartitioned, exon-only data, 25% occupancy
Resulting phylogeny from the RAxML, unpartitioned, exon-only data, 25% occupancy analysis.
RAxML_bipartitions_rename.tre
RAxML, partitioned, combined data, 70% occupancy
Partition file for the RAxML, partitioned, combined data, 70% occupancy analysis.
partition.txt
RAxML, partitioned, combined data, 70% occupancy
Resulting phylogeny from the RAxML, partitioned, combined data, 70% occupancy analysis.
RAxML_bipartitions.Combined_70_analysis.tre
RAxML, partitioned, combined data, 50% occupancy
Partition file for the RAxML, partitioned, combined data, 50% occupancy analysis.
partition.txt
RAxML, partitioned, combined data, 50% occupancy
Resulting phylogeny from the RAxML, partitioned, combined data, 50% occupancy analysis.
RAxML_bipartitions.Combined_50_analysis.tre
RAxML, partitioned, combined data, 25% occupancy
Partition file for the RAxML, partitioned, combined data, 25% occupancy analysis.
partition.txt
RAxML, partitioned, combined data, 25% occupancy
Resulting phylogeny from the RAxML, partitioned, combined data, 25% occupancy analysis.
RAxML_bipartitions.Combined_25_analysis.tre
RAxML, partitioned, UCE-only data, 70% occupancy
Partition file for the RAxML, partitioned, UCE-only data, 70% occupancy analysis.
partition.txt
RAxML, partitioned, UCE-only data, 70% occupancy
Resulting phylogeny from the RAxML, partitioned, UCE-only data, 70% occupancy analysis.
RAxML_bipartitions.UCE_70_analysis.tre
RAxML, partitioned, UCE-only data, 50% occupancy
Partition file for the RAxML, partitioned, UCE-only data, 50% occupancy analysis.
partition.txt
RAxML, partitioned, UCE-only data, 50% occupancy
Resulting phylogeny from the RAxML, partitioned, UCE-only data, 50% occupancy analysis.
RAxML_bipartitions.UCE_50_analysis.tre
RAxML, partitioned, UCE-only data, 25% occupancy
Phylip file for the RAxML, partitioned, UCE-only data, 25% occupancy analysis.
partition.txt
RAxML, partitioned, UCE-only data, 25% occupancy
Resulting phylogeny from the RAxML, partitioned, UCE-only data, 25% occupancy analysis.
RAxML_bipartitions.UCE_25_analysis.tre
RAxML, partitioned, exon-only data, 70% occupancy
Partition file for the RAxML, partitioned, exon-only data, 70% occupancy analysis.
partition.txt
RAxML, partitioned, exon-only data, 70% occupancy
Resulting phylogeny from the RAxML, partitioned, exon-only data, 70% occupancy analysis.
RAxML_bipartitions.Exon_70_analysis.tre
RAxML, partitioned, exon-only data, 50% occupancy
Partition file for the RAxML, partitioned, exon-only data, 50% occupancy analysis.
partition.txt
RAxML, partitioned, exon-only data, 50% occupancy
Resulting phylogeny from the RAxML, partitioned, exon-only data, 50% occupancy analysis.
RAxML_bipartitions.Exon_50_analysis.tre
RAxML, partitioned, exon-only data, 25% occupancy
Partition file for the RAxML, partitioned, exon-only data, 25% occupancy analysis.
partition.txt
RAxML, partitioned, exon-only data, 25% occupancy
Resulting phylogeny from the RAxML, partitioned, exon-only data, 25% occupancy analysis.
RAxML_bipartitions.Exon_25_analysis.tre
MrBayes, partitioned, combined data, 70% occupancy
Nexus file for the MrBayes, partitioned, combined data, 70% occupancy analysis.
Combined_70per_nexus.nex
MrBayes, partitioned, combined data, 70% occupancy
Resulting phylogeny from the MrBayes, partitioned, combined data, 70% occupancy analysis.
Combined_70per_nexus.nex.con.tre
MrBayes, partitioned, combined data, 50% occupancy
Nexus file for the MrBayes, partitioned, combined data, 50% occupancy analysis.
Combined_50per.nex
MrBayes, partitioned, combined data, 50% occupancy
Resulting phylogeny from the MrBayes, partitioned, combined data, 50% occupancy analysis.
Combined_50per.nex.con.tre
MrBayes, partitioned, combined data, 25% occupancy
Nexus file for the MrBayes, partitioned, combined data, 25% occupancy analysis.
Combined_25per_X.nex
MrBayes, partitioned, combined data, 25% occupancy
Resulting phylogeny from the MrBayes, partitioned, combined data, 25% occupancy analysis.
Combined_25per.nex.con_correctBurnIn40000.tre
MrBayes, partitioned, UCE-only data, 70% occupancy
Nexus file for the MrBayes, partitioned, UCE-only data, 70% occupancy analysis.
UCE_70per_taxa.nex
MrBayes, partitioned, UCE-only data, 70% occupancy
Resulting phylogeny from the MrBayes, partitioned, UCE-only data, 70% occupancy analysis.
UCE_70per_taxa.nex.con.tre
MrBayes, partitioned, UCE-only data, 50% occupancy
Nexus file for the MrBayes, partitioned, UCE-only data, 50% occupancy analysis.
UCE_50per.nex
MrBayes, partitioned, UCE-only data, 50% occupancy
Resulting phylogeny from the MrBayes, partitioned, UCE-only data, 50% occupancy analysis.
UCE_50per.nex.con.tre
MrBayes, partitioned, UCE-only data, 25% occupancy
Nexus file for the MrBayes, partitioned, UCE-only data, 25% occupancy analysis.
UCE_25per_X.nex
MrBayes, partitioned, UCE-only data, 25% occupancy
Resulting phylogeny from the MrBayes, partitioned, UCE-only data, 25% occupancy analysis.
UCE_25per.nex.con.tre
MrBayes, partitioned, exon-only data, 70% occupancy
Nexus file for the MrBayes, partitioned, exon-only data, 70% occupancy analysis.
Exon_70per_taxa_X.nex
MrBayes, partitioned, exon-only data, 70% occupancy
Resulting phylogeny from the MrBayes, partitioned, exon-only data, 70% occupancy analysis.
Exon_70per_taxa.nex.con.tre
MrBayes, partitioned, exon-only data, 50% occupancy
Nexus file for the MrBayes, partitioned, exon-only data, 50% occupancy analysis.
Exon_50per.nex
MrBayes, partitioned, exon-only data, 50% occupancy
Resulting phylogeny from the MrBayes, partitioned, exon-only data, 50% occupancy analysis.
Exon_50per.nex.con.tre
MrBayes, partitioned, exon-only data, 25% occupancy
Nexus file for the MrBayes, partitioned, exon-only data, 25% occupancy analysis.
Exon_25per_X.nex
MrBayes, partitioned, exon-only data, 25% occupancy
Resulting phylogeny from the MrBayes, partitioned, exon-only data, 25% occupancy analysis.
Exon_25per.nex.con.tre
Table 1 from manuscript
Use 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.xlsx
ASTRAL results, combined data, 70% occupancy
ASTRAL results, combined data, 70% occupancy
ASTRAL_results.tre
ASTRAL results, combined data, 50% occupancy
ASTRAL results, combined data, 50% occupancy
ASTRAL_results.tre
ASTRAL results, combined data, 25% occupancy
ASTRAL results, combined data, 25% occupancy
ASTRAL_results.tre
ASTRAL results, UCE-only data, 70% occupancy
ASTRAL results, UCE-only data, 70% occupancy
ASTRAL_results.tre
ASTRAL results, UCE-only data, 50% occupancy
ASTRAL results, UCE-only data, 50% occupancy
ASTRAL_results.tre
ASTRAL results, UCE-only data, 25% occupancy
ASTRAL results, UCE-only data, 25% occupancy
ASTRAL_results.tre
ASTRAL results, exon-only data, 70% occupancy
ASTRAL results, exon-only data, 70% occupancy
ASTRAL_results.tre
ASTRAL results, exon-only data, 50% occupancy
ASTRAL results, exon-only data, 50% occupancy
ASTRAL_results.tre
ASTRAL results, exon-only data, 25% occupancy
ASTRAL results, exon-only data, 25% occupancy
ASTRAL_results.tre