DOI: 10.5061/dryad.5027d
title: Data from: Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life

description: Background: Despite considerable effort, progress in spider molecular
 systematics has lagged behind many other comparable arthropod groups,
 thereby hindering family-level resolution, classification, and testing of
 important macroevolutionary hypotheses. Recently, alternative targeted
 sequence capture techniques have provided molecular systematics a powerful
 tool for resolving relationships across the Tree of Life. One of these
 approaches, Anchored Hybrid Enrichment (AHE), is designed to recover
 hundreds of unique orthologous loci from across the genome, for resolving
 both shallow and deep-scale evolutionary relationships within non-model
 systems. Herein we present a modification of the AHE approach that expands
 its use for application in spiders, with a particular emphasis on the
 infraorder Mygalomorphae. Results: Our aim was to design a set of probes
 that effectively capture loci informative at a diversity of phylogenetic
 timescales. Following identification of putative arthropod-wide loci, we
 utilized homologous transcriptome sequences from 17 species across all
 spiders to identify exon boundaries. Conserved regions with variable
 flanking regions were then sought across the tick genome, three published
 araneomorph spider genomes, and raw genomic reads of two mygalomorph taxa.
 Following development of the 585 target loci in the Spider Probe Kit, we
 applied AHE across three taxonomic depths to evaluate performance:
 deep-level spider family relationships (33 taxa, 327 loci); family and
 generic relationships within the mygalomorph family Euctenizidae (25 taxa,
 403 loci); and species relationships in the North American tarantula genus
 Aphonopelma (83 taxa, 581 loci). At the deepest level, all three major
 spider lineages (the Mesothelae, Mygalomorphae, and Araneomorphae) were
 supported with high bootstrap support. Strong support was also found
 throughout the Euctenizidae, including generic relationships within the
 family and species relationships within the genus Aptostichus. As in the
 Euctenizidae, virtually identical topologies were inferred with high
 support throughout Aphonopelma. Conclusions: The Spider Probe Kit, the
 first implementation of AHE methodology in Class Arachnida, holds great
 promise for gathering the types and quantities of molecular data needed to
 accelerate an understanding of the spider Tree of Life by providing a
 mechanism whereby different researchers can confidently and effectively
 use the same loci for independent projects, yet allowing synthesis of data
 across independent research groups.
description: Araneae_lociAlignment files for the Araneae dataset (both .fasta & .phy)Araneae_treesAll tree files for RAxML and ASTRAL analyses of the Araneae datasetsEuctenizidae_lociAlignment files for the Euctenizidae dataset (both .fasta & .phy)Euctenizidae_treesAll tree files for RAxML and ASTRAL analyses of the Euctenizidae datasetsAphonopelma_lociAlignment files for the Aphonopelma dataset (both .fasta & .phy)Aphonopelma_treesAll tree files for RAxML and ASTRAL analyses of the Aphonopelma datasetsAraneae taxa nameslist of taxa names for those in the Araneae datasetsAraneae.txtEuctenizidae taxa nameslist of taxa names for those in the Euctenizidae datasetsEuctenizidae.txtAphonopelma taxa nameslist of taxa names for those in the Aphonopelma datasetsAphonopelma.txt