DOI: 10.5061/dryad.34tmpg4kv
title: Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies

description: Resource specialization and host-associated genetic differentiation (HAD)
 are frequently invoked as an explanation for the high diversity of
 plant-feeding insects and other organisms with a parasitic lifestyle.
 While genetic studies have demonstrated numerous examples of HAD in insect
 herbivores, the general rarity of comparative studies means that we still
 lack an understanding of how deterministic HAD is, and whether patterns of
 host shifts can be predicted over evolutionary time scales. We applied
 genome-wide SNP data obtained through low-coverage genome resequencing to
 define species limits and to compare host-plant use in population samples
 of leaf- and bud-galling sawflies collected from seven shared willow
 (Salix) host species. To infer the repeatability of long-term
 cophylogenetic patterns, we also contrasted the phylogenies of the two
 galler groups with each other as well as with the phylogeny of their Salix
 hosts estimated based on RADseq data. We found clear evidence for host
 specialization and HAD in both of the focal galler groups, but also that
 leaf gallers are more specialized to single host species than are most bud
 gallers. In contrast to bud gallers, leaf gallers also exhibit
 statistically significant cophylogenetic signal with their Salix hosts.
 The observed discordant patterns of resource specialization and long-term
 host use in two related galler groups that have radiated in parallel
 across a shared resource base indicate a general lack of evolutionary
 repeatability and suggest that short- and long-term host use and
 ecological diversification in plant-feeding insects are dominated by
 stochasticity and/or lineage-specific effects.
description: Contained in this dataset are the three filtered VCF files, two
 tree files for the cophylogenetic analysis, an example script using the
 combined VCF file and the metadata. 
 Bud_galler_Vs_own = Bud galler samples mapped to the
 <em>Euura lappo</em> reference genome followed by variant
 calling. Leaf_galler_Vs_own = Leaf galler samples
 mapped to the <em>Eupontania</em>
 <em>aestiva</em> reference genome followed by variant
 calling. Bud_and_Leaf_gallers_Vs_bud_reference = Bud
 and leaf galler samples mapped to the <em>Euura</em>
 <em>lappo</em> reference genome followed by variant
 calling. Salix_concatRADloci.phy = phylip file
 containing the concatenated <em>Salix</em> RAD loci
 Galler_raxml_tree = The galler raxml tree used for the
 cophylogenetic analysis. Salix_raxml_tree = Salix
 tree used for the cophylogenetic analysis.
 ALL_Galler_MT_Concat.phy = Phylip alignment of concatendated
 mitochondrial genes.
 Galler_mtDNA_data_for_Arlequin.arp = Mitochondrial gene data for
 use in Arlequin.
 Statistical-analysis-Clustering_and_cophylogeny = Script used to
 perform the DAPC and sNMF analysis. Additionally, contains the script for
 the PACo cophylogenetic analysis based on
 the Bud_and_Leaf_gallers_Vs_bud_reference.vcf file.
 Metadata.txt = A comma-delimited file with the metadata for the
 combined galler dataset.