Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies

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..., , 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 Euura lappo reference genome followed by variant calling.
Leaf_galler_Vs_own = Leaf galler samples mapped to the Eupontania aestiva reference genome followed by variant calling.
Bud_and_Leaf_gallers_Vs_bud_reference = Bud and leaf galler samples mapped to the Euura lappo reference genome followed by variant calling.
Salix_concatRADloci.phy = phylip file containing the concatenated Salix 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...