DOI: 10.5061/dryad.rn8pk0pbj
title: VCF files of loci in approximate linkage equilibrium for two common spruce budworm larval parasitoids: Apanteles fumiferanae (Hymenoptera: Braconidae) and Glypta fumiferanae (Hymenoptera: Ichneumonidae)

description: Periodic and spatially synchronous outbreaks of insect pests have dramatic
 consequences for boreal and sub-boreal forests. Within these multitrophic
 systems, parasitoids can be stabilizing agents by
 dispersing toward patches containing higher host density
 (the so-called birdfeeder effect). However, we know little about
 the dispersal abilities of parasitoids in continuous forested landscapes,
 limiting our understanding of the spatiotemporal dynamics of
 host–parasitoid systems, and constraining our ability to predict forest
 resilience in the context of global changes. In this study, we investigate
 the spatial genetic structure and spatial variation in genetic diversity
 of two important species of spruce budworm larval parasitoids during
 outbreaks: Apanteles fumiferanae Viereck
 (Braconidae) and Glypta fumiferanae (Viereck)
 (Ichneumonidae). Using parasitoids sampled in
 2014 from 26 and 29 locations across a study
 area of 350,000 km2, we identified 1,012 and 992 neutral SNP loci
 for A. fumiferanae (N = 279
 individuals)
 and G. fumiferanae (N = 382),
 respectively. Using DAPC, PCA, AMOVA, and
 IBD analyses, we found evidence for panmixia and high genetic
 connectivity for both species, matching the previously described genetic
 structure of the spruce budworm within the same context, suggesting
 similar effective dispersal during outbreaks and high parasitoid
 population densities between outbreaks. We also found a significant
 negative relationship between genetic diversity and latitude
 for A. fumiferanae but not for G.
 fumiferanae, suggesting that northern range limits may vary by species
 within the spruce budworm parasitoid community. These spatial dynamics
 should be considered when predicting future insect outbreak severities in
 boreal landscapes.
description: Spruce budworm larvae were collected from late May to mid-July
 2014 from 29 sites located within and around six distinct outbreak areas
 in the province of Québec, Canada. Larvae were reared individually on
 artificial diet until egression of <em>Apanteles
 fumiferanae</em> and <em>Glypta fumiferanae</em> larvae.
 Adult parasitoids were then stored individually in dry conditions at -80°C
 prior to DNA extraction. Because both <i>A.
 fumiferanae</i> and <i>G. fumiferanae</i> are
 haplodiploid, total genomic DNA was extracted only from females (1–23
 females per species per site). Genotyping-by-sequencing libraries were
 constructed using the protocol of Poland, Brown, Sorrells, and Jannink
 (2012), and then single-end sequenced (100 bp reads) using an Illumina
 HiSeq2000. Because there is no reference genome available for <i>A.
 fumiferanae</i> and <i>G. fumiferanae</i>, we used the
 TASSEL 3.0 UNEAK (Universal Network-Enabled Analysis Kit) pipeline for
 single-nucleotide-polymorphism (SNP) calling (Lu et al., 2013). Only sequences with five or more reads over all individuals were kept, creating a master list of sequences which serves as a ‘pseudo reference genome’. During alignment, a 0.03 error tolerance rate. SNP loci with a minor allele frequency &lt; 5% were removed. Genotypes were corrected using the program <i>Uneak_filter</i> to consider low allele frequencies that could have resulted from sequencing errors. Loci absent in &gt; 25% of individuals and individuals with &gt; 10% missing loci were pruned out of the data matrix using TASSEL 5. We then created a pruned dataset of SNP loci for each species by removing SNPs in high linkage disequilibrium (correlation coefficient ≥ 0.3) were dropped to remove highly correlated variants.
description: We provide two VCF files of loci in approximate linkage
 equilibrium: one for <i>Apanteles
 fumiferanae</i> (Apanteles_fumiferanae_279inds_1056loci_LD_filtered.vcf) and one for <i>Glypta fumiferanae </i>(Glypta_fumiferanae_382inds_1044loci_LD_filtered.vcf)<i>. </i>We also provide the associated metadata from Table 1 of the article (outbreak areas, sites numbers, and latitude and longitude) in two text files (Apanteles_fumiferanae_Metadata.txt and Glypta_fumiferanae_Metadata.txt).