DOI: 10.5061/dryad.3560pr3
title: Data from: Using host-associated differentiation to track source population and dispersal distance among insect vectors of plant pathogens

description: Small, mobile insects are notoriously challenging to track across
 landscapes and manage in agricultural fields. However, genetic
 differentiation among insect populations and host-plants acquired through
 host-associated differentiation could be exploited to infer movement
 within crop systems and damage potential. Although many insects exhibit
 host-associated differentiation, management strategies for insect vectors
 of plant pathogens assume a homogenous population. Nevertheless,
 phenotypic changes derived from host-associated differentiation could
 manifest in altered behavior or physiology affecting the likelihood of
 vector-pathogen-plant interactions, or the subsequent efficiency of
 pathogen transmission. We used SNPs to assess genotypic structure and
 host-associated differentiation in the cowpea aphid, Aphis craccivora Koch
 (Hemiptera: Aphididae). To do so, we sampled A. craccivora across the
 Midwestern U.S. from two host-plants, alfalfa (Medicago sativa) and black
 locust (Robinia pseudoacacia) — putative source populations for winged
 migrants. Simultaneously, we sampled winged A. craccivora landing in
 pumpkin fields where they transmit viruses. Structure analyses supported
 host-associated differentiation by identifying two major genotypic groups:
 an alfalfa group containing a single multilocus genotype, and a locust
 group containing all others. Winged locust-group aphids landed at a much
 greater magnitude within focal fields during year 2 than year 1, while
 those in the alfalfa-group remained fairly consistent. Spatial
 autocorrelation analyses indicated locust-group aphid movementwas
 characterized by small-scale dispersal during year 2, likely originating
 from populations within 10 km. We also detected strong temporal
 differences in colonization from the two host-plants. Early in the summer,
 most winged aphids (79.4%) derived from the locust group, whereas late in
 the summer more (58.3%) were from the alfalfa group. Because early crop
 growth stages are more susceptible to damage from aphid-vectored viruses,
 these data implicate locust as the more important source and illustrate
 how host-associated differentiation can be used to track dispersal and
 inform management of heterogeneous pest populations.
description: 43 Validated
 SNPsDataset
 "Ac_43validatedSNPs.csv" presents 43 validated SNP sequences
 screened for use in the analyses conducted in our manuscript. RAD tags
 (please see NCBI SRA BioProject #PRJNA503177, BioSample #SAMN10354042)
 were used to identify de novo candidate SNPs with Stacks v. 1.19 (Catchen
 et al. 2011; Catchen et al. 2013). We allowed a maximum of two mismatches
 between stacks within individuals and a minimum depth of coverage of three
 nucleotides for ustacks, and allowed no mismatches between stacks between
 individuals for cstacks. We then used Stacks script export_sql.pl
 (snps_l=1 -F snps_u=1 -F pare_l=3) to create a whitelist of all loci
 containing one snp with a minor variant present in at least three samples.
 The whitelist was used to select a subset of 50 candidate SNPs, of which
 seven failed validation (LGC Genomics LLC, Beverly, MA). Dataset
 "Ac_43validatedSNPs.csv" presents the 43 validated SNP
 sequences. Further filters were applied prior to the analyses detailed in
 the manuscript (please see Methods: RAD Library Preparation, SNP
 dentification and Assessment of Function).Ac_43validatedSNPs.csvComprehensive Dataset 21 LociDataset "Ac_2012-13_21loci.csv" presents the genotypic, geographic (Lat, Long), population, and host-plant or pan collection source (Origin) for each Aphis craccivora sample used in manuscript analyses.Ac_2012-13_21loci.csv