DOI: 10.5061/dryad.w9ghx3fxt
title: Data from: Landscapes with higher crop diversity have lower aphid species richness but higher plant virus prevalence

description: Diversifying agricultural systems by growing more than one crop species in
 an area can decrease pest and disease pressure and increase crop yields.
 However, there is a lack of information on how crop diversity at larger
 spatial scales influences pest and disease pressure. Here, we investigated
 how landscape-scale crop diversity affects aphid vector communities and
 prevalence of non-persistently transmitted potato virus Y
 (PVY). To test the influence of landscape-scale crop diversity on
 PVY prevalence and aphid communities, we conducted a field study during
 the 2020 and 2021 field seasons in the San Luis Valley, Colorado where we
 quantified aphid communities and PVY incidence at multiple sites. We then
 determined the association of aphid species richness and abundance and PVY
 incidence with landscape variables (crop diversity metrics and percentage
 cover of crop species) within 1, 2 and 3 km buffers from study
 sites. Higher crop diversity (measured as Shannon diversity
 index) led to decreased aphid species richness at a 3 km buffer in the
 2021 field season. Percentage of alfalfa was positively associated with
 aphid species richness in 2020 and aphid abundance in 2021 within a 1 km
 buffer. Higher crop diversity led to increased PVY incidence at a
 2 km buffer in 2021 and 3 km buffer in 2020 and 2021. At a 3 km buffer in
 2021, we found a positive influence of crop species richness on PVY
 incidence and a negative influence of crop species evenness on PVY
 incidence. Also in 2021, we found a positive influence of percentage of
 potato (virus host) on PVY incidence and a negative influence of
 percentage of barley (virus non-host) on PVY incidence. Synthesis and
 applications: In summary, we found that landscape-scale crop diversity
 impacts plant virus prevalence at spatial scales of &gt;1 km. This
 suggests that potato growers could reduce PVY prevalence by geographically
 isolating potato fields from other potato or other PVY-hosts. Crop
 diversity had a negative influence on aphid vector communities so growers
 could reduce risk of virus spread by aphid vectors by using certified
 potato seed in a diversified landscape.
description: A two-year field study (during the years 2020 and 2021) was
 conducted in the San Luis Valley, Colorado, a major potato producing
 region in the United States. Potato fields were sampled and tested for the
 presence of PVY biweekly (i.e., once every two weeks) at 17 fields (eight
 fields in 2020 and nine fields in 2021) using TAS-ELISA, and aphid
 communities were sampled weekly, using yellow pan traps, at 10 sites
 during both years. Potato fields were pivot-irrigated and most fields were
 either ~24-25 hectares or ~49-54 hectares in area. The mean distance from
 sampled potato plants to corresponding aphid traps was 567.4 m. Each
 sampling site, for both aphids and PVY, was at least 1.5 km away from the
 next closest sampling site. In 2020, one field (“6N6E”) was sampled which
 did not have corresponding aphid traps; this site was included for tests
 of PVY-landscape associations but not PVY-aphid abundance or species
 richness associations. Also in 2020, one field (“RS-1”) was composed of
 the PVY-resistant potato variety “Rocky Mountain Russet”, so this field
 was excluded from analyses. This dataset contains .csv
 files of weekly values of abundance and species composition of aphids from
 yellow pan traps at each trapping site, results from biweekly sampling and
 testing for PVY incidence in potato fields, and values of landscape
 composition surrounding aphid and PVY sampling sites, obtained from
 landscape composition data provided by the Rio Grande Water Conservation
 District. Associations between PVY incidence and aphid communities were
 determined using binomial (logit) generalized linear mixed-effects models
 (GLMM). Associations between PVY incidence and landscape composition were
 determined using logistic regression models. Associations between aphid
 communities and landscape composition were determined using linear
 regression models. Further details on statistical analyses can be found in
 Pitt et al. (2024), “Landscapes with higher crop diversity have lower
 aphid species richness but higher plant virus prevalence” published in
 Journal of Applied Ecology.
description: # Data from: Landscapes with higher crop diversity have lower aphid
 species richness but higher plant virus prevalence **Overview of
 data** This dataset contains weekly values of abundance and species
 composition of aphids from yellow pan traps at each trapping site, results
 from biweekly sampling and testing for PVY incidence in potato fields, and
 values of landscape composition surrounding aphid and PVY sampling sites,
 obtained from landscape composition data provided by the Rio Grande Water
 Conservation District. This study was conducted from May – September in
 2020 and 2021. Associations between PVY incidence and aphid communities
 were determined using binomial (logit) generalized linear mixed-effects
 models (GLMM). Associations between PVY incidence and landscape
 composition were determined using logistic regression models. Associations
 between aphid communities and landscape composition were determined using
 linear regression models. Further details on statistical analyses can be
 found in Pitt et al. (2024), “Landscapes with higher crop diversity have
 lower aphid species richness but higher plant virus prevalence” published
 in the Journal of Applied Ecology. **Descriptions of files**
 aphid.counts.2020.csv aphid.counts.2021.csv These .csv files contain the
 raw data from aphid trapping during 2020 and 2021. Column “Week” is the
 week during which an aphid was trapped; Column “Site” is the site where an
 aphid was trapped; Column “Species” is the species/genus group that an
 aphid belonged to; Column “Count” is the number of individual aphids that
 were trapped; Column “Number of active traps” is the number of active
 traps at that site during that week. In the column “Species”, values of
 “?”, “? Damaged”, "Unknown species (apterous)", and
 "Apterous - ?" indicate that aphids weren’t able to be
 identified to species or genus. PVY.testing.results.2020.csv
 PVY.testing.results.2021.csv These files contain results from biweekly
 testing for PVY for 2020 and 2021. Column “Field” indicates the potato
 field site were sampling was conducted; Column “Potato variety” indicates
 the variety of potato that was sampled; All other columns indicate the
 number of plants that tested positive for PVY (out of 20 plants that were
 sampled and tested) for each sampling date. landscape.aphid.sites.2020.csv
 landscape.aphid.sites.2021.csv These files contain data of landscape
 composition surrounding each aphid trapping site for 2020 and 2021. Column
 “site” indicates the aphid trapping site. All other columns indicate
 values of landscape composition surrounding sites; the suffix “1”, “2”,
 and “3” in column names indicate values of landscape composition within
 buffers of 1, 2, and 3 km, respectively. “sd” represents the Shannon
 diversity index of crop species; “richness” represents crop species
 richness; “crop.evar” represents crop species evenness calculated using
 the E<sub>var</sub> metric; “potato”, “barley”, and “alfalfa”
 represent the percent cover of each crop species.
 landscape.PVY.sites.2020.csv landscape.PVY.sites.2021.csv These files
 contain data of landscape composition surrounding each PVY sampling site
 for 2020 and 2021. Column “site” indicates the potato field site. All
 other columns indicate values of landscape composition surrounding sites;
 the suffix “1”, “2”, and “3” in column names indicate values of landscape
 composition within buffers of 1, 2, and 3 km, respectively. “sd”
 represents the Shannon diversity index of crop species; “richness”
 represents crop species richness; “crop.evar” represents crop species
 evenness calculated using the E<sub>var</sub> metric;
 “potato”, “barley”, and “alfalfa” represent the percent cover of each crop
 species.