DOI: 10.5061/dryad.5x69p8dj1
title: TuMV infection in <em>Hesperis matronalis</em> across Kingston, Ontario

description: Understanding the factors that influence pathogen prevalence is essential
 to mitigating the negative consequences of disease. Infection prevalence
 should be influenced by the abundance and distribution of the pathogen’s
 hosts, yet tests of this general expectation from natural populations are
 few. Furthermore, human activity is profoundly altering species
 distributions, which may have consequences for the pathogens that are
 associated with them. We investigated whether urbanization influences
 infection prevalence by, in part, affecting host population size and
 density in a study that surveyed the occurrence of turnip mosaic virus
 (TuMV) infection across 132 populations of the invasive mustard plant
 Hesperis matronalis in Ontario, Canada, along an urban-rural gradient. We
 scored TuMV infection by the appearance of overcolor breaking for a total
 of ∼38,000 plants across three generations. Overall, 39% of populations
 included at least one infected individual, and 10% of individuals were
 infected within these populations. As predicted, the probability of
 population infection increased with human activity, even after controlling
 for the positive effect of population size. Larger populations in areas of
 high human activity were also more likely to remain infected across
 generations. The effect of human activity on the infection frequency
 within populations was less consistent. Within populations, the
 probability of individuals being infected increased with local density of
 conspeci cs, yet mean density did not influence population infection or
 infection frequency within infected populations. Our results highlight how
 urbanization can influence the prevalence of infection due to an
 economically important plant virus.
description: # TuMV infection in *Hesperis matronalis* across Kingston, Ontario Dataset
 DOI: [10.5061/dryad.5x69p8dj1](https://doi.org/10.5061/dryad.5x69p8dj1) ##
 Description of the data and file structure We surveyed naturalized
 populations of the plant *Hesperis matronalis* over three years along an
 urban-rural gradient throughout Kingston, ON, Canada. We used night sky
 brightness (NSB) as a proxy for human activity. At each population, we
 estimated the prevalence of TuMV infection by scoring the colour morph of
 an individual as either normal (uniform white, pink, or violet) or colour
 broken. We estimated the reproductive census size as the total number of
 flowering individuals (N). We also counted the number of flowering stems
 within a 1-m radius (D ) of every third plant sampled for infection status
 during 2022 and 2023. In 22 populations surveyed in 2021, we also randomly
 tagged plants, scored them as infected or not, and then harvested the
 aboveground portion of the plant to estimate correlates of fitness.  ###
 Files and variables #### File: Infection_between_sites.csv
 **Description:** Survey data of TuMV infection prevalence in populations
 of *Hesperis matronalis* surveyed from 2021-2023.  Missing values are
 denoted as NA ##### Variables * order: row number * sitecode: Code for the
 location where the sample was taken. We know the GPS coordinates of these
 sites * gen_location: Road name for each population that was surveyed. *
 date_sampled: Date data was collected * year: Year data was collected *
 three_yrs: Binary variable describing whether a site was surveyed in all 3
 sampling years (1= yes, 0 = no) * fate: Describes the number of years a
 site was surveyed (s3y = sampled 3 years, ns = not sampled, inacc = not
 accessible) * lon: Longitude * lat: Latitude * N: Estimated population
 size * W: Number of plants with white colour morph * LP: Number of plants
 with light pink colour morph * DP: Number of plants with dark pink morph *
 V: Number of plants with white violet morph * S: Number of plants with
 colour-broken (infected) morph * morph_freqs: Binary variable describing
 if morph frequencies were counted (yes or no) * other_mustards: Binary
 variable describing if other mustard species were detected at the
 population * site_distinctness: Binary variable describing if a site was a
 distinct cluster of plants (1 = yes, 0 = no) * notes: Notes column * SQM:
 Night sky brightness measured in Sky Quality Meteres * dist_cc_km:
 Distance of population to Kingston city centre (city hall) in km * n:
 Number of plants surveyed * fW: Frequency of white morph * fLP: Frequency
 of light pink morph * fDP: Frequency of dark pink morph * fV: Frequency of
 violet morph * nwS: Number of plants that are not infected * fS: Frequency
 of infected plants * Sgt0: Binary variable stating if population had
 infected plants detected or not (0 = no, 1 = yes) * log10_N:
 Log10-transformed population size * negSQM: Negative values of Sky Quality
 metres * med_den: Median density of a population * mlog10_den: Mean of
 log10-transformed density of conspecific plants within a 1 m radius *
 mden: Mean density of conspecific plants within a 1 m radius #### File:
 Within_stand_density.csv **Description:** Density data of individual
 *Hesperis matronalis* around a given focal plant measured across
 populations. ##### Variables * year: Year data was collected *
 sitecode: Code for the location sample was taken. We know the GPS
 coordinates of these sites * morph: Describes colour morph of plant that
 was measured (W = white, LP = light pink, DP = dark pink, V = violet, S =
 infected/colour-broken) * density_pmr: number of conspecific plants within
 a 1 m radius of a focal plant * dens_pm2: number of conspecific plants
 within a 1 m radius of a focal plant * broken: Binary variable describing
 whether the focal plant was colour-broken (i.e. infected), where 1 = yes,
 0 = no. #### File: Fitness_data.csv **Description:** Fitness correlates
 of* Hesperis matronalis* plants measured in 2021 ##### Variables * order:
 Row number * year: Year data was collected * sitecode: Code for the
 location where the sample was taken. We know the GPS coordinates of these
 sites * plant: the ID that was on the tag of the plant. Unique for the
 location, but not across locations * plant_id:  Sitecode and plant
 combined for a unique ID * colour_morph: The colour of the plant's
 flowers. V is violet/purple, LP is light pink, DP is dark pink, W is
 white, and S is sectored/multicoloured/variegated * total_stem_mass_g: 
 Mass in g of everything above the first inflorescence stem ( main stem,
 fruit, seeds, inflorescence stems) * fruit_number: Total number of
 developed fruit on the plant * flower_number: Fruit number + aborted fruit
 number * ppn_parasitized: Proportion of fruit for an individual that had
 dark marks or frass * mseptumindents: Number of potential seeds (the
 number of indentations in the outer layer of fruit that were made by
 developing seeds) * fruit_set: Number of fruit that successfully set seed
 * total_seeds: The number of seeds * ppn_seedsdestroyed: Proportion of
 seeds that were destroyed * log10_total_stem_mass_g: Log10-transformed
 stem mass * log10_fruit_number: Log10-transformed fruit number *
 log10_total_seeds: Log10-transformed total seed number * infected: Binary
 variable describing whether a plant was infected (yes or no) * N:
 Population size * fW: Frequency of white colour morph at that population *
 fP: Frequency of pink colour morph at that population * fV: Frequency of
 violet colour morph in that population * NSB: Night Sky Brightness
 (negative Sky Quality Metres) ## Code/software All analyses were performed
 using the R statistical environment (ver. 4.4.1) run in RStudio (ver.
 2024, 09.01375; Posit Software, Boston, MA).