Data and code from: Impacts of urbanization on pathogens and pests of wild and cultivated plants
Data files
Apr 14, 2026 version files 57.26 KB
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MainText_and_Supplemental_Script_Figures_20260223.Rmd
28.53 KB
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Metadata.zip
20.91 KB
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README.md
7.82 KB
Abstract
Understanding how urbanization affects plant interactions with pathogens and herbivores is important for clarifying how changes in land use, climate, and biodiversity affect ecological and evolutionary processes, and for managing urban plants to maximize ecosystem services. We performed a systematic literature review of relationships between urbanization and pathogens or pests of wild and cultivated plants. We identified k = 171 relationships from n = 54 studies in which pathogen or pest abundance was quantified in both urban and non-urban areas, and summarized their distribution across taxa, geographic regions, and directions and mechanisms of effects proposed by the authors. Most studies featured tree hosts and their arthropod pests or fungal pathogens. Grasses and forbs were the next most commonly studied hosts, followed by crops and shrubs. We then performed a meta-analysis limited to trees, which had the most studies with sufficient statistical information (k = 55 relationships, n = 14 studies). In that meta-analysis, we found no overall effect of urbanization on tree pest or pathogen abundance. However, there was a significant interaction between urbanization and type of pest/pathogen, with arthropod pests trending toward lower abundance in urban areas and fungal pathogens trending toward higher abundance. Drawing on literature from the broader fields of urban ecology, disease ecology, and plant pathology, we synthesize our findings and offer insights into mechanisms by which urbanization influences disease and herbivory in wild and cultivated plants. We conclude by identifying research gaps, with the goal of informing management strategies that prioritize food security, environmental health, and global biodiversity.
Dataset DOI: 10.5061/dryad.brv15dvn4
Date of Data Collection
2023-2025
Contributors
Authors: Kaylee M. H. Arnold1,2, Mahal J. Bugay1, Quinn N. Fox1, Cheyenne M. Morris1,
William D. Hutson1,3, Alexis Durant1,4, Anthony V. Basta1,5, Christopher P. Tomera1, Sara E. Pierce1, Grace Z. Armstrong1,6, Devon Chen1,7, Daniel J. Chertow1,8 Richard L. Hofstra1,9, Cooper Johnson1, Katie Talbert1, Kayla R. Wallace1,10, Anna Wassel1, and Rachel M. Penczykowski1
1Department of Biology, Washington University in St. Louis
2Living Earth Collaborative, Washington University in St. Louis
3School of Medicine, University of Pittsburgh
4School of Veterinary Medicine, University of California-Davis, Davis, CA
5McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX
6Indiana University School of Medicine
7Warren Alpert Medical School of Brown University
8School of Medicine, Kaiser Permanente
9The Ohio State University College of Medicine, Columbus, Ohio
10 School of Public Health, University of MichiganDescription of the data and file structure
Overview
A systematic literature search of the effects of urbanization on wild and cultivated plant pests and pathogens was first completed in March 2023. Subsequent efforts were completed in April 2024 and February 2025 to search for and gather the most up to date literature. A meta-analysis on a small subset of these data was then performed to more formally assess the effects of urbanization on tree pests and fungal pathogens. Finally, we synthesized our findings and offered insights into mechanisms by which urban environmental factors influence disease and herbivory in wild and cultivated plants. We conclude the manuscript by identifying research gaps, with the goal of informing management strategies that prioritize food security, environmental health, and global biodiversity.
Description
These files include the supplementary figures to our manuscript and detailed tables of the eligible papers included in both our systematic literature review and meta-analysis. We included formatted Excel tables as well as the CSV files to reproduce the data and analyses in the R script.
R Scripts and Metadata
File: MainText_and_Supplemental_Script_Figures_20260223.Rmd
File Format
R markdown (.rmd)
Content Overview
RMD file to reproduce main text figures and supplemental figures, effect size calculations, and meta-regression.
File: Metadata.zip
File Format
Zip File (.zip)
Content Overview
The files in this zip folder are the metadata to be used to reproduce each figure and analyses.
Files included
File 1: TableS1.csv
Description
CSV file of the 54 eligible studies and 171 urbanization–host–pest and urbanization–host–pathogen included in the systematic literature review. This file is used to create Figures 2a and 3. Columns 1-16 describe the study system, column 17 includes the direction of the urban-disease relationship as stated by the authors, columns 18-23 include 5 categories of urban-disease relationship as stated by the authors across the dataset of eligible studies (precipitation and humidity, pollution, temperature, biodiversity changes, altered landscape and population connectivity or unspecified), and columns 24-27 include each study's title, Journal, Volume, and DOI. Each row corresponds to a unique host-pest or host-pathogen pairing for each Study ID.
Table Columns
- Authors: First author(s)
- Year: Year of publication
- STUDY_ID: Unique ID as assigned during initial data curation for each study
- City: Study city
- Country: Study country
- Host.plant.type: Category of host
- Tree, crop, forb, shrub, or grass
- Host.plant.common.name: Common name for host study organism
- Host.plant.family: Host family
- Host.plant.genus: Host genus
- Host.plant.species: Host species
- Pathogen.transmission.mode: Category of pathogen transmission
- Insect vector, wind, water, or NA (non-vector pest)
- Pest.pathogen.type: Category of pest or pathogen type
- Bacterium, fungus, or insect
- Pest.or.pathogen.common.name: Pest or pathogen common name
- Pest.or.pathogen.family: Pest or pathogen family name
- Pest.or.pathogen.genus: Pest or pathogen genus
- Pest.or.pathogen.species: Pest or pathogen species
- Urban.disease.relationship: Direction of urban-disease relationship as specified by the authors
- positive, negative, or no relationship
- Biodiversity_Changes: Mechanism of urban-disease relationship as stated by authors
- yes or no
- Altered.Landscape.Or.Population.Connectivity: Mechanism of urban-disease relationship as stated by authors
- yes or no
- Contamination.Or.Pollution: Mechanism of urban-disease relationship as stated by authors
- yes or no
- Temperature.UrbanHeatIsland: Mechanism of urban-disease relationship as stated by authors
- yes or no
- Precipitation.Humidity: Mechanism of urban-disease relationship as stated by authors
- yes or no
- Unspecified: Mechanism of urban-disease relationship was not stated
- yes or no
- Title
- Journal
- Volume
- DOI
File 2: TableS2.csv
Description
CSV file of the cities, countries, and coordinates for each eligible study and their corresponding study sites. This file is used to create Figure 2b.
Table Columns
- STUDY_ID: Unique study ID as assigned during initial data curation
- City.name: Study city
- Country.name: Study country
- Latitude: Latitude of data collection or nearest city
- Longitude: Longitude of data collection or nearest city
File 3: TableS3.csv
Description
A detailed CSV file of each eligible study in our meta-analysis (14 studies) and their corresponding urbanization–host–pest or urbanization–host–pathogen relationships (55 relationships), including sample sizes and the effect sizes between paired urban and non-urban relationships. This file is used to create Figure S1, Figure S2, Figure S3, and the meta-regression analyses.
Table Columns
- STUDY_ID: Unique study ID as assigned during initial data curation
- Figure.number: Figure number for extracted data in each study
- Independent.variable: Specifies repeated sampling methods or biological replicates
- Host.plant.type: Category of host type
- Tree, forb, shrubs, grasses, or crops
- Host.common.name: Host common name
- Host.plant.genus: Host plant genus
- Host.plant.species: Host plant species
- Parasite.guild: Feeding or parasitism guild
- fungi, galling insects, miners, chewers, wood borers, sap sucking, or general herbivory
- Pest.pathogen.type: Category of pest or pathogen type
- insect, fungus, bacterium
- Transmission.mode: Category of pest or pathogen transmission mode
- Vector, non-vector pest, or wind
- urbanization: Urbanization classification as stated by the authors
- urban, rural, forest, natural, etc
- SampleSize: Sample size of each urban-disease relationship
- Severity.or.abundance: Specifies what type of data was collected
- Severity (individual plant level, e.g., number of galls on each plant at each site) or abundance (population level, e.g., average number of galls at each site)
- value.calculation: Specifies what type of data was extracted
- percentages or proportions
- value: Raw values extracted from each urban-disease relationship
- error: Error calculation
- Standard error or standard deviation
- upper: 95 % confidence interval upper bound
Code/software
R version 4.4.2
Version 2023.12.1+402
Access information
Databases used
Web of Science and Journal of Urban Ecology
