Data from: Functional vertebrate group diversity, tick-borne pathogen ecology and genetic diversity
Data files
Apr 24, 2025 version files 18.41 KB
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diversity_disease_code.R
2.85 KB
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diversity_pathogen_data.csv
2.89 KB
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README.md
2.74 KB
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variable_keys.xlsx
9.93 KB
Abstract
Anthropogenic land use change has led to considerable biodiversity loss, affecting ecosystem functions with unresolved consequences for zoonotic disease transmission. Functional diversity is understudied but potentially important for understanding the role of biodiversity because many zoonotic disease systems are maintained by species with different roles in disease transmission. Here, we explore how functional groups and pathogen genetic diversity influence transmission and human disease risk within the Lyme disease system. Our field and molecular ecology study examined ticks and vertebrates across a fragmented landscape and evaluated several metrics of disease risk. For predicting vector and infected vector density, rodent host richness had a positive effect and was most important, but vector infection prevalence was best predicted by rodent and predator richness together, reflecting how indirect effects may alter tick-host interactions and disease risk. These results indicate that examining species richness generally may obscure important interactions driven by richness within functional groups. Pathogen genotype richness was best predicted by overall vertebrate richness, providing support for the multiple niche polymorphism hypothesis. Our study offers an important perspective on the relationship between biodiversity and disease risk, suggesting that richness within functional groups may offer more nuanced insight into pathogen transmission dynamics than overall biodiversity.
Dataset DOI: 10.5061/dryad.vdncjsz61
Description of the data and file structure
This repository contains the full data set and contains code to analyze the data in the preparation of the associated manuscript. All the missing data are mentioned as "NA".
Description of the data and file structure
The "diversity_disease_code.R" document contains the R code used to generate the final models presented in our results section.
"diversity_pathogen_data.csv" contains the raw and processed data used for figure generation and model building.
Files and variables
File: diversity_pathogen_data.csv
Description:
- vert_year: Year that vertebrates were sampled (lagged so that this year is one year prior to nymphal tick cohort sampling)
- site: Abbreviation for site name
- area: Site area in hectares
- log_area: Log base 10 of site area in hectares
- ospC_richness_BBSS: Number of ospC genotypes for B. burgdorferi sensu strictu
- ospC_N_BBSS: Sample size of ospC genotypes sequenced for B. burgdorferi sensu strictu
- ospC_HIS_richness: Number of human infecting ospC genotypes for B. burgdorferi sensu strictu
- ospC_HIS_prev: Prevalence of human infecting ospC genotypes for B. burgdorferi sensu strictu
- DON: Density of Ixodes pacificus nymphs collected across 995 square meters
- DON_tested: Number of Ixodes pacificus nymphs collected tested for pathogens
- NIP_BBSS: Prevalence of Ixodes pacificus nymphs infected with B. burgdorferi sensu strictu
- DIN_BBSS: Density of Ixodes pacificus nymphs infected with B. burgdorferi sensu strictu collected across 995 square meters
- predator_richness: Number of predator species detected at the site via camera trapping
- rodent_richness: Number of rodent species detected at the site via live trapping
- mammal_richness: Number of mammal species detected at the site via live trapping and camera trapping
- Scoc_abundance: Abundance of Sceloporus occidentalis
- vertebrate_richness: Number of vertebrate species detected at the site via live trapping and camera trapping
- Nefu_abundance_est: Abundance of Neotoma fuscipes
- Pero_abundance: Abundance of Peromyscus sp.
- PredAbundance: Abundance of predators
- DeerAbundance: Abundance of deer
Code/software
Models were created in R studio (Version 4.3.2) using the ‘glmmTMB’ package and 'lme4' packagge. Code for model development is contained in the file "diversity_disease_code.R"
Access information
Other publicly accessible locations of the data:
- GenBank, or contained within the associated manuscript
Location: California, U.S.A.
Time Period: 2017-2020
Major taxa studied: Ixodes pacificus, zoonotic bacterial pathogens, large vertebrates, lizards, and rodent communities
Methods:
We collected I. pacificus ticks and tested them for Borrelia burgdorferi, the causative agent of Lyme disease. We additionally genotyped the outer surface protein C (ospC) gene of B. burgdorferi. We also measured wildlife variables for 14 sites in northern California over 4 years. Methods involved surveys of host-seeking ticks, wildlife camera trapping, mark-recapture rodent surveys and mark-recapture lizard surveys.
