DOI: 10.5061/dryad.vdncjsz61
title: Data from: Functional vertebrate group diversity, tick-borne pathogen ecology and genetic diversity

description: 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.
description: Location<em>: </em>California, U.S.A.
 Time Period<em>: </em>2017-2020
 Major taxa studied<em>: </em><em>Ixodes
 pacificus</em>, zoonotic bacterial pathogens, large vertebrates,
 lizards, and rodent communities Methods:
 We collected <em>I. pacificus </em>ticks and tested
 them for <em>Borrelia burgdorferi</em>, the causative agent of
 Lyme disease. We additionally genotyped the outer surface protein C (ospC)
 gene of <em>B. burgdorferi. </em>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.
description: # Functional vertebrate group diversity, tick-borne pathogen ecology and
 genetic diversity Dataset DOI:
 [10.5061/dryad.vdncjsz61](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:** 
 ###### *Variables* * 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