Landscape connectivity, habitat isolation, and tick-borne pathogen ecology

Habitat loss and forest fragmentation are often linked to increased pathogen transmission, but the extent to which habitat isolation and landscape connectivity affect disease dynamics through movement of disease vectors and reservoir hosts has not been well examined. Tick-borne diseases are the most prevalent vector-borne diseases in the US and on the West Coast, Ixodes pacificus is one of the most epidemiologically important vectors. We investigated the impacts of habitat fragmentation on pathogens transmitted by I. pacificus and sought to disentangle the effects of wildlife communities and landscape metrics predictive of pathogen diversity, prevalence, and distribution. We collected pathogen data for four co-occurring bacteria transmitted by I. pacificus and measured wildlife parameters. We also used spatial data and cost-distance analysis integrating expert opinions to assess landscape metrics of habitat fragmentation. We found that landscape metrics were significant predictors of ti..., Location: California, U.S.A.
Time Period: 2016-2021
Major taxa studied: Ixodes pacificus, zoonotic bacterial pathogens, large vertebrate and rodent communities
Methods:
We collected pathogen data for four co-occurring bacteria transmitted by I. pacificus; Borrelia burgdorferi sensu stricto, Borrelia bissettiae, Borrelia miyamotoi, and Rickettsia tillamookensis. Additionally we measured wildlife and landscape variables for 19 sites in northern California over six years. Methods involved surveys of host-seeking ticks, wildlife camera trapping, and mark-recapture rodent surveys. We used spatial data and cost-distance analysis integrating expert opinions to assess landscape metrics of habitat fragmentation.
Results:
Landscape metrics, i.e., habitat size, measurements of surrounding green space, and habitat isolation, are significant predictors for tick density and pathogen prevalence. However, wildlife variables, i.e., wildlife, predator, and rodent diversity, also contribute to understandi..., , # Landscape connectivity, habitat isolation, and tick-borne pathogen ecology

[https://doi.org/10.5061/dryad.63xsj3v9b](https://doi.org/10.5061/dryad.63xsj3v9b)

This repository contains code to analyze the data and prepare individual figures. It also contains the full data sets analyzed in the preparation of the associated manuscript. 

## Description of the data and file structure

The \"FragPathDiv_script.R\" document contains the R code used to generate the final models and all figures presented in our results section. 

\"Full_summary.csv\", \"Full_summary_NoWP100.csv\", \"biFrag.csv\", and \"2021pathogen_data.csv\" contain the raw and processed data used for figure generation and model building. 

For all spreadsheets, empty cells represent years or sites in which a metric was not collected, or for pathogen prevalence metrics, a blank cell may mean that no relevant ticks were collected from that year/site and therefore no pathogen assays were run. Ticks from years prior to 2021 may not have...