DOI: 10.5061/dryad.h18931zwp
title: Indirect pathogen transmission underlies an emerging infectious fungal disease outbreak in a wild reptile population

description: Infectious diseases present a growing risk to wildlife biodiversity.
 Predicting outbreak dynamics and developing effective management tools
 requires knowledge on the mechanisms of infection transmission.
 Specifically, understanding the relative contributions of direct
 host-to-host transmission versus indirect environmental transmission is
 critical. Here, we leverage a large dataset from long-term monitoring of a
 free-living population of eastern water dragons (Intellagama lesueurii)
 experiencing an outbreak of the fungal pathogen Nannizziopsis barbatae, to
 investigate this pathogens’ transmission. Using different host behaviours
 to model direct and indirect transmission of infection in this population,
 we demonstrate N. barbatae’s ability to infect hosts through indirect
 transmission. Our findings shed light on the danger N. barbatae poses to
 Australian reptiles, but also provide insights into how outbreaks should
 be managed. Additionally, we provide a methodology to elucidate the
 transmission mechanisms of driving the spread of emerging fungal
 pathogens.
description: # Indirect pathogen transmission underlies an emerging infectious fungal
 disease outbreak in a wild reptile population
 [https://doi.org/10.5061/dryad.h18931zwp](https://doi.org/10.5061/dryad.h18931zwp) ## Description of the data and file structure Investigating transmission of a recently emerged fungal disease (Nannizziopsis barbata) among a population of Eastern Water Dragons (Intellagama lesueurii) using separate host behaviours to model direct (social) and indirect (environmental) disease transmission. Data comes from observational surveys of a population of dragons recording the GPS locations of where individual dragons were sighted on specific dates at specific times. There are two data files - initial raw data from observational surveys (Dragon_Sight_Data.csv), and data ready for analysis (INLA_Data.csv). ### Files and variables #### File: INLA\_Data.csv **Description:** Data ready for analysis in INLA model ##### Variables * Name: Identity of individual dragon (de-identified - 523 unique levels) * Season: Number of research season (range: 1-13) * ActiveFungus: Case/control of disease status of dragon. 0 = negative for N. barbartae; 1 = positive for N. barbartae * Sightings: Number of sightings for that individual in that research season * X: Latitude of sighting converted to meters * Y: Latitude of sighting converted to meters * Sex: Sex of the individual sighted (2 levels: Female, Male) * AgeClass: Age class of the individual sighted (2 levels: Adult, Juvenile) * Time.in.pop: Age of the individual sighted measured in number of days spent in the population from first sighting (average of season) * InfectedDensity.Annual: Average density of diseased conspecifics of space utilised by an individual for a given season (units: No. of infected conspecifics / square meter) * Infect_Assoc_Sight: Number of diseased conspecific interactions for an individual in a given season divided by the number of times the individual was sighted (units: No. of interactions / No. of sightings) * SeasonNumeric: Season column repeated but in numeric format #### File: Dragon\_Sight\_Data.csv **Description:** Data collected from behavioural surveys - GPS coordinates of where dragons were sighted at specific times and dates ##### Variables * Name: Identity of individual dragon (de-identified - 1218 unique levels) * Date: Date of when individual was sighted (dd/mm/yyyy) * Season: Number of research season (range: 1-13) * Time: Time of day when individual was sighted (2 levels: 7am-10am, 1pm-3pm) * Lat: Latitude of sighting (first three decimal places of minutes in decimal minutes) * Long: Longitude of sighting (first three decimal places of minutes in decimal minutes) * Date.diagnosed: Date when individual was first diagnosed as diseased (dd/mm/yyyy - NA for individuals who were never diagnosed) * Sex: Sex of the individual sighted (2 levels: Female, Male) * AgeClass: Age class of the individual sighted (2 levels: Adult, Juvenile) * Time.in.pop: Age of the individual sighted measured in number of days spent in the population from first sighting #### Supplementary Material: SuppInfo\_Fig1\_Table1\_Table2.pdf **Description:** Supplementary information for the published paper ## Code/software Analysis is undertaken in RStudio (R version 4.4.1). Modeling was completed using the R-INLA package to account for spatial and temporal autocorrelation in the data. Packages to calculate social and spatial metrics, and other required packages, can be found in the following code needed to reproduce this analysis. The scripts are numbered in order and contain the following: * 1a_Density_Code.R: Generate host spatial behavioural metric to model indirect transmission of fungal disease (Input is initial raw data from observational surveys (Dragon_Sight_Data.csv)) * 1b_Social_Metric_Code.R: Generate host social behavioural metric to model direct transmission of fungal disease (Input is the output data file from 1a) * 2_INLA_Model.R: Run INLA model to investigate how each of the host behavioural metrics explain fungal disease transmission in this population (Input is the output data file from 1b. Produces data ready for INLA analysis (INLA_Data.csv)) * 3_Generate_Figures.R: Produce figures The code was initially written by Greg Albery and Sam Becker. ## Supplementary Material The SuppInfo_Fig1_Table1_Table2.pdf file contains supplementary material (two tables and one figure) referenced but not explicitly shown in the main text of the paper.