Data from: Divergent population responses following salamander mass mortalities and declines driven by the emerging pathogen Batrachochytrium salamandrivorans

This folder includes the data and code associated with the manuscript "Divergent population responses following salamander mass mortalities and declines driven by the emerging pathogen Batrachochytrium salamandrivorans"Jesse Erens, Kathleen Preissler, Jeroen Speybroeck, Wouter Beukema, Annemarieke Spitzen-van der Sluijs, Tariq Stark, Arnaud Laudelout, Thierry Kinet, Benedikt R. Schmidt, An Martel, Sebastian Steinfartz, Frank PasmansProceedings of the Royal Society B (2023)https://doi.org/10.1098/rspb.2023.0510<br>--- 'encounter_rates.csv' lists all fire salamander (Salamandra salamandra) count data across study populations from completed transect visits. The three-letter abbreviations refer to the focal outbreak sites Bunderbos (BUN), Putberg (PUT), Liège (BDC) and Robertville (ROB), and the reference sites Argenteau (ARG) and Nonceveux (NCV). All other abbreviations refer to sites monitored as part of the Flemish monitoring program, for which specific site names are left undisclosed at the discretion of the coordinator for the purpose of protection.--- 'bsal_detection.csv' lists the skin swab samples taken in focal outbreak sites and those that tested positive for Batrachochytrium salamandrivorans (Bsal) by means of qPCR. References in the table refer to data previously featured in Stegen et al. 2017 (doi: 10.1038/nature22059) and Spitzen-van der Sluijs et al. 2016 (doi: 10.3201/eid2207.160109) and 2018 (doi: 10.1038/s41598-018-22225-9).--- 'body_lengths_and_behaviour.csv' lists all body length data of measured fire salamanders included in demographic analyses. Data in focal outbreak sites and nearby reference sites were collected around the recent study period 2018-2020 (see the methods section in the manuscript for additional details). Further comparative data are included from: 1) The 2014 dataset of Robertville, which was obtained during the initial outbreak and demographic shift (see Stegen et al. 2017), providing a temporal comparison to recent observations; and 2) The 2013-2020 dataset of Luisdonk (LDB), included as a high-detailed reference of an uninfected population. Direct-contact behaviours describe observations of: Male-male combat (MM&amp;&amp;), courtship (AMPL) and larval deposition (BIRT).--- 'microsat_allele_calling.csv' presents the allele table of all included microsatellite loci as obtained from Genemarker, comprising the basis for all genetic analyses. In addition to the focal sites collected around the recent study period 2018-2020, ex-situ populations stemming from early-outbreak phases in Bunderbos in 2012 and Robertville in 2014 were sampled for temporal comparison. See the methods section in the manuscript for additional details and software use.--- 'zoospore_assay.csv' lists Bsal zoospore counts obtained following exposure to mucosome samples collected from salamanders in the field in focal outbreak and reference sites. These were performed in triplicate following the non-invasive assay described by Smith et al. 2018 (doi: 10.1371/journal.pone.0199295).--- The folder 'spatial_data' provides the shape files containing all GPS locations of encountered salamanders as used in spatial analyses (subfolder 'GPS'). These can be directly implemented in GIS software and packages, and list both WGS84 and Lambert1972 coordinates. It additionally contains the population transects and the 15m buffer areas that were used to correct for inaccurate GPS measurements ('outlier corrected') and generating null models for spatial comparisons (subfolder 'transects'). Environmental data were obtained from the LifeWatch dataset (2015, v2.10; http://maps.elie.ucl.ac.be/lifewatch/ecotopes.html).--- All R code was carried out in R version 4.1.2 "Bird Hippie", and the versions of the various software packages are listed within the code.<br>Additional notes:--- Analyses were partially performed in standalone GUI-based software. Please refer to the original manuscript and supplementary information for details. Most R plots were augmented using graphical software to improve color schemes and overall interpretation.--- Luisdonk (LDB) data were collected by, and Flemish monitoring data were curated by Jeroen Speybroeck (contact: [e-mail]).