Dataset DOI: 10.5061/dryad.xd2547dwt

Description of the data and file structure

The data shared here consists of field-collected amphibian locality, mass, developmental stage, and body size data; field observations on frogs' health status; corresponding Bd infection intensity data for sampled frogs from quantitative PCR; and field-collected temperature data from iButtons deployed in aquatic and terrestrial microhabitats.

Files and variables

File: ExtentPolygon_Vilcanota.shp, ExtentPolygon_Vilcanota.dbf, ExtentPolygon_Vilcanota.shx, ExtentPolygon_Vilcanota.qpj, ExtentPolygon_Vilcanota.prj, ExtentPolygon_Vilcanota.cpg

Description: Shapefile and supporting files delineating the extent of the study region. File created by the authors. 

File: VilcanotaWaterFeatures.kml

Description: KML file containing polygons for water features in the Vilcanota. This file was generated by drawing vectors and polygons in Google Earth, using satellite imagery as a template.

File: TreeInfo_All_encoded.csv

Description: Code to plot the phylogeny of global Bd samples. 

Variables

• sampleID: For my samples, Bd sample name (matches the frog it was sampled from), or for previously-published sequences, sample name used in previous publications (as cited in text)
• Lineage: Bd lineage. Lineage names are consistent with previous publications (as cited in manuscript text), and "mine" refers to samples we are phylogenetically placing (from the Vilcanota, and generated in this study)
• GPL: Whether* Bd*GPL strains are BdGPL-1 or BdGPL-2
• Continent: Continent assignment, coded as numbers. Encoding is explained in the Global_phylogeny_plot.R script. 

File: Panama_primer_lookup_table.csv

Description: Mapping between primer tube numbers and primer names used in amplicon sequencing.

Variables:

• Primer_Number_Tube: Tube number for primer
• Primer_Number_PANA: Name of primer

File: Pleurodema_Split_LatLon_SiteNumbers.csv

Description: Locality data for frogs sampled.

Variables

• sampleID: individual IDs for frogs
• elevation: in m a.s.l.
• lon: longitude (WGS84), generalized to 0.1 decimal degree
• lat: latitude (WGS84), generalized to 0.1 decimal degree
• site.num: individual number assigned to the sampling site

File: parfile_Vilcanota.txt

Description:  Parameter file needed for running smartPCA on just the Vilcanota samples. 

File: parfile.txt

Description:  Parameter file needed for running smartPCA on a panel of GPL samples includes those from the Vilcanota. 

File: AllData.csv

Description: Temperature data gathered by field-deployed iButtons

Variables

• Site: Individual code for each iButton. Name is composed of "IB", for iButton; a number representing the unique site (1-20); then a suffix "_ACUA" or "TERR", to represent whether the iButton was deployed aquatically or terrestrially.
• Time: Date and time in DD/MM/YYYY HH:MM format
• Temp: Temperature in degrees Celcius

File: iButtons.csv

Description: iButton locality data

Variables

• iButton Number: Individual code for each iButton. Name is composed of "IB", for iButton; a number representing the unique site (1-20); then a suffix "_ACUA" or "TERR", to represent whether the iButton was deployed aquatically or terrestrially.
• Elevacion: Elevation
• Lat: Latitude (WGS84), generalized to 0.1 decimal degree
• Lon: Longitude (WGS84), generalized to 0.1 decimal degrees
• Microhabitat: Aquatic or Terrestrial deployment

File: Pleuro_field.csv

Description: Field data for Pleurodema marmoratum

Variables

• Number_ID: Frog individual ID, without the 'ES' prefix.
• sampleID: Frog individual ID, with the 'ES' prefix.
• Year: Sampling year
• Date: Complete date, in MM/DD/YYYY
• species: species sampled
• tissue: tissue type. Toe (dedo) or tail (cola)
• elevation: elevation in m a.s.l.
• weight: mass (g)
• svl: body length (snout vent length), mm
• condition: notes on health condition. Translations in Infection_elevation.R script. 
• lifeStage: developmental status, expressed as adult ("adulto"), juvenile ("juv"), or tadpole (a number representing Gosner developmental stage)
• sex: M, F, or x (undetermined)
• Swab..D.W.B.: swab taken was ethanol-stored (wet, 'W'), dry-stored ('D'), or both kinds of swab were taken ('B')
• notes: Any additional notes taken in the field

File: Bd.csv

Description: qPCR data from Bd samples

Variables

• sampleID: sample ID for Bd sample (matches the frog from which sampled)
• Sethanolapaired (dry/ethanol/paired): was the swab for this individual dry-stored, ethanol-stored, or both (paired)?
• Swab extracted?: Was DNA extracted from this swab
• 2nd swab extracted?: For paired samples, was DNA extracted from the second swab?
• Zsp_est1: zoospores estimated in reaction from replicate 1
• Zsp_est2: zoospores estimated in reaction from replicate 2
• Zsp_est3: zoospores estimated in reaction from replicate 3
• Zsp_est4: zoospores estimated in reaction from replicate 4
• Zsp_est5: zoospores estimated in reaction from replicate 5
• Zsp_est6: zoospores estimated in reaction from replicate 6
• Zoospore_Mean: mean zoospores across replicates
• Zoospore_SD: standard deviation of zoospores across replicates
• Zoospores in swab: from the mean zoospores in the reaction, what is the mean derived number of zoospores in the initial swab?
• DryPairZspEst1: For dry-stored swabs, zoospores estimated in reaction from replicate 1
• DryPairZspEst2: For dry-stored swabs, zoospores estimated in reaction from replicate 2
• DryPairZspEst3: For dry-stored swabs, zoospores estimated in reaction from replicate 3
• DryPairZspMean: For dry-stored swabs, mean zoospores across replicates
• DryPairZspSD: For dry-stored swabs, standard deviation of zoospores across replicates
• Plate#: Which qPCR plate was this sample processed on?

File: TreeInfo_PCA_global.csv

Description:  Metadata for plotting the PCA of global GPL samples

Variables

• sampleID: For Vilcanota samples, Bd sample name (matches the frog it was sampled from), or for previously-published sequences, sample name used in previous publications (as cited in manuscript)
• Lineage: Whether the sample is from this study ("mine") or previously published ("GPL)
• Continent: Continent that Bd sample is derived from
• GPL-1-2: Whether GPL samples that were previously published are from GPL-1 or GPL-2 (citations for these designations in manuscript)

Files to be derived from other sources:

Voyles2017_GPL.csv: Temperature-dependent logistic growth data derived from Fig. 5 and Supp. Table 7 of Voyles, J., Johnson, L. R., Rohr, J., Kelly, R., Barron, C., Miller, D., ... & Rosenblum, E. B. (2017). Diversity in growth patterns among strains of the lethal fungal pathogen Batrachochytrium dendrobatidis across extended thermal optima. Oecologia, 184(2), 363-373. We adapted as a CSV, with "Temperature" in degrees Celcius in the first column and "r" the logistic growth rate in the second column. 

DEMvilcanota.tif: Digital elevation model of the Cordillera Vilcanota. This TIF was produced for map-building only (elevations used in the study were measured in the field using GIS). The DEM for the study region was produced by intersecting the study area polygon (included above) with publicly available DEM data for Peru. 

Code/software

Included scripts are run with R (".R") or bash (".sh"). R packages needed for data processing are listed at the top of each script as calls to those libraries. This workflow also requires IQTree (https://github.com/iqtree/iqtree2), vcf2eigenstrat.py(https://github.com/mathii/gdc/blob/master/vcf2eigenstrat.py), smartPCA (https://github.com/chrchang/eigensoft/blob/master/POPGEN/smartpca.info), FLASH2 (https://github.com/dstreett/FLASH2), and ANGSD (https://github.com/ANGSD/angsd). 

File: iButton_temp_figure.R

Description: Code to create the figure communicating temperature variability in aquatic and terrestrial microhabitats

File: iButton_sampling_map.R

Description: Creates a contour map of the study area, plotting the location of iButtons deployed for temperature measurement. Rios_Quebradas shapefile can be downloaded from this source: https://data.humdata.org/dataset/hidrografia-de-peru

File: Sampling_map.R

Description: Creates a DEM of the study area, plotting the sampling locations for Pleurodema marmoratum. A simple shapefile of South America indicating country borders (SouthAmerica.shp) can be downloaded from this or a number of sources: https://databasin.org/datasets/cc743dcc1b7641aba2a5d2cf42431f84/. Watershed polygon shapefiles for Peru can be downloaded from this source: https://www.geogpsperu.com/2018/07/mapa-de-subcuencas-hidrograficas-ana.html 

File: Trim_merge.R

Description: Trim and merge raw sequencing data.

File: Bd_mapping.sh

Description: Map trimmed, merged sequencing data.

File: Variant_calling.sh

Description: Compute genotype likelihoods in angsd. 

File: Global_phylogeny_concatenate_fasta.sh

Description: Concats global Bd samples for global phylogeny. 

File: Global_phylogeny_MSA.R

Description: Creates a multiple sequence alignment of global Bd samples. 

File: Global_phylogeny_plot.R

Description: Plots the global phylogeny of Bd samples, including representative sequences from other lineages. 

File: create_smartPCA_inputs.R

Description: commands for creating the .ind files required as input into smartPCA

File: Local_PCA_AMOVA.R

Description: commands for conducting and visualizing PCA in smartPCA, and for conducting AMOVA. 

File: Infection_elevation.R

Description: Analyses modelling relationships between infection intensity or sublethal impacts and elevation. Also summarizes infection and health status information for sampled frogs.