DOI: 10.5061/dryad.83bk3j9zv
title: Data for: Epidemiological landscape of Batrachochytrium dendrobatidis and its impact on amphibian diversity at global scale

description: Chytridiomycosis, caused by the fungal pathogen Batrachochytrium
 dendrobatidis (Bd), is a major driver of amphibian decline worldwide. The
 global presence of Bd is driven by a synergy of factors, such as climate,
 species life history, and amphibian host suscep­tibility. Here, using a
 Bayesian data-mining approach, we modeled the epidemiologi­cal landscape
 of Bd to evaluate how infection varies across several spatial, ecological,
 and phylogenetic scales. We compiled global information on Bd occurrence,
 climate, species ranges, and phylogenetic diversity to infer the potential
 distribution and preva­lence of Bd. By calculating the degree of
 co-distribution between Bd and our set of environmental and biological
 variables (e.g. climate and species), we identified the factors that could
 potentially be related to Bd presence and prevalence using a geo­graphic
 correlation metric, epsilon (ε). We fitted five ecological models based on
 1) amphibian species identity, 2) phylogenetic species variability values
 for a given species assemblage, 3) temperature, 4) precipitation and 5)
 all variables together. Our results extend the findings of previous
 studies by identifying the epidemiological landscape features of Bd. This
 ecological modeling framework allowed us to generate explicit spatial
 predictions for Bd prevalence at the global scale and a ranked list of
 species with high/low probability of Bd presence. Our geographic
 model identified areas with high potential for Bd prevalence (potential
 Bd-risk areas) and areas with low potential Bd prevalence as potential
 refuges (free Bd). At the amphibian assemblage level, we found a
 non-relationship with amphibian phylogenetic signals, but a significantly
 negative correlation between observed species richness and Bd prevalence
 indicated a potential dilution effect at the landscape scale. Our model
 may identify species and areas potentially susceptible and at risk for Bd
 presence, which could be used to prioritize regions for amphibian
 conservation efforts and to assess species and assemblage at risk.
description: Usage notes These datasets
 include the geographic data used to build ecological and geographical
 models for <em>Batrachochytrium dendrobatidis</em>, as well as
 supplementary results of the following paper: Basanta et al.
 Epidemiological landscape of <em>Batrachochytrium</em>
 <em>dendrobatidis</em> and its impact on amphibian diversity
 at the global scale. Missing values are denoted by NA.
 Details for each dataset are provided in the README file.
 Datasets included: Information
 of <em>Bd</em> records. Table S1.xls
 contains *Bd* occurrence records and prevalence of infection from the
 Bd-Maps online database (http://www.bd-maps.net), Olson et al. 2013) accessed in 2013, and searched Google Scholar for recent papers with *Bd* infection reports using the keywords ‘*Batrachochytrium dendrobatidis’*. We excluded records from studies of captive individuals and those without coordinates, keeping only records in which coordinates reflected site-specific sample locations. Supplementary figures Supplementary information S1.docx contains supplementary figures of results obtained in this study. Description of methods and figures interpretation are in the Method and Results sections of the manuscript. Ecological traits of global amphibians and score-trait values. Table S2.xlsx contains information of amphibians' ecological traits obtained from AmphiBIO (Oliveira et al., 2017), as well as Score-trait values for each species. Methods for calculating Score-trait values are described in the section Methods of the manuscript. Values of ε (C|X) and S(C|X) of each <em>Bd</em>-variable pair combination. Table S3.xlsx contains epsilon and score values obtained by each pair combination of <em>Bd</em> and temperature, precipitation, phylogenetic and amphibian species. Methods for calculating epsilon and score values are described in the section Methods of the manuscript. List of new species confirmed positives for <em>Bd</em> (Olson et al. 2021). Table S4.xlsx contains a list of species recently confirmed positives for *Bd* (Olson et al. 2021) as well as score values and score quantiles.
description: # 1. Title of Dataset: Epidemiological landscape of *Batrachochytrium
 dendrobatidis* and its impact on amphibian diversity at global scale
 ## 2. Authors Information
 M. Delia Basanta Department of Biology, University of Nevada Reno. Reno,
 Nevada, USA. Julián A. Velasco Instituto de
 Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma
 de México. Ciudad de México, México. 
 Constantino González-Salazar. Instituto de Ciencias de la Atmósfera y
 Cambio Climático, Universidad Nacional Autónoma de México. Ciudad de
 México, México. ## 3. Date of data
 collection (single date, range, approximate date): 2019-2022 ## 4.
 Geographic location of data collection: Global ## DATA & FILE OVERVIEW
 ### 1. File List: 1. Table S1.xls 2. Supplementary information S1.docx 3.
 Table S2.xlsx 4. Table S3.xlsx 5. Table S4.xlsx ### DATA-SPECIFIC
 INFORMATION FOR: Table S1.xls Table S1.xls contains *Bd* occurrence
 records and prevalence of infection from the Bd-Maps online database
 ([www.bd-maps.net](http://www.bd-maps.net), Olson et al. 2013) accessed in
 2013, and searched Google Scholar for recent papers with *Bd* infection
 reports using the keywords ‘*Batrachochytrium dendrobatidis’*. We excluded
 records from studies of captive individuals and those without coordinates,
 keeping only records in which coordinates reflected site-specific sample
 locations. 1. Number of variables: 10 2. Number of cases/rows: 2674 3.
 Variable List: * Order: taxonomic Orders of amphibians. * Family:
 taxonomic Families of amphibians. * Species: species scientific name. *
 Positive: number of individuals positives for Bd * Negative: number of
 individuals negatives for Bd * N: total of individuals tested for Bd *
 Prevalence: prevalence of Bd infection. Obtained as positive/N * Latitude:
 geographic latitude of field sampling in decimal degrees * Longitude:
 geographic longitude of field sampling in decimal degrees * ID cell grid:
 identifier of each cell of our grid used to sample our geographic data ###
 DATA-SPECIFIC INFORMATION FOR: Supplementary information S1.docx
 Supplementary information S1.docx is a Word file, which contains
 supplementary figures of results obtained in this study. 1. number of
 figures: 4 2. Figures list: * Figure S1. Full score model of Bd presence.
 * Figure S2. Relationship between weighted prevalence (pw) and amphibian
 richness. * Figure S3. Score trait-based model for Bd. * Figure S4. Linear
 regression of percentage of species recently confirmed positives for Bd
 and score-trait quantile. Description of methods and figures
 interpretation are in the Method and Results sections of the manuscript.
 ### DATA-SPECIFIC INFORMATION FOR: Table S2.xls Table S2.xlsx contains
 information of amphibians ecological traits obtained from AmphiBIO
 (Oliveira et al., 2017), as well as Score-trait values for each species.
 Methods for calculating Score-trait values are described in the section
 Methods of the manuscript. 1. Number of variables: 26 2. Number of
 cases/rows: 6108 3. Variable List: * Order: taxonomic Orders of
 amphibians. * Family: taxonomic Families of amphibians. * Genus: names of
 amphibian Genus * Species: species scientific name. * Species decline:
 species for which population decline has been documented * Positives for
 Bd: species confirmed positives for Bd * Habitat: Overall vertical
 foraging stratum classification. We used four classes,
 Fosorial/Terrestrial/Aquatic/Arboreal. * Activity: TOverall diel period as
 active. We used three classes, Diurnal/Nocturnal/Crepuscular * Diet: Food
 items from the eating habits of adults using qualitative dietary
 categories. Specialist Carnivores Arthro-Hervib, Specialist Herbivores,
 Generalist. * Seasonality: Seasonal period as active. We used four
 classes, Wet_cold, Wet_warm, Dry_warm, Dry_cold
 Wet_warm/Wet_cold/Dry_warm. * Breding strategy: Whether the species
 reproduce via direct, larval development or is viviparous. *
 Body_size_mm1: classification of species based on body size, large,
 medium, small. * Epsilon (Bd): epsilon values of each pair of Bd-species
 association * Epsilon quantil: number of quantiles into which the list of
 species is divided based on epsilon values. We used 20-quantiles *
 Geographic score: score values of each pair of Bd-species association *
 Score geographic quantile: number of quantiles into which the list of
 species is divided based on score values. We used 20-quantiles * Score
 Order: score values of each pair of Bd-order association * Score Family:
 score values of each pair of Bd-familiy association * Score Genus: score
 values of each pair of Bd-genus association * Score Habitat: score values
 of each pair of Bd-habitat trait association * Score Activity: score
 values of each pair of Bd-activity trait association * Score Seasonality:
 score values of each pair of Bd-seasonality trait association * Score
 Breeding strategy: score values of each pair of Bd-breeding strategy trait
 association * Score Body_size: score values of each pair of Bd-body size
 trait association * Total Score traits: sum of score values of each
 amphibian trait. * Score Trait Quantile: number of quantiles into which
 the list of species is divided based on score trait values. We used
 20-quantiles ### DATA-SPECIFIC INFORMATION FOR: Table S3.xls Table S3.xlsx
 contains epsilon and score values obtained by each pair combination of
 *Bd* and temperature, precipitation, phylogenetic and amphibian species.
 Methods for calculating epsilon and score values are described in the
 section Methods of the manuscript. This file contains three sheets: Sheet
 1: Species 1. number of variables: 3 2. Number of cases/rows: 6108 3.
 Variable List: * Species: species scientific name. * Epsilon: epsilon
 values of each pair of Bd-species association * Score: score values of
 each pair of Bd-species association Sheet 2: PSV 1. number of variables: 3
 2. Number of cases/rows: 20 3. Variable List: * Phylogenetic metric:
 ranges of PSV-index. * Epsilon: epsilon values of each pair of Bd-PSV
 range association * Score: score values of each pair of Bd-PSV range
 association Sheet 3: Temperature 1. number of variables: 4 2. Number of
 cases/rows: 120 3. Variable List: * BIO: abbreviation of the six
 temperature variables used. BIO5, BIO6, BIO8, BIO9, BIO10, BIO11. Their
 names are BIO5: Max Temperature of Warmest Month, BIO6: Min Temperature of
 Coldest Month, BIO8: Mean Temperature of Wettest Quarter, BIO9: Mean
 Temperature of Driest Quarter, BIO10: Mean Temperature of Warmest Quarter,
 BIO11: Mean Temperature of Coldest Quarter. * Name: range: names and range
 of each of the six temperature variables. Units are degrees Celsius *
 Epsilon: epsilon values of each pair of Bd-temperature range association *
 Score: score values of each pair of Bd-temperature range association Sheet
 4: Precipitation 1. number of variables: 4 2. Number of cases/rows: 118 3.
 Variable List: * BIO: abbreviation of the six precipitation variables
 used. BIO13, BIO14, BIO16, BIO17, BIO18, BIO19. Their names are BIO13:
 Precipitation of Wettest Month, BIO14: Precipitation of Driest Month,
 BIO16: Precipitation of Wettest Quarter, BIO17: Precipitation of Driest
 Quarter, BIO18: Precipitation of Warmest Quarter, BIO19: Precipitation of
 Coldest Quarter. * Name: range: names and range of each of the six
 precipitation variables. Units are millimetres * Epsilon: epsilon values
 of each pair of Bd-precipitation range association * Score: score values
 of each pair of Bd-precipitation range association ### DATA-SPECIFIC
 INFORMATION FOR: Table S4.xls Table S4.xlsx contains a list of species
 recently confirmed positives for *Bd* (Olson et al. 2021) as well as score
 trait values and score trait quantiles. 1. Number of variables: 3 2.
 Number of cases/rows: 571 3. Variable List: * New Bd records (Olson et al
 2021): scientific names of new amphibians confirmed positives for Bd *
 Score traits: sum of score values of each amphibian trait * Score Trait
 Quantile: corresponding quantile number according to the total list of
 amphibian species. Missing values in all files are denoted by NA.