Data for: Epidemiological landscape of Batrachochytrium dendrobatidis and its impact on amphibian diversity at global scale
Data files
Dec 13, 2023 version files 2.14 MB
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README.md
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Supplementary_information_S1.docx
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Table_S1.xlsx
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Table_S2.xlsx
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Table_S3.xlsx
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Table_S4.xlsx
Abstract
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.
README: 1. Title of Dataset: Epidemiological landscape of Batrachochytrium dendrobatidis and its impact on amphibian diversity at global scale
https://doi.org/10.5061/dryad.83bk3j9zv
2. Authors Information
M. Delia Basanta
Department of Biology, University of Nevada Reno. Reno, Nevada, USA.
delibasanta@gmail.com
Julián A. Velasco
Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México. Ciudad de México, México.
javelasco@atmosfera.unam.mx
Constantino González-Salazar.
Instituto de Ciencias de la Atmósfera y Cambio Climático, Universidad Nacional Autónoma de México. Ciudad de México, México.
cgsalazar@atmosfera.unam.mx
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:
- Table S1.xls
- Supplementary information S1.docx
- Table S2.xlsx
- Table S3.xlsx
- 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, 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.
Number of variables: 10
Number of cases/rows: 2674
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.
- number of figures: 4
- 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.
Number of variables: 26
Number of cases/rows: 6108
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
- number of variables: 3
- Number of cases/rows: 6108
- 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
- number of variables: 3
- Number of cases/rows: 20
- 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
- number of variables: 4
- Number of cases/rows: 120
- 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
- number of variables: 4
- Number of cases/rows: 118
- 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.
Number of variables: 3
Number of cases/rows: 571
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.
Methods
Usage notes
These datasets include the geographic data used to build ecological and geographical models for Batrachochytrium dendrobatidis, as well as supplementary results of the following paper: Basanta et al. Epidemiological landscape of Batrachochytrium dendrobatidis 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 Bd 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 Bd-variable pair combination.
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.
List of new species confirmed positives for Bd (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.