Batrachochytrium salamandrivorans thermal phenotypic variation
Data files
Sep 30, 2024 version files 1.44 MB
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Combined_data_for_temp_growth_tests_DRYAD.csv
589.23 KB
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Combined_data_for_temp_growth_tests.csv
771.92 KB
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combined_qpcr_loads.csv
77.17 KB
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README.md
5.61 KB
Abstract
Recognizing the influence of pathogen diversity on infection dynamics is crucial for mitigating emerging infectious diseases. Characterising such diversity is often complex, for instance when multiple pathogen variants exist that interact differently with the environment and host. Here, we explore genotypic and phenotypic variation of Batrachochytrium salamandrivorans (Bsal), an emerging fungal pathogen that is driving declines among an increasing number of European amphibian species. For thirteen isolates, spanning most of the known temporal and geographical Bsal range in Europe, we mapped phenotypic diversity through numerous measurements that describe varying reproductive rates in vitro across a range of temperatures. Bsal isolates are revealed to have different thermal optima and tolerances, with phenotypic variation correlating with genomic diversity. Using a mechanistic niche model of the fire salamander (Salamandra salamandra) as an example, we illustrate how host steady-state body temperature and Bsal thermal range variation may influence pathogen growth through space and time across Europe. Our combined findings show how the identity of emergent pathogen variants may strongly influence when and which host populations are most at risk.
README: Batrachochytrium salamandrivorans thermal phenotypic variation
https://doi.org/10.5061/dryad.4xgxd25j5
Description of the data and file structure
Data was derived from the following sources:
- Raw counts based on in vitro phenotypic experiments. This is the data supporting the manuscript "High phenotypic diversity correlated with genomic variation across the European Batrachochytrium salamandrivorans epizootic" by Kelly et al. Full methodology can be found in the manuscript.
- qPCR results from in vitro phenotypic experiments. This is the data supporting the manuscript "High phenotypic diversity correlated with genomic variation across the European Batrachochytrium salamandrivorans epizootic" by Kelly et al. Full methodology can be found in the manuscript.
File:
Combined_qpcr _loads.csv <- CSV of qPCR results from plate of in vitro *phenotypic growth tests of various *Bsal isolates
Variables:
row: row number
Isolate: Isolate of *Bsal *(see table below for isolate details)
experiment: experiment replicate
Plate: plate in experiment (3 plates seeded per experiment, 1 processed for qPCR on day 0, other two remain in experiment until day 10)
Well: well within the 24 well plate
day: which time point in experiment (0 or day 10 for qPCR counts)
temp: temperature that plate was cultured at (celsius)
SQ: starting quantity
QE: genomic equivalent
Combined_data_for_growth_tests.csv
image: photo id
"day": day of experiment photo taken (0,3,5,7,10)
"experiment": experient replicate
"temp": temperature plate cultured at (celsius)
"spore_count": number of spores counted in photo
"sporangia_count" : number of sporangia counted in photo
"sporangia_coverage": the area of the photo covered by sporangia (um^2)
"sporang_area_min": size of smallest sporangia in photo (um^2)
"sporang_area_max":size of largest sporangia in photo (um^2)
"sporan_area_mean": average area of sporangia in photo (total area/number sporangia) (um^2)
"sporang_area_sd": standard deviation of sporangia size in image (um^2)
"bottom_surface": is photo of bottom ("B") or surface ("S") of the well (surface photos taken only on day 3)
"Well": well id within 24 well plate
"Plate": plate number (2 plates per experiment)
"time_series": is this an isolate for which we have multiple isolates from the same outbreak site at different times (y = Yes, n = No)
"outbreak_root": name of the site of the outbreak - see table below for isolate site details
"Isolate": *Bsal *isolate cultured in well - see table below:
Isolate (Outbreak site) | Year of Isolation | Location | Passage | GenBank Sample | Accession Numbers |
---|---|---|---|---|---|
BundBos2013 (AMFP) | 2013 | Bunde, Netherlands | 14,20,26,29 | AMFP13/1 | PRJNA797022, GCA_021556675.1, |
Rob2014 (Rob) | 2014 | Robertville, Belgium | 17 | AMFP14/1 | PRJNA610831 |
Luik2014 (Luik) | 2014 | Liege (Luik), Belgium | 10,22 | AMFP14/2 | PRJNA797021, |
Captive2015-1 (NA- 1 isolate) | 2015 | Captive amphibian collection | 10,12 | AMFP15/1 | PRJNA610831, GCA_020617715.1 |
Captive2015-2 (NA- 1 isolate) | 2015 | Captive amphibian collection | 15 | AMFP15/2 | PRJNA610831, GCA_020617195.1 |
Rob2015 (Rob) | 2015 | Robertville, Belgium | 8,15 | AMFP15/3 | PRJNA610831, |
Captive2015-3 (NA- 1 isolate) | 2015 | Captive amphibian collection | 6,9 | AMFP15/4 | PRJNA845763 |
Luik2017 (Luik) | 2017 | Liege (Luik), Belgium | 8,16 | AMFP17/1 | PRJNA610831 |
BundBos2018 (AMFP) | 2018 | Bunde, Netherlands | 8,20 | AMFP18/1 | PRJNA610831 |
Catalan2018 (NA- 1 isolate) | 2018 | Montnegre i el Corredor Natural Park, Catalonia, Spain | 7,13 | AMFP18/2 | PRJNA610831, GCA_020617735.1 |
Essen2019 (NA- 1 isolate) | 2019 | Essen, Germany | 8,12 | AMFP19/1 | PRJNA845763, |
Eifel2019 (NA- 1 isolate) | 2019 | Brandscheid (Watzbach), Eifel, Germany | 11 | AMFP19/2 | PRJNA845763 |
Olne2020 (NA- 1 isolate) | 2020 | Olne, Belgium | 4,7 | AMFP20/1 |
"Observer" : photo counts were performed by 2 observers, observer ID (O1,O2) included her to allow inclusion as random effect in mixed effect model.
Analysis_script_growth_test_figures_for_publication_resubmitting_2.R: R script for analyses and figure generation
Code/Software
The analysis, figure production etc. used for manuscript generation is included.
Methods
This dataset represents the raw counts and qPCR data from in vivo phenotypic experiments. This is the data supporting the manuscript "High phenotypic diversity correlated with genomic variation across the European Batrachochytrium salamandrivorans epizootic" by Kelly et al. Full methodology can be found in the manuscript.