DOI: 10.5061/dryad.4xgxd25j5
title: Batrachochytrium salamandrivorans thermal phenotypic variation

description: 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.
description: This dataset represents the raw counts and qPCR data from
 <em>in vivo </em> phenotypic experiments. This is the data
 supporting the manuscript "High phenotypic diversity correlated with
 genomic variation across the European <em>Batrachochytrium
 salamandrivorans</em> epizootic" by Kelly <em>et
 al.</em> Full methodology can be found in the manuscript.
description: # Batrachochytrium salamandrivorans thermal phenotypic variation
 [https://doi.org/10.5061/dryad.4xgxd25j5](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** &lt;- 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.