This DATSETNAMEreadme.txt file was generated on [2021-01-14] by [Matthew J Gray] ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Winter is Coming – Temperature Affects Immune Defenses and Susceptibility to Batrachochytrium salamandrivorans 2. Author Information Principal Investigator Contact Information Name:Matthew J Gray Institution:Center for Wildlife Health, University of Tennessee Institute of Agriculture, Knoxville Address:UT Department of FWF 2505 E. J. Chapman Drive Rm 427 Plant Biotech Building, Knoxville, TN 37996 Email:mgray11@utk.edu Principal Investigator Contact Information Name:Debra L Miller Institution:Center for Wildlife Health, University of Tennessee Institute of Agriculture, Knoxville; Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville Address:UT Department of FWF 2505 E. J. Chapman Drive Rm 427 Plant Biotech Building, Knoxville, TN 37996 Email:dmille42@utk.edu Principal Investigator Contact Information Name:Doug C Woodhams Institution:University of Massachusetts, Boston Address:UMass Boston, Department of Biology 100 Morrissey Blvd. Boston, Massachusetts 02125 Email: douglas.woodhams@umb.edu Principal Investigator Contact Information Name:Louise Rollins-Smith Institution:Department of Microbiology and Immunology,Vanderbilt University Medical Center Address: A-5301 Medical Center North, Nashville, TN 37232 Email: louise.rollins-smith@Vanderbilt.Edu Associate or Co-investigator Contact Information Name: Molly C Bletz Institution:University of Massachusetts, Boston Address:UMass Boston, Department of Biology 100 Morrissey Blvd. Boston, Massachusetts 02125 Email:molly.bletz@umb.edu Associate or Co-investigator Contact Information Name:Brandon LaBumbard Institution:University of Massachusetts, Boston Address:UMass Boston, Department of Biology 100 Morrissey Blvd. Boston, Massachusetts 02125 Email:Brandon.LaBumbard001@umb.edu Associate or Co-investigator Contact Information Name: Mitchell Le Sage Institution:Department of Microbiology and Immunology,Vanderbilt University Medical Center Address: A-5301 Medical Center North, Nashville, TN 37232 Email:mitchell.lesage@vumc.org Associate or Co-investigator Contact Information Name: E. Davis Carter Institution:Center for Wildlife Health, University of Tennessee Institute of Agriculture, Knoxville Address:UT Department of FWF 2505 E. J. Chapman Drive Rm 427 Plant Biotech Building, Knoxville, TN 37996 Email:ecarte27@utk.edu 3. Date of data collection (single date, range, approximate date) 2018-2020 4. Geographic location of data collection (where was data collected?): University of Tennessee, Knoxville, TN Vanderbilt University, Nashville, TN University of Massachusetts, Boston, MA 5. Information about funding sources that supported the collection of the data: This research was supported by a National Science Foundation Division of Environmental Biology (Ecology and Evolution of Infectious Disease Program) grant (#1814520) awarded to MJG, DLM, DCW, and LRS, and the U.S. Department of Defense SERDP (Award #W912HQ-16-C-0033, C. Richards-Zawacki, PI). MJG and DLM also were supported by Hatch Project 1012932 of the U.S. Department of Agriculture National Institute of Food and Agriculture. 6. Abstract/description of the dataset: Environmental temperature is a key factor driving various biological processes, including immune defenses and host-pathogen interactions. Here, we evaluated the effects of environmental temperature on the pathogenicity of the emerging fungus, Batrachochytrium salamandrivorans (Bsal), using controlled laboratory experiments, and measured components of host immune defense to identify regulating mechanisms. We found that adult and juvenile Notophthalmus viridescens died faster due to Bsal chytridiomycosis at 14 ºC than at 6 and 22 ºC. Pathogen replication rates, total available proteins on the skin, and microbiome composition likely drove these relationships. Temperature-dependent skin microbiome composition in our laboratory experiments matched seasonal trends in wild N. viridescens, adding validity to these results. We also found that hydrophobic peptide production after two months post-exposure to Bsal was reduced in infected animals compared to controls, perhaps due to peptide release earlier in infection or impaired granular gland function in diseased animals. Using our temperature-dependent infection results, we performed a geographic analysis that suggested that N. viridescens populations in the northeastern United States and southeastern Canada are at greatest risk for Bsal invasion. Our results indicate that environmental temperature will play a key role in the epidemiology of Bsal and provide evidence that temperature manipulations may be a viable Bsal management strategy. 7: Keywords for the dataset (provide 3 - 5): Amphibian Diseases, Microbiome, Amphibian Immunity -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: 2. Links to publications that cite or use the data: 3. Links to other publicly accessible locations of the data: 4. Links/relationships to ancillary data sets: 5. Was data derived from another source? If yes, list source(s):Yes Files:L and M Climate data: Fick, S.E. and R.J. Hijmans, 2017. Worldclim 2: New 1-km spatial resolution climate surfaces for global land areas. International Journal of Climatology. Species Range data: IUCN SSC Amphibian Specialist Group. 2015. Notophthalmus viridescens. The IUCN Red List of Threatened Species 2015: e.T59453A78906143. https://dx.doi.org/10.2305/IUCN.UK.2015-4.RLTS.T59453A78906143.en. 6. Recommended citation for the data: --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: 16S_Metadata_AlphaDiv_AntiFungalPred_TimePre.txt Short description: Sample metadata for newts sampled prior to Bsal exposure along with alpha diversity metrics and anti-Batrachochytrium predictions calculated from an 16S OTU table rarefied to 5000 reads. B. Filename:16S_TimePre_EEID_AdultTempExp_OTUTable_deblur_tr245.txt Short description: 16S unrarefied sOTU table for newts sampled prior to Bsal exposure; samples are columns, sOTUs are rows C. Filename: 16S_Taxonomy.txt Short description: Taxonomic classification of 16S sOTUs D. Filename: ITS_Metadata_AlphaDiv_TimePre.txt Short description: Sample metadata for newts sampled prior to Bsal exposure along with alpha diversity metrics calculated from an ITS OTU table rarefied to 1000 reads. E. Filename: ITS_TimePre_EEID_AdultTempExp_OTUTable_ITSXprocessed_DADA2_tr100.txt Short description: ITS unrarefied sOTU table for newts sampled prior to Bsal exposure; samples are columns, sOTUs are rows F. Filename: ITS_Taxonomy.txt Short description: Taxonomic classification of ITS sOTUs G. 16S_Metadata_AlphaBetaDiv_AntiFungal_Vermont_Field2017.txt Short description: Sample metadata for newts sampled in 2017 in Colchester Vermont, along with alpha and beta diversity metrics and anti-Batrachochytrium predictions calculated from an 16S OTU table rarefied to 4600 reads H. Filename:16S_Vermont_Field2017_OTU-table.txt Short description: 16S unrarefied sOTU table for newts sampled in 2017 from Colchester, Vermont; samples are columns, sOTUs are rows I. Filename: NOVISSData Short description: This datafile includes the following data collected on Eastern Newt adults: body condition (mass, SVL, Tail length); skin secretion recovery (Total Protein, Hydrophobic Peptide), inhibition of Bsal by skin secretions (using CellTiterGlo assay for Total Protein, and 7-day Growth Inhibition Assay for Hydrophobic Peptides). J. Filename:EEID_NOVI_Survival Short description: Survival times for each individual newt used in the temperature experiments. K. Filename:EEID_NOVI_Copy_Analysis Short description: Bsal load data measured by performing qPCR on DNA extracted from swab samples. L. Filename:NOVI_Temp_Data_Distribution Short description: This datafile includes the output of merged average annual temparture and maximum temperature rasters created from WorlClim2 temperature data rasters and a rasterized IUCN N. viridescens polygon. M. Filename:NOVI_Range_Data_Temp Short description: This datafile consists of the scaled (1-4) temperature data used to inform the final map. The scaled data was created using the methods outlined in the supplemental file. N. Filename:WorlClim2.zip Short description: This zip folder contains temperature rasters obtained from the Worldclim2 website. O. Filename:EEID_R_AdultExp_PlosPathogens_Code.Rmd Short description: This code was written to perform analysis on Files A-F. P. Filename:EEID_R_AdultExp_PlosPathogens_Code.txt Short description: This .txt file contains Rmd written to perform analysis on Files A-F. Q. Filename:EEID_R_AdultExp_PlosPathogens_Code.html Short description: This html document contains Rmd code and ouput of analyses performed on Files A-F. R. Filename:Newt_16S_2017Vermont.Rmd Short description: This code was written to perform analysis on Files G and H. S. Filename:NSF_EEID_NewtSecretions.txt Short description: This text file contains Rmd code for analysis of File I. T. Filename:NSF_EEID_NewtSecretions.html Short description: This html file contains Rmd code and output for analysis of File I. U. Filename:EEID_NOVI_Temperature_Survival_Analysis.R Short description: This R file contains code for analysis of File J. V. Filename:EEID_NOVI_Bsal_Copy_Analysis.R Short description: This R file contains code for analysis of File K. W. Filename:EEID_Bsal_Habitat_Suitability_Map_Scaling.R Short description: This R file contains code for habitat suitability scaling performed on File L which resulted in the ouput found in File M. 2. Relationship between files: Files A-C are associated with the 16S microbiomes and Files D-F are associated ITS microbiomes and the code used to perform analyses on these data can be found in Files O-Q. Files G-H are associated with the 16S microbiomes and the code used to perform analyses on these data can be found in File R. File I is associated with newt protein and hydrophobic peptide secretions and File T can be used to analyze these data. File J is associated with the survival of newts exposed during the course of this work and the code used for analysis can be found in File U. File K relates to Bsal loads detected on adult and eft stage newts exposed at three environmental temperatures (6,14 and 22C) and the code used to analyze the data are found in File V. File L and M relate to the Bsal risk map produced for Notophthalmus viridescens based on the temperature dependent susceptibility of the species. The code used to create File M from File L can be found in File W. File N contains the WorlClim2 temperature raster files used to create file L. 3. Additional related data collected that was not included in the current data package: NA 4. Are there multiple versions of the dataset? NO If yes, list versions: Name of file that was updated: i. Why was the file updated? ii. When was the file updated? Name of file that was updated: i. Why was the file updated? ii. When was the file updated? -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: Files A-F: We quantified differences in skin bacterial and fungal communities among temperatures for adult N. viridescens by sequencing extracted gDNA from swabs taken after one-week acclimation to temperatures but prior to Bsal exposure. Files G and H: We quantified differences in skin bacterial communities among adult N. viridescens that were sampled in Colchester, Vermont in 2017 as part of another study. We sequenced extracted gDNA from these collected skin swabs. File I: We induced skin secretion production in adult Eastern Newts using a subcutaneous injection of acetylcholine at 25nmol/gram body mass. Skin secretions were divided into two fractions: Total Proteins (unfiltered) which were quantified, and lyophilized to challenge Bsal zoospores, and Hydrophobic Peptides, which were filtered through a C-18 SepPak, quantified, and then used to challenge Bsal zoospores. Files J-K: We exposed adult and eft stage N. viridescens to Bsal at three temperatures 6, 14 and 22C. We then monitored the health of the exposed animals for until death, euthanasia or the termination of the experiment. Swabs were collected from each animal and tested for Bsal DNA using qPCR. Files L: This file was created by merging temperature raster data retrieved from the WorldClim2 data source with a rasterized version of the N. viridescens range polygon retrieved from the IUCN database. File M: This data was produced by scaling temperature data found in File L to a risk range between 1 and 4 using methods described in the supplemental methods section provided in the publication. File N: These temperature raster files were downloaded from the WorldClim2 website and imported into ArcGIS 10.7. Cell statistics were then used to calculate the average annual temperature and the maximum annual temperature for each raster cell. The resulting rasters were then used to form File L along with the rasterized N. viridescens range polygon. 2. Methods for processing the data: Files A-F: We PCR-amplified the V4 region of the 16S rRNA gene for bacterial communities and the ITS1 region for fungal communities with single index barcoded primers (bacterial:515f–806r, fungal: ITS1f-ITS2r) as described in the Earth Microbiome Protocol (EMP, 2018) with a few modifications to increase PCR efficiency. The PCR cycle conditions followed Bletz et al. [73] for bacterial community amplification and the EMP for fungal communtiy amplification. PCR products were purified and equalized using the Omega Biotek MagBead Normalization Kit (Omega biotek, Norcross, GA USA). We pooled equal-molar PCR products and these were sequenced on an Illumina MiSeq (Illumina, San Diego, CA USA) at University of Massachusetts Boston using 2x250 paired-end v2 chemistry kit. We processed generated sequence data in Quantitative Insights into Microbial Ecology 2 (QIIME2, Bolyen et al. [74]). Briefly, we demultiplexed, quality filtered (minimum q-score of 10), and clustered raw sequence data into sub-Operational Taxonomic Units (sOTU) using deblur for bacterial communities [75] and DADA2 for fungal communities [76]. For ITS data, we trimmed the conserved flanking regions from sequences using ITSxpress as recommended for amplicon sequencing [77,78]. After filtering, 1,242,115 bacterial 16S sequence reads remained (average: 9,269.5 reads/sample) representing 1,142 sOTUs and 895,217 fungal ITS reads (average 6,781.9 reads/sample) and 1,901 ASVs. We subsequently rarefied all samples at 5,000 reads per sample for bacteria and 1,000 reads for fungal communities to adequately capture sample diversity and retain the majority of sequenced samples. We assigned taxonomy with classify-sklearn [79], built a phylogenetic tree using mafft and fasttree2 [80], and calculated alpha and beta diversity metrics (sOTU richness and Faith's phylogenetic diversity), weighted and unweighted UniFrac metrics (16S only), and Bray-Curtis and binary Jaccard metrics in QIIME2. Files G and H: We PCR-amplified the V4 region of the 16S rRNA gene for bacterial communities with single index barcoded primers (bacterial:515f–806r) as described in the Earth Microbiome Protocol (EMP, 2018) with a few modifications to increase PCR efficiency. The PCR cycle conditions followed Bletz et al. [73] for bacterial community amplification. PCR products were purified and equalized using the SequalPrep Normalization Kit (ThermoFisher Scientific, USA). We pooled equal-molar PCR products and these were sequenced on an Illumina MiSeq (Illumina, San Diego, CA USA) at University of Massachusetts Boston using 2x150 paired-end v2 chemistry kit. We processed generated sequence data in Quantitative Insights into Microbial Ecology 2 (QIIME2, Bolyen et al. [74]). Briefly, we demultiplexed, quality filtered (minimum q-score of 10), and clustered raw sequence data into sub-Operational Taxonomic Units (sOTU) using deblur for bacterial communities. We subsequently rarefied all samples at 4600 reads per sample for bacteria communities to adequately capture sample diversity and retain the majority of sequenced samples. We assigned taxonomy with classify-sklearn [79], built a phylogenetic tree using mafft and fasttree2 [80], and calculated alpha and beta diversity metrics (weighted UniFrac metrics) in QIIME2. File I: Total Proteins were quantified using a BSA standard in a microBCA assay, and Hydrophobic Peptides were quantified using a bradykinin standard in a microBCA assay. Total Proteins were used to challenge Bsal zoospores to determine percent inhibition using a CellTitreGlo assay. Hydrophobic Peptides were used to challenge Bsal zoospores and calculate percent inhibition using a 7-day Growth Inhibition assay. File J: We randomly assigned animals to one of four Bsal exposure doses (5x10^3, 5x10^4, 5x10^5 and 5x10^6 Bsal zoospores per 10 mL) or to a control group. After exposure, we placed the animals in Conviron® environmental growth chambers (Winnipeg, Canada) which were set to one of the three target temperatures (6, 14, 22C).The experiments lasted between 45 and 90 days, which has been shown to be a sufficient duration for Bsal chytridiomycosis to develop. Animals were humanely euthanized loss of righting reflex. Natural mortalities were also noted. Animals that were euthanized or died naturally prior to the end of an experiment were recorded as mortalities for the data analysis. File K: We collected swabs from animals every 6 days and at death/euthanasia. Our swabbing procedure involved swabbing the ventrum and feet of each individual using a rayon tipped swab with a plastic shaft. We extracted genomic DNA from the swab samples using Qiagen DNeasy Blood and Tissue kits. The extracted DNA was then tested for Bsal DNA via qPCR and Bsal load data determined based off comparison to a standard curve. Each qPCR reaction was run in duplicate. File L: This datafile was created by merging together multiple raster data files which were created using the WorldClim2 data and a rasterized species range produced from an IUCN species polygon for N. viridescens. The rasters were merged together using the combine function in the spatial analysis toolbox. For each unique combination of raster input values there is a unique output value produced. File M: This datafile was created by scaling the unique output values found in File L. The values of File L were scaled in R using the methods described in the supplemental text. 3. Instrument- or software-specific information needed to interpret the data: Files A-H: Initial processing was completed in QIIME2 - see Qiime2.org for data processing information. File L was created using ArcMap version 10.7. 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: Files A-F and I-K: Newts were housed at four temperatures: 6°C, 14°C, 22°C. Files: G and H: Seasonal sampling of aquatic adult newts from 2017 in Colchester, Vermont. We sampled in the spring, summer, and fall for newts. 6. Describe any quality-assurance procedures performed on the data: Files A-H: Negative PCR controls were included to ensure quality of sequencing data and control for possible contamination File I: Negative controls and growth standards were included in all assays to ensure Bsal growth was standardized. File J: Control newts were mock inoculated with 1/mL of water and held in exposure containers and housing containers which matched those used for exposed animals. File K: Positive and negative controls were included on each qPCR plate ran to estimate Bsal load found on each swab sample. 7. People involved with sample collection, processing, analysis and/or submission: Files A-F, :Molly Bletz, Doug Woodhams Files G and H: Brandon LaBumbard, Doug Woodhams Files I: Louise Rollins-Smith, Mitchell LeSage Files J-M: Matthew J Gray, Davis Carter ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [16S_Metadata_AlphaDiv_AntiFungalPred_TimePre] ----------------------------------------- 1. Number of variables: 16 2. Number of cases/rows: 134 (+ header) 3. Variable List A. Name: SampleID Description: unique sample ids B. Name: BarcodeSequence Description: unique barcode associated with illumina sequencing C. Name: LinkerPrimerSequence Description: Linker sequences associated with illumina sequencing D. Name: Temperature Description: Temperature at which the newts were housed during the experiments E. Name: TimeWeek Description: The time point at which sampling occurred F. Name: CollectionLocation Description: Location where newt was collected G. Name: Propor_TotalAntiFungal_Full Description: proportion of community predicted to have Bactrachochytrium-inhibitory function from full data including Bd- and Bsal-inhibitory isolates H. Name: faith_pd Description: phylogenetic diversity value for bacterial community I. Name: observed_otus Description: OTU richness value for bacterial community J. Name: Propor_TotalAntiFungal_BSALonly Description: proportion of community predicted to have Bactrachochytrium-inhibitory function from only known Bsal-inhibitory isolates 4. Missing data codes: Code/symbol NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 16S_TimePre_EEID_AdultTempExp_OTUTable_deblur_tr245.txt ----------------------------------------- 1. Number of variables: 135; Column 1 is OTU ID codes; Column 2-135 represent individuals newts 2. Number of cases/rows: 1143, Row 1 is column headers; 2-1143 represent OTU IDs 3. Variable List A. Name: OTUID Description: OTU ID codes B. Name: Column 2-134 Description: individual newt IDS corresponding to metadata SampleIDs 4. Missing data codes: NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 16S_Taxonomy.txt ----------------------------------------- 1. Number of variables:3 2. Number of cases/rows: 1143 3. Variable List A. Name: OTUID Description: OTU ID codes B. Name: Taxon Description: Taxonomic string associated with OTU ID C. Name: Confidence Description: confidence value is taxonomic identification 4. Missing data codes: NA 5. Specialized formats of other abbreviations used NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ITS_Metadata_AlphaDiv_TimePre.txt ----------------------------------------- 1. Number of variables: 7 2. Number of cases/rows: 90, first is column header 3. Variable List A. Name: SampleID Description: unique sample ids B. Name: BarcodeSequence Description: unique barcode associated with illumina sequencing C. Name: LinkerPrimerSequence Description: Linker sequences associated with illumina sequencing D. Name: Temperature Description: Temperature at which the newts were housed during the experiments E. Name: TimeWeek Description: The time point at which sampling occurred F. Name: CollectionLocation Description: Location where newt was collected G. Name: observed_otus Description: OTU richness value for bacterial community 4. Missing data codes: NA 5. Specialized formats of other abbreviations used NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ITS_TimePre_EEID_AdultTempExp_OTUTable_ITSXprocessed_DADA2_tr100.txt ----------------------------------------- 1. Number of variables: 90 2. Number of cases/rows: 1902, first is column header 3. Variable List A. Name: OTUID Description: OTU ID codes B. Name: Column 2-90 Description: individual newt IDS corresponding to metadata SampleIDs 4. Missing data codes: NA 5. Specialized formats of other abbreviations used NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: ITS_Taxonomy.txt ----------------------------------------- 1. Number of variables: 2 2. Number of cases/rows: 3724, first is column header 3. Variable List A. Name: OTUID Description: OTU ID codes B. Name: Taxon Description: Taxonomic string associated with OTU ID C. Name: Confidence Description: confidence value is taxonomic identification 4. Missing data codes:NA 5. Specialized formats of other abbreviations used NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [16S_Metadata_AlphaBetaDiv_AntiFungal_Vermont_Field2017.txt] ----------------------------------------- 1. Number of variables: 23 2. Number of cases/rows: 134 (+ header) 3. Variable List A. Name: SampleID Description: unique sample ids B. Name: BarcodeSequence Description: unique barcode associated with illumina sequencing C. Name: LinkerPrimerSequence Description: Linker sequences associated with illumina sequencing D. Name: Date Description: Date skin swab was taken of animal E. Name: Season Description: The season at which sampling occurred F. Name: Site Description: Location where newt was collected G. Name: Species Description: Notophthalmus viridescens H. Name: Bd_Total Description: ITS copies of Batrachochytrium dendrobatidis estimated through qPCR of newts' skin swab DNA extract I. Name: log_BdLoad Description: ITS copies (log transformed) of Batrachochytrium dendrobatidis estimated through qPCR of newts' skin swab DNA extract J. Name: Infected Description: Detection of Batrachochytrium dendrobatidis DNA estimated through qPCR of newts' skin swab DNA extract K. Name: observed_otus Description: OTU richness value for bacterial community L. Name: faith_pd Description: phylogenetic diversity value for bacterial community M. Name: AntiFungal_Richness Description: Number of sOTUs that match the Bactrachochytrium-inhibitory database N. Name: TotalAntiFungal Description: Total number of reads to have Bactrachochytrium-inhibitory function from full data O. Name: Propor_TotalAntiFungal Description: proportion of community predicted to have Bactrachochytrium-inhibitory function from full data P. Name: W_PCoA1 Description: Weighted Unifrac ordination value for the PCoA 1 axis Q. Name: W_PCoA2 Description: Weighted Unifrac ordination value for the PCoA 2 axis R. Name: W_PCoA3 Description: Weighted Unifrac ordination value for the PCoA 3 axis 4. Missing data codes: Code/symbol NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: 16S_Vermont_Field2017_OTU-table.txt ----------------------------------------- 1. Number of variables: 91; Column 1 is OTU ID codes; Column 2-90 represent individuals newts 2. Number of cases/rows: 1143, Row 1 is column headers; 2-6498 represent OTU IDs 3. Variable List A. Name: OTUID Description: OTU ID codes B. Name: Column 2-90 Description: individual newt IDS corresponding to metadata SampleIDs 4. Missing data codes: NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [NOVISSData.csv] ----------------------------------------- 1. Number of variables: 24 2. Number of cases/rows: 451 3. Variable List A. Name: VID Description: unique ID label of an individual newt Value labels if appropriate: (L01 - L86) B. Name: Trtmt Description: exposure treatment of the newt, in number of Bsal zoospores (or Control, for unexposed newts) Value labels if appropriate: 5*10^3, 5*10^4, 5*10^5, 5*10^6, Control C. Name: Temp Description: temperature of the housing of the newt Value labels if appropriate: 22°C, 14°C, 6°C D. Name: Secretion Description: type of induced secretion Value labels if appropriate: Hydrophobic Peptide, Total Protein E. Name: InduceType Description: method used to induce skin secretions Value labels if appropriate: ACh injection, Massage, APBS F. Name: InduceConc Description: concentration of Acetylcholine (ACh) used to induce secretion (or Massage for massaged newts, or APBS for newts injected with Amphibian Phosphate-Buffered Saline) Value labels if appropriate: 25.0nmol/g, 50.0nmol/g, 12.5nmol/g, Massage, APBS G. Name: DPI Description: days Post Inducement, number of days since the most recent previous inducement for this newt (000 if this is the first time) Value labels if appropriate H. Name: InjDate Description: date of inducement Value labels if appropriate I. Name: Mass Description: mass of the newt in grams at time of inducement Value labels if appropriate J. Name: SVL Description: snout-vent length measurement at time of inducement Value labels if appropriate K. Name: Tail Description: tail length measurement at time of inducement Value labels if appropriate L. Name: mBCADate Description: date of microBCA quantification assay Value labels if appropriate M. Name: mBCAConc Description: concentration of sample according to microBCA assay µg/ml Value labels if appropriate N. Name: SampVol Description: volume of sample quantified by microBCA in ml Value labels if appropriate O. Name: Totalug Description: micrograms of secretion product in sample Value labels if appropriate P. Name: uggbw Description: micrograms of secretion product per gram body mass produced by this newt Value labels if appropriate Q. Name: CellGloDate Description: date on which a CellTiterGlo assay was carried out to determine inhibitory effectiveness on Bsal (only for Total Protein samples) Value labels if appropriate R. Name: CellGloConc Description: concentration of secretion product used in CellTiterGlo assay, in micrograms per ml Value labels if appropriate S. Name: CellGloPctInhib Description: percent of growth inhibition of Bsal caused by this concentration of secretion product Value labels if appropriate T. Name: CellGloEffectiveness Description: effectiveness of the secretion product to inhibit Bsal growth (CellGloPctInhib * uggbw) Value labels if appropriate U. Name: GIA Date Description: date on which a 7-day Growth Inhibition assay (GIA) was carried out to determine inhibitory effectiveness on Bsal (only for Hydrophobic Peptides) Value labels if appropriate V. Name: GIA250 Description: if "Y", a GIA was carried out challenging Bsal zoospores with 250µg/ml secretion product Value labels if appropriate W. Name: GIAPctInhib250 Description: percent of growth inhibition of Bsal caused by this concentration of secretion product Value labels if appropriate X. Name: GIA250Effectiveness Description: effectiveness of the secretion product to inhibit Bsal growth (GIAPctInhib250 * uggbw) Value labels if appropriate 4. Missing data codes: NA Code/symbol Definition Code/symbol Definition 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [EEID_NOVI_Survival.csv] ----------------------------------------- 1. Number of variables: 7 2. Number of cases/rows: 210 3. Variable List A. Name:ID Description:Animal identification character and number. B. Name: Treatment Description:This variable indicates the exposure treatment the animal was assigned to. C. Name:DaysSurvived Description: This variable indicates the number of days each animals survived after Bsal exposure. D. Name: Life_Stage Description: This variable indicates the life-stage of newt being tested. E. Name: Stage_Treatement Description: This variable indicates both the life-stage and exposure treatment each animal belonged to. F. Name: Temp Description: This variable indicates the temperature each animal was exposed at. 4. Missing data codes: Code/symbol NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [EEID_NOVI_Copy_Analysis.csv] ----------------------------------------- 1. Number of variables: 9 2. Number of cases/rows: 210 3. Variable List A. Name:Sample Description:Animal ID for the sample. B. Name:Treatment Description:This variable indicates the exposure group assigned to each animal. C. Name: Temp Description:This variable indicates the temperature each animal was being housed at during each experiment. D. Name: CT Mean Description: This variable indicates which cycle the cycle threshold was reached. Samples which did not reach the cycle threshold prior to 40 cycle are indicated as having a CT Mean of 50. E. Name: Quantity Description: This variable indicates the quantity () of Bsal detected on each swab sample. F. Name: Pos Description: This binary variable indicates whether or not the animal tested positive for Bsal. G. Name: Neg Description: This binary variable indicates whether or not the animal tested postive for Bsal. H. Name:LifeStage Description: This variable indicates the life-stage of newt each sample was collected from. 4. Missing data codes: Code/symbol NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [NOVI_Temp_Data_Distribution.csv] ----------------------------------------- 1. Number of variables: 6 2. Number of cases/rows: 131 3. Variable List A. Name:ObjectID Description: Identification code for each unique combination of raster inputs. B. Name: Value Description: Duplicate output of identification code. C. Name: Count Description: The count variable refers to the number of unique raster cells combined into the new output level. D. Name: MaxTemp Description: The average temperature of the warmest month for each of the object outputs formed during the merging of the raster inputs. E. Name: AverageAnnualTemp Description: The average annual temperature for each of the object outputs formed during the merging of the raster inputs. F. Name: NOVIRasterCreation Description: This variable indicates whether N. viridescens are present in the new object output formed during the merging of the raster inputs. 4. Missing data codes: Code/symbol NA 5. Specialized formats of other abbreviations used: NA ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: [NOVI_Range_Data_Temp_Revised.csv] ----------------------------------------- 1. Number of variables: 7 2. Number of cases/rows: 131 3. Variable List A. Name:OBJECTID Description:Identification code for each unique combination of raster inputs. B. Name: MaxTemp Description: The average temperature of the warmest month for each of the object outputs formed during the merging of the raster inputs. C. Name: AverageAnnualTemp Description: The average annual temperature for each of the object outputs formed during the merging of the raster inputs. D. Name: NOVIRasterCreation Description: This variable indicates whether N. viridescens are present in the new object output formed during the merging of the raster inputs. E. Name: MeanTempScale Description: The MeanTempScale variable indicates the Bsal risk score given to each value of AverageAnnualTemp. The scale ranges from 1-4 with scores of 1 indicating less suitable temperatures for Bsal while areas closer to 4 indicate ideal temperatures for the pathogen. F. Name: MaxTempScale Description: The MaxTempScale variable indicates the Bsal risk score given to each value of MaxTemp. The scale ranges from 1-4 with scores of 1 indicating less suitable warmest month temperatures for Bsal while areas given scores closer to 4 indicate ideal temperatures for the pathogen. G. Name: OverallHabitatSuitability Description: The average of the MeanTempScale and MaxTempScale values for each OBJECTID. 4. Missing data codes: Code/symbol NA 5. Specialized formats of other abbreviations used: NA