Data from: Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns

This readme file was generated on 2022-09-14 by Tamilie Carvalho GENERAL INFORMATION Title of Dataset: Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns. Author Information Name: Tamilie Carvalho ORCID: https://orcid.org/0000-0001-7300-2777 Institution: University of Michigan Address: 2220 Biological Science Building, 1105 North University, Ann Arbor, MI 48109-1085, USA. Email: [e-mail]; [e-mail] Co-author Information Name: Daniel Medina Institution:The Pennsylvania State University Address: University Park, PA 16802, USA. Email: [e-mail] Co-author Information Name: Jessica Hite Institution: University of Wisconsin-Madison Address: 2015 Linden Dr, Madison, WI 53706, USA. Email: [e-mail] Date of data collection: 2018-04-01 to 2018-07-01 Geographic location of data collection: São Paulo, Brazil. Latitude: 23°38'02"S; Longitude: 46°40'54" Information about funding sources that supported the collection of the data: Grants and fellowships were provided by Sao Paulo Research Foundation (FAPESP #2016/25358-3; #2018/08650-8; #2018/236220; #2019/18335-5), the National Council for Scientific and Technological Development (CNPq #300896/2016-6; #302834/2020-6), and the Coordination for the Improvement of Higher Education Personnel (CAPES - Finance Code 001). Recommended citation for this dataset: Carvalho, T; Medina, D; Ribeiro, LP; Rodriguez, D; Jenkinsom, TS; Becker, CG; Toledo, LF; Hite, J.2022. Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns. DATA & FILE OVERVIEW File List: 1. Survival\_analysis\_comp\_exp\_with\_triple\_coinfections\_to\_upload.csv 2. Suvival\_analysis.Rmd 3. all\_GPLxBrazil.csv 4. 01\_PairwiseCompPart1.Rmd 5. 02\_PairwiseCompPart2.Rmd 6. 03\_MortalityStats.Rmd 7. 04\_Plots.Rmd Relationship between files: Use file number 1 to run R code number 2, and file number 3 to run R code numbers 4,5,6, and 7. DATA-SPECIFIC INFORMATION FOR: Survival\_analysis\_comp\_exp\_with\_triple\_coinfections\_to\_upload.csv Number of variables: 6 Number of rows: 298 Variable List: 1. Mortality\_day: Values reflect the number of days until death after exposure to the pathogen. 2. Censor\_corrected: 1 when the frog died, and 0 when it survived until the end of the experiment. 3. Field\_number: Frog identification number. 4. Genotype: Genotype(s)ID and combination of genotype(s) used in the exposure treatment. P - Panzootic, E - Enzootic, and R - recombinant. P1 (single infection with genotype CLFT168), P2 (single infection with genotype CLFT198), E1 (single infection with genotype CLFT041), E2 (single infection with genotype CLFT172), R (single infection with genotype CLFT024\_02), E1-R (coinfection with genotypes CLFT41 and CLFT024\_02), E2-R (coinfection with genotypes CLFT172 and CLFT024\_02),P1-R (coinfection with genotypes CLFT168 and CLFT024\_02),P2-R (coinfection with genotypes CLFT198 and CLFT024\_02),P1-E1 (coinfection with genotypes CLFT168 and CLFT041), P1-E2 (coinfection with the genotypes CLFT168 and CLFT172),P2-E1 (coinfection with the genotypes CLFT198 and CLFT041),P2-E2 (coinfection with genotypes CLFT198 and CLFT172),E1-P1-R (coinfection with genotypes CLFT041, CLFT168 and CLFT024\_029¡), E1-P2-R (coinfection with genotypes CLFT041, CLFT198 and CLFT024\_02), E2-P1-R (coinfection with genotypes CLFT172, CLFT168 and CLFT024\_02), E2-P2-R (coinfection with genotypes CLFT172, CLFT198 and CLFT024\_02), and Control (No genotype used). 5. Lineage\_type: lineage(s) ID and combination used in the exposure treatment. Panzootic - Batrachochytrium dendrobatidis Global Panzootic Lineage (Bd-GPL) - includes the P1 and P2 genotypes. Enzootic - Bd-Asia2/Brazil lineage - includes the E1 and E2 genotypes. Hybrid - Bd recombinant genotype. Together means that one or more lineages or genotype were used in the exposure experiment. Control (No lineages/genotypes used). 6: Strains\_number: Number of pathogen strains/genotyes used in the exposure experiment. DATA-SPECIFIC INFORMATION FOR: all\_GPLxBrazil.csv Number of variables: 23 Number of rows: 529 Variable List: 1. ID\_Field: Id (B) and FieldN (C) columns combined 2. ID: Frog identification number. 3. FieldN: When the animal was swabbed. M - Day of death, # - day 21 after pathogen exposure, F - End of experiment. 4. FieldN\_2: S1 - frog was swabbed on the day 21 after pathogen exposure; and S2 - frog swabbed on either the day of death or at the end of the experiment. 5. Day\_swab: Represents the number of days after pathogen exposure in which the frog was swabbed. 6. Treatment: Single (frog infected with a single strain/genotype), Coinfected (frog coinfected with more than one strain/genotype). 7. TotalInitialDoseZoosporesPermL: Number of total Bd zoospores each animal was exposed to during infection. 8. StrainSpecificInitialDoseZoosporesPermL: Number of Bd zoospores from each strain/genotype used for exposure during infection. 9. Lineage\_type: lineage(s) and genotypes IDs and combination used in the exposure treatment. Panzootic - single infection with P1 (CLFT168) or P2 (CLFT198), Enzootic - single infection with E1 (CLFT041) or E2 (CLFT172), Recombinant - single infection with the recombinant genotype (CLFT024\_02), E-P Coinfection - Coinfection with panzootic (P1 or P2) and enzootic (E1 or E2) genotypes, R Coinfection - Coinfection with the recombinant and panzootic (P1 or P2) or enzootic (E1 or E2) genotypes, and P-E-R Coinfection - Coinfection with panzootic (P1 or P2), enzootic (E1 or E2) and recombinant genotypes. 10. Lineage: genotypes IDs and combination used in the exposure treatment. B172xH - Coinfection with CLFT172 and recombinant genotypes, B41xH Coinfection with CLFT041 and recombinant genotypes, Brazil - single infection with E1 (CLFT041) or E2 (CLFT172), GPL - single infection with P1 (CLFT168) or P2 (CLFT198), GPL168xH - Coinfection with CLFT168 and recombinant genotypes, GPL198xH - Coinfection with CLFT198 and recombinant genotypes, GxB - Coinfection with panzootic (P1 or P2) and enzootic (E1 or E2) genotypes, GxBxH - Coinfection with panzootic (P1 or P2), enzootic (E1 or E2) and recombinant genotypes, and R - single infection with the recombinant genotype. 11. Strains: genotypes IDs and combination used in the exposure treatment. 198 (single infection with the strain CLFT198), 41 (single infection with the strain CLFT041),168 (single infection with the strain CLFT168),172 (single infection with the strain CLFT172), 24 (single infection with the strain CLFT024\_02), 172\_24(coinfection with the strains CLFT172 and CLFT024\_02), 41\_24 (coinfection with the strains CLFT41 and CLFT024\_02), 168\_24 (coinfection with the strains CLFT168 and CLFT024\_02), 168\_41 (coinfection with the strains CLFT168 and CLFT041), 168\_172 (coinfection with the strains CLFT168 and CLFT172), 198\_24 (coinfection with the strains CLFT198 and CLFT024\_02), 198\_41 (coinfection with the strains CLFT198 and CLFT041), 198\_172 (coinfection with the strains CLFT198 and CLFT172), 168\_172\_24 (coinfection with the strains CLFT168, CLFT172 and CLFT024\_02), 168\_41\_24 (coinfection with the strains CLFT168, CLFT041 and CLFT024\_02), 198\_41\_24 (coinfection with the strains CLFT198, CLFT041 and CLFT024\_02), 198\_172\_24 (coinfection with the strains CLFT198, CLFT172 and CLFT024\_02). 12. StrainID: lineage(s) and genotypes IDs and combination used in the exposure treatment. P - Panzootic, E - Enzootic, and R - recombinant. P1 (single infection with the genotype CLFT168), P2(single infection with the genotype CLFT198), E1 (single infection with the genotype CLFT041), E2 (single infection with the genotype CLFT172), R (single infection with the genotype CLFT024\_02), E1-R (coinfection with the genotypes CLFT41 and CLFT024\_02), E2-R (coinfection with the genotypes CLFT172 and CLFT024\_02),P1-R (coinfection with the genotypes CLFT168 and CLFT024\_02),P2-R (coinfection with the genotypes CLFT198 and CLFT024\_02),P1-E1 (coinfection with the genotypes CLFT168 and CLFT041), P1-E2 (coinfection with the genotypes CLFT168 and CLFT172),P2-E1 (coinfection with the genotypes CLFT198 and CLFT041),P2-E2 (coinfection with the genotypes CLFT198 and CLFT172),E1-P1-R (coinfection with the genotypes CLFT041, CLFT168 and CLFT024\_02),E1-P2-R (coinfection with the genotypes CLFT041, CLFT198 and CLFT024\_02), E2-P1-R (coinfection with the genotypes CLFT172, CLFT168 and CLFT024\_02), and E2-P2-R (coinfection with the genotypes CLFT172, CLFT198 and CLFT024\_02). 13. Number\_of\_lineages: Number of lineages/genotypes used in the exposure experiment. 14. GPL\_pg: Bd-GPL lineage pathogen load (concentration) in picograms. 15. Brazil\_pg: Bd-Asia-2/Brazil lineage pathogen load (concentration) in picograms. 16. Hybrid: recombinant genotype pathogen load (concentration) in picograms. 17. TotalBd: Total Bd pathogen load (concentration) in picograms. 18. Susceptible: 0 - Frog got infected after exposure to the pathogen, or 1 - frog did not get infected after exposure to the pathogen. 19. Infected: 1 - Frog got infected after exposure to the pathogen, or 0 - frog did not get infected after exposure to the pathogen. 20. Dead: 1- Frog died during the experiment, or 0 - frog survived until the end of the experiment. DATA-SPECIFIC INFORMATION FOR: Suvival\_analysis.Rmd, 01\_PairwiseCompPart1.Rmd, 02\_PairwiseCompPart2.Rmd, 03\_MortalityStats.Rmd, and 04\_Plots.Rmd These are R Markdown files used for conducting statistical analyses and creating an interactive report that combines R code and explanatory text. They generate charts and visualizations of the analysis results. Software Versions and Packages Used: R (version 1.4.11) R Packages: survival\_3.5-5 survminer\_0.4.9 patchwork\_1.1.2 here\_1.0.1 car\_3.1-2 conflicted\_1.2.0 fitdistrplus\_1.1-11 AICcmodavg\_2.3-2 multcomp\_1.4-23 mgcv\_1.8-42 nlme\_3.1-162 ggplot2\_3.4.2 tidyverse\_2.0.0 lmtest\_0.9-40 extrafontdb\_1.0