DOI: 10.5061/dryad.cc2fqz693
title: Data from: Coinfection with chytrid genotypes drives divergent infection dynamics reflecting regional distribution patterns

description: By altering the abundance, diversity, and distribution of species — and
 their pathogens — globalization may inadvertently select for more virulent
 pathogens. In Brazil’s Atlantic Forest, a hotspot of amphibian
 biodiversity, the global trade has facilitated the co-occurrence of
 previously isolated enzootic and panzootic lineages of the pathogenic
 amphibian-chytrid (Batrachochytrium dendrobatidis, ‘Bd’) and generated new
 virulent recombinant genotypes (‘hybrid’). Epidemiological data indicate
 that amphibian declines are most severe in hybrid zones, suggesting that
 coinfections are causing more severe infections or selecting for higher
 virulence. We investigated how coinfections involving these genotypes
 shaped virulence and transmission. Overall, coinfection favored the more
 virulent and competitively superior panzootic genotype, despite dampening
 its transmission potential and overall virulence. However, for the least
 virulent and least competitive genotype, coinfection increased both
 overall virulence and transmission. Thus, by integrating experimental and
 epidemiological data, our results provide a mechanistic insight into how
 globalization can select for, and propel, the emergence of introduced
 hypervirulent lineages, such as the globally distributed panzootic lineage
 of Bd.
description: 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: tamiliec@gmail.com; tamilie@umich.edu
 Co-author Information Name: Daniel Medina Institution:The Pennsylvania
 State University Address: University Park, PA 16802, USA. Email:
 medinald19@gmail.com Co-author Information Name: Jessica Hite Institution:
 University of Wisconsin-Madison Address: 2015 Linden Dr, Madison, WI
 53706, USA. Email: jessicahite@gmail.com 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