DOI: 10.5061/dryad.9ghx3ffxw
title: Many roads to reservoirs? How susceptibility and shedding shape host competence in amphibians

description: Host competence—the ability to acquire, harbor, and transmit
 infections—drives pathogen spread and persistence in multi-host
 communities. Evaluating species-specific competence is critical for
 predicting transmission, particularly for generalist fungal pathogens like
 Batrachochytrium dendrobatidis (Bd). Despite its central role in disease
 dynamics, we lack an epidemiologically grounded competence metric that
 rigorously accounts for how infection intensity affects a host's
 competence. This knowledge gap limits our ability to compare mechanisms
 across species and assess their roles in pathogen persistence. To address
 these challenges, we developed a novel, load-dependent competence metric
 using host-pathogen Integral Projection Models (IPMs) that integrates
 variation in susceptibility, within-host pathogen growth, and pathogen
 shedding dynamics. We applied this metric to lab-based challenge
 experiments with three common North American amphibians (Notophthalmus
 viridescens, Rana clamitans, and Rana catesbeianus) that persist
 endemically with Bd. Using dose-response assays and repeated pathogen
 shedding measurements across species, we asked: i) is there a consistent,
 non-linear relationship between infection intensity and pathogen shedding
 across species? and ii) which load-based traits best predict host
 competence? We quantified four of five components of host
 competence—susceptibility, pathogen growth, pathogen survival, and
 load-dependent shedding—and used these to parameterize species-specific
 IPMs, integrating competence into a single relative metric across species.
 We found that Bd shedding increased non-linearly with infection intensity,
 contradicting the standard assumption that Bd shedding is linearly related
 to infection intensity. N. viridescens and R. catesbeianus were the most
 competent hosts but through distinct pathways: high susceptibility in N.
 viridescens and elevated shedding rates in R. catesbeianus. In contrast,
 density dependent reductions in pathogen growth and shedding limited R.
 clamitans competence. Thus, species-level competence is not determined by
 a single trait, but emerges from interactions among multiple load-based
 processes. Our results demonstrate that variation in competence emerges
 from distinct, species-specific processes across multiple dimensions of
 competence. By linking individual infection dynamics to population-level
 transmission potential, our integrative framework provides a more
 mechanistic approach to predicting host contributions to community-level
 pathogen persistence
description: We conducted a controlled dose-response experiment to assess Bd
 susceptibility and shedding across species (details in Appendix S1). After
 confirming Bd-free status via qPCR following heat treatment, adult
 <em>R. clamitans</em>, <em>N. viridescens</em>,
 and <em>R. catesbeianus</em> were exposed to one of four Bd
 zoospore doses ($1\times10<sup>4$</sup> to
 $1\times10<sup>7$</sup>) or a control. All exposures occurred
 at $21^\circ C$ in individual containers under standardized housing and
 feeding conditions. We exposed individuals to a
 Tennessee Bd isolate (<em>FMB003</em>,
 <em>GPL-1</em>), with zoospore concentrations enumerated using
 a hemocytometer. Individuals were exposed for 24 hours, then monitored for
 infection and zoospore shedding repeatedly. Skin swabs to measure Bd
 infection load were taken every 6 days, followed by 24-hour water exposure
 in separate containers to quantify shedding. Experiment duration varied
 among species (56-79 days post-exposure). Swab and shedding samples were
 processed for Bd detection via qPCR using established protocols
 [@Boyle2004; @Blooi2013]. DNA extractions and Bd quantification methods
 are detailed in Appendix S1.
description: This README describes various files: 1. The file
 "comp_figures.Rmd" provides the Bayesian hierarchical models
 used to construct the plots for the manuscript and appendix. 2. The files
 'bull_comp_master.csv', 'newt_comp_master_data.csv',
 and 'comp_green_master.csv' are the data files from the each
 challenge experiment where bull = R. catesbeianus, newt = N. viridescens,
 and green = R. clamitans. The necessary columns are described below:
 'ID': A unique identifier for individual hosts within a species.
 'trt": The dose (zoospores per mL) of Bd to which the hosts were
 exposed. This columns is given in scientific notation and will be read as
 a string. There were four unique doses: 1x10^4, 1x10^5, 1x10^6, and
 1x10^7. 'temp': The temperature at which the hosts were held at
 for the duration of the experiment 'day & waterday': The day
 of the experiment at which the swab (day) and shedding sample (waterday)
 were taken. 'swabZE': The Bd load as measured by qPCR on the
 given individual at the day of the experiment given in column
 'day'. 'waterZE10': The Bd shed as measured by qPCR on
 the given individual at the day of the experiment given in column
 'waterday'. 'species' The anuran or caudate species of
 the given individual. There were 2 anuran species that were used:
 R.clamitans (green frogs), R. catesbeianus (bullfrogs) and one caudate
 species N. viridescens (eastern newt). 'mass' : The weight in
 grams of the animal upon capture 'svl': the length as measured
 by snout to vent length of the animal upon capture in cm. 1.
 'ipm_comp_calc.R': This script is uses the functions contained
 in script 'ipm_fxns_comp.R' along with rds files that contain
 trait distributions: 'newt_dist.rds', 'bull_dist.rds',
 and 'green_dist.rds'. To calculate the species level competence
 value for each species based on host traits. All rds files (i.e.,
 'newt_dist.rds', 'bull_dist.rds',
 'green_dist.rds' are standard  rds files that contain the
 parameter values and distributions used in the competence measure. Once
 loaded in, code is provided in 'ipm_comp_calc.R' to properly
 prepare the data contained in the rds files for use.  2. Stan file:
 'shedding_model2.stan' is the missing swab/shed model that is
 used in the 'comp_figures.Rmd' to correctly calculate the
 shedding for each species.