DOI: 10.5061/dryad.f127gp0
title: Data from: Opening the file drawer: Unexpected insights from a chytrid infection experiment

description: Infection experiments are critical for understanding wildlife disease
 dynamics. Although infection experiments are typically designed to reduce
 complexity, disease outcomes still result from complex interactions
 between host, pathogen, and environmental factors. Cryptic variation
 across factors can lead to decreased repeatability of infection
 experiments within and between research groups and hinder research
 progress. Furthermore, studies with unexpected results are often relegated
 to the “file drawer” and potential insights gained from these experimental
 outcomes are lost. Here, we report unexpected results from an infection
 experiment studying the response of two differentially-susceptible but
 related frogs (American Bullfrog Rana catesbeiana and the Mountain
 yellow-legged frog Rana muscosa) to the amphibian-killing chytrid fungus
 (Batrachochytrium dendrobatidis, Bd). Despite well-documented differences
 in susceptibility between species, we found no evidence for
 antibody-mediated immune response and no Bd-related mortality in either
 species. Additionally, during the study, the sham-inoculated R.
 catesbeiana control group became unexpectedly Bd-positive. We used a
 custom genotyping assay to demonstrate that the aberrantly-infected R.
 catesbeiana carried a Bd genotype distinct from the inoculation genotype.
 Thus R. catesbeiana individuals were acquired with low-intensity
 infections that could not be detected with qPCR. In the Bd-inoculated R.
 catesbeiana treatment group, the inoculated genotype appeared to
 out-compete the cryptic infection. Thus, our results provide insight into
 Bd coinfection dynamics, a phenomenon that is increasingly relevant as
 different pathogen strains are moved around the globe. Our experiment
 highlights how unexpected experimental outcomes can serve as both
 cautionary tales and opportunities to explore unanswered research
 questions. We use our results as a case study to highlight common sources
 of anomalous results for infection experiments. We argue that
 understanding these factors will aid researchers in the design, execution,
 and interpretation of experiments to understand wildlife disease
 processes.
description: Concatenated aligned
 sequences for all swab and isolate samples.We concatenated
 sequences from 90 nuclear loci for all 16 swab samples and 26 Bd isolates.
 We aligned the concatenated sequences using MUSCLE v3.8 (38) and visually
 checked the alignments for errors. These data were used to create Figure 3
 in the manuscript.rc_rm_concatenate_shared_all_isolates alignment.fastaBody Mass Measurements for all frogsWe measured body mass (in grams) for each frog every week of the experiment. These data were used to create figure 1 (boxplot of percent change in body weight).body_mass_results.xlsxELISA ResultsWe measured as optical density at 450 nm at different sampling points. Plate layouts and raw data are listed in the first two tabs, calculated averages are in the third tab, and t-test results are in the fourth tab.ELISA_data.xlsxBd qPCR results from swab samplesWe collected skin swab samples before inoculation and every week for the 10-week duration of the experiment. We analyzed skin swab samples for Bd presence using quantitative polymerase chain reaction (qPCR) for Bd using standard protocols (Taqman real-time qPCR assay). All qPCR results are listed as log zoospre equivalents (ZE). These data were used to create figure 2.qpcr_results_rcrm_inf_experiment.xlsx