DOI: 10.5061/dryad.g1jwstqtb
title: Recovered frog populations coexist with endemic Batrachochytrium dendrobatidis despite load-dependent mortality

description: Novel infectious diseases, particularly those caused by fungal pathogens,
 pose considerable risks to global biodiversity. The amphibian chytrid
 fungus (Batrachochytrium dendrobatidis, Bd) has demonstrated the scale of
 the threat, having caused the greatest recorded loss of vertebrate
 biodiversity attributable to a pathogen. Despite catastrophic declines on
 several continents, many affected species have experienced population
 recoveries after epidemics. However, the potential ongoing threat of
 endemic Bd in these recovered or recovering populations is still poorly
 understood. We investigated the threat of endemic Bd to frog populations
 that recovered after initial precipitous declines, focusing on the
 endangered rainforest frog Mixophyes fleayi. We conducted extensive field
 surveys over four years at three independent sites in eastern Australia.
 First, we compared Bd infection prevalence and infection intensities
 within frog communities to reveal species-specific infection patterns.
 Then, we analyzed capture-recapture data of M. fleayi to estimate the
 impact of Bd infection intensity on apparent mortality rates and Bd
 infection dynamics. We found that M. fleayi had lower infection
 intensities than sympatric frogs across the three sites, and cleared
 infections at higher rates than they gained infections throughout the
 study period. By incorporating time-varying individual infection
 intensities, we show that healthy M. fleayi populations persist despite
 increased apparent mortality associated with infrequent high Bd loads.
 Infection dynamics were influenced by environmental conditions, with Bd
 prevalence, infection intensity, and rates of gaining infection associated
 with lower temperatures and increased rainfall. However, mortality
 remained constant year-round despite these fluctuations in Bd infections,
 suggesting major mortality events did not occur over the study period.
 Together, our results demonstrate that while Bd is still a potential
 threat to recovered populations of M. fleayi, high rates of clearing
 infections and generally low average infection loads likely minimize
 mortality caused by Bd. Our results are consistent with pathogen
 resistance contributing to the coexistence of M. fleayi with endemic Bd.
 We emphasize the importance of incorporating infection intensity into
 disease models rather than infection status alone. Similar population and
 infection dynamics likely exist within other recovered amphibian-Bd
 systems around the globe, promising longer-term persistence in the face of
 endemic chytridiomycosis.
description: We conducted robust design capture-recapture surveys
 for <em>Mixophyes fleayi</em> at three sites from 2017–2021.
 Swab samples were collected from individuals during each capture and
 analysed with qPCR, which informed infection status
 with <em>Bd</em>. From these results, we constructed a capture
 history for analysis. Some columns, corresponding to primary occasions,
 were padded with missing values to align primary occasions across sites.
 Details of the data handling are in the Quarto document m2-cmr.qmd.
 Additionally, up to 15 individuals of sypatric frog species were swabbed
 during each primary occasion at each site from 2019–2021. These data are
 analysed in the Quarto document m1-infections.qmd. For more details, see
 the manuscript.
description: All code for data manipulation, analysis, and figure creation is
 included in the two Quarto files. All analysis was conducted in R using
 RStudio. Data analysis was conducted using NIMBLE.