Environmental DNA-based detection of Batrachochytrium salamandrivorans in captive settings

Detecting pathogens in the live animal trade is critical for tracking and preventing their movement, introduction, and spillover into susceptible fauna. However, the scale of the live animal trade makes individually testing animals infeasible for all but the most economically important taxa. For instance, while the fungal pathogen, Batrachochytrium salamandrivorans (Bsal), threatens amphibian, particularly caudate diversity, in Europe and the Americas, screening even a fraction of the millions of live amphibians imported into the United States, alone, is impractically laborious and expensive. A promising alternative to individual-level sampling (e.g., swabbing the skin of salamanders) is to instead collect DNA from the animals’ environment (e.g., housing container or water) which allows us to screen a whole group of animals at a time. 
We used a series of experiments with Bsal-spiked water and substrates and experimentally infected rough-skinned newts (Taricha granulosa) to determine ho..., Water or housing substrates were spiked with Batrachochytrium salamandrivorans (Bsal) and then recovered with filtering water or pelletizing materials by centrifugation. In other studies rough-skinned newts were experimentally infected with Bsal and samples were collected from their water, housing substrates, or from skin swabs. In each case DNA was extacted and then screened for Bsal genes with a quantitative realtime PCR assay. Data are estimated copy number from the qPCR assay, as well as columns specifying whether we had detected inhibition in an exogenous internal positive control assay added to the third well of each triplicate of wells used per sample and then whether the sample was cleaned up with a Zymo PCR Inhibitor Removal kit or diluted 1-to-10 (in which case the quantity was adjusted). See the main text for details. , The analysis files are generated from Quarto documents run in R. They include all of the code needed to reporduce the results in R. , # \# Environmental DNA\-based detection of Batrachochytrium salamandrivorans in captive settings

These data come from a series of experiments designed to understand how best to collect use environmental DNA (eDNA) to detect the amphibian pathogen, *Batrachochytrium salamandrivorans* (Bsal), in captive settings (e.g., trade or collections). Water or housing substrates were spiked with Batrachochytrium salamandrivorans (Bsal) and then recovered with filtering water or pelletizing materials by centrifugation. In other studies rough-skinned newts (*Taricha granulosa*) were experimentally infected with Bsal and samples were collected from their water, housing substrates, or from skin swabs. In each case DNA was extacted and then screened for Bsal genes with a quantitative realtime PCR (qPCR) assay.

## Description of the data and file structure

Data are estimated copy number from the qPCR assay, as well as columns specifying whether we had detected inhibition in an exogenous internal posit...