DOI: 10.5061/dryad.jwstqjqhp
title: Code and data for: Are novel or locally adapted pathogens more devastating and why? : resolving opposing hypotheses

description: The naive host syndrome hypothesis suggests that pathogens are able to
 easily invade and become deadly to novel hosts because of a lack of
 co-evolutionary history, whereas the local adaptation hypothesis suggests
 that pathogens are better able to invade local hosts because of their
 co-evolutionary history, but rarely do studies on these two hypotheses
 cite one another or acknowledge their ostensibly mixed messages. By
 combining a continental-scale, factorial, common garden experiment with a
 global-scale meta-analysis, each on the amphibian-chytrid fungus
 host-pathogen system, we show that local host-pathogen interactions
 typically resulted in higher host mortality, greater infection success,
 and higher pathogen loads, but that there was substantial variation in
 novel host-pathogen outcomes and thus moving pathogens around the planet
 increases the likelihood of exposure to particularly virulent pathogen
 strains and particularly deadly host-pathogen combination. Therefore, we
 provide support for both the local adaptation and naïve host syndrome
 hypotheses, highlight how the two hypotheses are complementary rather than
 conflicting, and emphasize the need for greater integration of these
 hypotheses and their associated semi-disparate literature.
description: Data from the 5x6 experiment: "5x6 experimental
 data.csv" Data used the meta analysis, previously
 published in Sauer et al. 2020: "Sauer et al. 2020 data
 subset.csv" See metadata file for
 details Code for all analyses: "Code for Sauer et
 al Pathogen novelty.R"
description: # Code and data for:Are novel or locally adapted pathogens more
 devastating and why?: resolving opposing hypotheses
 [https://doi.org/10.5061/dryad.jwstqjqhp](https://doi.org/10.5061/dryad.jwstqjqhp) "5x6 experimental data.csv" contains all the data from the 5x6 experiment that is used in all analyses of that experiment described in the main text and supplement. Detailed information about the dataset (units, variation definitions, etc) can be found in "Sauer et al novelty metadata.csv" "Sauer et al. 2020 data subset.csv" contains the data used in the meta analysis described in the main text. This data is a subset of the previously published database from Sauer et al. 2020: [https://doi.org/10.1002/ecy.2979](https://doi.org/10.1002/ecy.2979) Code for all analyses described in the main text and supplement can be found in the following R script file: "Code for Sauer et al Pathogen novelty.R" Library load lines are included in the script for all the packages needed to run the code. Both the "5x6 experimental data.csv" and "Sauer et al. 2020 data subset.csv" data files need to be read in for the code to run, lines to load this data are included. ## Information about missing data "5x6 experimental data.csv": There are blank cells in the "mass2" and "dmass" columns in this data set. Those are purposeful and occur because mass at the of the experiment or at death ("mass2") could not be collected for some individuals after death due to the state of the remains. For ever row missing "mass2", the change in mass from prior to exposure ("mass") to the end of the experiment or death ("mass2") is missing because it could not be calculated ("dmass"). See metadata file for further descriptions of these columns. Neither of these columns are used in any analysis for this manuscript and thus the blank cells do not affect the code. "5x6 experimental data.csv": There are "#N/A" cells in columns "HostGenDist", "IB", "LB", and "EB". All the N/As align with treatment that include the QC Bd isolate. This isolate did not have a local paired host species, making it impossible to include in the "HostGenDist" calculations, and could not be sequenced, making it impossible to include in the "IB", "LB", and "EB" calculations. None of these rows are used the analyses that required these columns and the N/As do not affect the code. See the manuscript for more details on the various phylogenetic distance analyses and the subsets they were performed on. "Sauer et al. 2020 data subset.csv": There are blank cells in this data set in the "Linage" and "Species.isolated.from" columns. Those are purposeful and represent Bd isolates where either the phylogenetic linage ("Linage") is unknown or was unreported by the authors the manscript where the row of data was collected from or the amphibian species the isolate was originally collected from ("Species.isolated.from") was not reported by the authors the manscript where the row of data was collected from. Neither of these columns are used in the analyses for this manuscript and thus the blanks do not affect the code. # Sharing/Access information Links to other publicly accessible locations of the data and code: * [https://github.com/erinsauer/Sauer-et-al.-Bd-novelty](https://github.com/erinsauer/Sauer-et-al.-Bd-novelty)