DOI: 10.5061/dryad.37pvmcvsp
title: Code and data: Evidence for the vacated niche hypothesis in parasites of invasive mammals

description: Species redistribution and invasion are becoming increasingly common due
 to climate change and anthropogenic impacts. Understanding the resultant
 shifts in host-parasite associations is important for anticipating
 disruptions to host communities, disease cycles, and conservation efforts.
 In this paper, we bring together the enemy release and vacated niche
 hypotheses to relate parasite acquisition and retention, two distinct yet
 intertwined processes that play out during host invasion. Using the Global
 Mammal Parasite Database, we test for net enemy release based on
 differences in parasite species richness, and we develop a novel taxonomic
 null modeling approach to demonstrate that parasites fill vacated niches.
 We find evidence of net enemy release, and our taxonomic null models
 indicate replacement of lost parasites by taxonomically similar acquired
 ones, over and above what might be expected by chance. Our work suggests
 that both enemy release and vacated niche hypotheses provide valuable
 frameworks through which to understand and predict changing host-parasite
 associations, which may include insights on how climate change and
 anthropogenic influences perturb and reorganize communities and
 ecosystems.
description: # Code and data: Evidence for the vacated niche hypothesis in parasites of
 invasive mammals #### Annakate M. Schatz and Andrew W. Park
 [https://doi.org/10.5061/dryad.37pvmcvsp](https://doi.org/10.5061/dryad.37pvmcvsp) --- All data preparation, analysis, and modeling were done in R v3.5.1-4.2.1. NOTE: Before running code, please move the data from Dryad into a "data" subfolder in the same parent folder as the code from Zenodo ("Schatz_Park_code"), as this is the structure via which the code files will try to load data. --- CODE 0.data-prep.R: filter and clean host-parasite data on acquistion and retention for analyses * Data loaded: cluster-data-previous-work.Rda * Data created: data-prep.Rda 0a.ecoregion-bioclim.R: extract bioclimatic data for all relevant ecoregions associated with focal hosts * Data loaded: range-data-previous-work.Rda, wc2.1_10m_bio (folder) * NOTE: The WorldClim data in the folder "wc2.1_10m_bio" cannot be uploaded to Dryad due to differences in license. To download this data, go to [https://www.worldclim.org/data/worldclim21.html](https://www.worldclim.org/data/worldclim21.html). Scroll down to the table that offers "Bioclimatic variables" and download the "bio 10m" version. Open the downloaded zip file ("wc2.1_10m_bio.zip") and place the "wc2.1_10m_bio" folder in the "data" subdirectory for easy loading in these scripts. If the data is not available online, please contact Annakate Schatz (corresponding author; [schat22a@mtholyoke.edu](mailto:schat22a@mtholyoke.edu)). * Data citations * Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005 Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25, 1965–1978. (doi:[https://doi.org/10.1002/joc.1276](https://doi.org/10.1002/joc.1276)) * Fick, S.E. and R.J. Hijmans, 2017. WorldClim 2: new 1km spatial resolution climate surfaces for global land areas. International Journal of Climatology 37 (12): 4302-4315. * Data created: ecoregion-bioclim.Rda 0b.range-data.R: filter and define ecoregion data associated with native and non-native ranges for each focal host * Data loaded: cluster-data-previous-work.Rda, data-prep.Rda, range-data-previous-work.Rda * Data created: range-data.Rda 1a.er-data-prep.R: prepare data for enemy release analyses (filter data to relevant parasites per focal host, collect and calculate predictor and response variables) * Data loaded: data-prep.Rda, ecoregion-bioclim.Rda, PanTHERIA_1-0_WR05_Aug2008.txt, range-data.Rda * Data created: part1-data-prep.Rda 1b.er-tests.R: perform enemy release analyses (phylogenetic t-test, simple linear regressions) * Data loaded: data-prep.Rda, part1-data-prep.Rda, WR_2005_ST.txt * Data created: none 2a.vn-tests.R: perform vacated niche analyses for parasite type (Fisher test), transmission mode (Fisher test), and phylogenetic specificity (Mann-Whitney U test) * Data loaded: data-prep.Rda * Data created: part2-data-analyses.Rda 2b.vn-arth.Rmd: collect, format, and clean taxonomic parasite data for arthropods; build taxonomic trees; build and run taxonomic null models; calculate z-scores * Data loaded: data-prep.Rda * Data created: tax-data-arth.Rda, tax-trees-arth.Rda, null-models-arth.Rda 2b.vn-bact.Rmd: collect, format, and clean taxonomic parasite data for bacteria; build taxonomic trees; build and run taxonomic null models; calculate z-scores * Data loaded: data-prep.Rda * Data created: tax-data-bact.Rda, tax-trees-bact.Rda, null-models-bact.Rda 2b.vn-helm.Rmd: collect, format, and clean taxonomic parasite data for helminths; build taxonomic trees; build and run taxonomic null models; calculate z-scores * Data loaded: data-prep.Rda * Data created: tax-data-helm.Rda, tax-trees-helm.Rda, null-models-helm.Rda 2b.vn-prot.Rmd: collect, format, and clean taxonomic parasite data for protozoa; build taxonomic trees; build and run taxonomic null models; calculate z-scores * Data loaded: data-prep.Rda * Data created: tax-data-prot.Rda, tax-trees-prot.Rda, null-models-prot.Rda 2b.vn-virus.Rmd: collect, format, and clean taxonomic parasite data for viruses; build taxonomic trees; build and run taxonomic null models; calculate z-scores * Data loaded: data-prep.Rda * Data created: tax-data-virus.Rda, tax-trees-virus.Rda, null-models-virus.Rda 2c.vn-follow-ups: check for correlations between null model z-scores and number of comparisons; calculate quantiles for null model z-scores * Data loaded: data-prep.Rda, null-models-arth.Rda, null-models-bact.Rda, null-models-helm.Rda, null-models-prot.Rda, null-models-virus.Rda * Data created: vn-follow-ups.Rda figures&tables (folder): contains Rmd files for all figures and tables created in R (Figures 3, 4, A1-A4, Tables A1, A2) --- DATA cluster-data-previous-work.Rda: host-parasite and community data from previous work on parasite acquisition and retention (Schatz and Park 2021, 2023) data-prep.Rda: host-parasite data cleaned for all analyses ecoregion-bioclim.Rda: filtered and prepped bioclimatic data for use in enemy release analyses null-models-arth.Rda: null model results for arthropods (true and null pairwise distances, z-scores) null-models-bact.Rda: null model results for bacteria (true and null pairwise distances, z-scores) null-models-helm.Rda: null model results for helminths (true and null pairwise distances, z-scores) null-models-prot.Rda: null model results for protozoa (true and null pairwise distances, z-scores) null-models-virus.Rda: null model results for viruses (true and null pairwise distances, z-scores) PanTHERIA_1-0_WR05_Aug2008.txt: PanTHERIA data (Jones et al 2009) part1-data-prep.Rda: host-parasite data and predictor/response variables for enemy release analyses part2-data-analysis.Rda: filtered data and results of vacated niche analyses for parasite type, transmission mode, and phylogenetic specificity range-data-previous-work.Rda: range data (IUCN and ecoregions) for focal hosts from previous work on parasite acquisition and retention (Schatz and Park 2021, 2023) range-data.Rda: lists of native and non-native ecoregions for each focal host supp_table_data.Rda: data used to create Table S1 tax-data-arth.Rda: taxonomic data for all arthropods associated with focal hosts tax-data-bact.Rda: taxonomic data for all bacteria associated with focal hosts tax-data-helm.Rda: taxonomic data for all helminths associated with focal hosts tax-data-prot.Rda: taxonomic data for all protozoa associated with focal hosts tax-data-virus.Rda: taxonomic data for all viruses associated with focal hosts tax-trees-arth.Rda: taxonomic tree and corresponding distance matrix for arthropods tax-trees-bact.Rda: taxonomic tree and corresponding distance matrix for bacteria tax-trees-helm.Rda: taxonomic tree and corresponding distance matrix for helminths tax-trees-prot.Rda: taxonomic tree and corresponding distance matrix for protozoa tax-trees-virus.Rda: taxonomic tree and corresponding distance matrix for viruses vn-follow-ups.Rda: null model z-scores associated with number of comparisons that went into calculating each true pairwise distance; quantiles for null model z-scores; data organization for Table A2 WR_2005_ST.txt: mammalian supertree (Bininda-Emonds et al 2007) for enemy release phylogenetic paired t-test