Continent-wide recent emergence of a global pathogen in African amphibians

These datasets are associated with the study entitled, "Continent-wide recent emergence of a global pathogen in African amphibians." In this study we describe the historical and recent biogeographical spread of a fungal pathogen of amphibians, Batrachochytrium dendrobatidis (Bd) and assess its risk to amphibians across the continent of Africa. The larger combined file, "AfricaBd_CombinedFile_LitReview_BdMaps_GhoseData.xlsx", contains Bd occurrence records processed by the authors of the study (N=4,623) and previously published records (N=12,297). Of the previously published records, 12,234 records came from studies reporting both Bd-negative and Bd-positive records (i.e. prevalence) that we used along with our data (N=4,623) to assess emergence of Bd in African amphibians. The file "AfricaBd_Ghosedata_Hirschfelddata_ZimkusCameroondata.xlsx" contains all georeferenced Bd records collected by the authors of this study, data from Hirschfeld et al. 2016, and data for Cameroon from Zimkus et al. 2020. This file includes more metadata including amphibian species tested, and includes infection intensity data detected by qPCR for Bd-positive records. Using these datasets we document a pattern of Bd emergence beginning largely at the turn of the century (the year 2000). From 1852–1999, we found low Bd prevalence (3.2% overall) and limited geographic spread, but after 2000 we documented a sharp increase in prevalence (18.7% overall), wider geographic spread, and our genotyping revealed multiple Bd lineages with indications of hybridization. Our habitat suitability model showed that Bd risk to amphibians was highest in much of eastern, central, and western Africa. Our study documents a largely overlooked yet significant increase in a fungal pathogen that could pose a threat to amphibians across an entire continent. We emphasize the need to bridge historical and contemporary datasets to better describe and predict host-pathogen dynamics over larger temporal scales.This research was funded by the National Science Foundation (Belmont Forum project NSF ICER-1633948 to V.T.V., NSF DEB-1202609 to D.C.B., NSF Graduate Research Fellowship Program to A.Q.B., and NSF IOS-1354241 to E.B.R.), the California Academy of Sciences (Hagey Venture Research Fund to D.C.B. and V.T.V.), and the National Institutes of Health (Animal Models of Infectious Diseases Training Program T32 AI060555 Ruth L. Kirschstein National Research Service Award to S.L.G.). DNA sequencing, conducted at the University of Idaho IBEST Genomics Resources Core, was supported in part by NIH COBRE Phase III grant P30GM103324. The content is solely the responsibility of the authors and does not necessarily represent the official views of funding agencies