Chronic infections can shape epidemic exposure: Pathogen co-occurrence networks in the Serengeti lions

Nicholas M. Fountain-Jones; Craig Packer; Maude Jacquot; F. Guillaume Blanchet; Karen Terio; Meggan E. Craft

Infra-community dynamics are also likely to vary with spatiotemporal scale. For example, pathogen associations in amphibian communities differed substantially at the host scale compared to the pond scale, but these effects can be reversed or undetected at other scales (Stutz et al. 2018) . In general, interactions between free-living species are more apparent at scales 7 7 Although pathogen co-occurrence networks are valuable for quantifying broad structural patterns, they do not account for environmental or host factors or differences in spatial or temporal scale. Joint species distribution models fill this gap by simultaneously assessing environmental influences and interspecific co-occurrences across multiple scales using hierarchical Bayesian mixed models (Warton et al. 2015; Ovaskainen et al. 2017 ). Here we use both co-occurrence network and joint species distribution models to examine the structure of pathogen-pathogen networks and quantify pathogen associations whilst controlling for environmental and host factors. We collate ten years of data on acute and chronic pathogens in 105 African lions (Panthera leo) as well as extensive host and environmental data from the Serengeti Lion Project (SLP, Packer et al. 2005) . The SLP datasets provides a unique opportunity to understand pathogen co-occurrence networks in a wild population whilst controlling for group, individual and environmental characteristics. We use this data to ask the following interlinked questions: