Using multi‐response models to investigate pathogen coinfections across scales: Insights from emerging diseases of amphibians

Associations among parasites affect many aspects of host–parasite dynamics, but a lack of analytical tools has limited investigations of parasite correlations in observational data that are often nested across spatial and biological scales. Here we illustrate how hierarchical, multiresponse modelling can characterize parasite associations by allowing for hierarchical structuring, offering estimates of uncertainty and incorporating correlational model structures. After introducing the general approach, we apply this framework to investigate coinfections among four amphibian parasites (the trematodes Ribeiroia ondatrae and Echinostoma spp., the chytrid fungus Batrachochytrium dendrobatidis and ranaviruses) and among >2,000 individual hosts, 90 study sites and five amphibian host species. Ninety‐two percent of sites and 80% of hosts supported two or more pathogen species. Our results revealed strong correlations between parasite pairs that varied by scale (from among hosts to among sites) and classification (microparasite versus macroparasite), but were broadly consistent across taxonomically diverse host species. At the host‐scale, infection by the trematode R. ondatrae correlated positively with the microparasites, B. dendrobatidis and ranavirus, which were themselves positively associated. However, infection by a second trematode (Echinostoma spp.) correlated negatively with B. dendrobatidis and ranavirus, both at the host‐ and site‐level scales, highlighting the importance of differential relationships between micro‐ and macroparasites. Given the extensive number of coinfecting symbiont combinations inherent to natural systems, particularly across multiple host species, multiresponse modelling of cross‐sectional field data offers a valuable tool to identify a tractable number of hypothesized interactions for experimental testing while accounting for uncertainty and potential sources of co‐exposure. For amphibians specifically, the high frequency of co‐occurrence and coinfection among these pathogens—each of which is known to impair host fitness or survival—highlights the urgency of understanding parasite associations for conservation and disease management.