Factors at multiple scales drive parasite community structure

1. Understanding how ecological communities are assembled remains a key goal of ecosystem ecology. Because communities are hierarchical, factors acting at multiple scales can contribute to patterns of community structure. Parasites provide a natural system to explore this idea, as they exist as discrete communities within host individuals, which are themselves part of a community and metacommunity. 2. We aimed to understand the relative contribution of multi‐scale drivers in parasite community assembly and assess how patterns at one level may mask those occurring at another. Specifically, we wanted to disentangle patterns caused by passive sampling from those determined by ecological drivers, and how these vary with scale. 3. We applied a Markov Random Fields model and assessed measures of β‐diversity and nestedness for 420 replicate parasite infracommunities (parasite assemblages in host individuals) across two freshwater mussel host species, three sites and two time periods, comparing our results to simulations from four different ecologically relevant null models. 4. We showed that β‐diversity between sites (explaining 25% of variation in parasite distribution) and host species (41%) is greater than expected, and β‐diversity between individual hosts is smaller than expected, even after accounting for parasite prevalence and characteristics of host individuals. Furthermore, parasite communities were significantly less nested than expected once parasite prevalence and host characteristics were both accounted for, but more nested than expected otherwise, suggesting a degree of modularity at the within‐host level that is masked if underlying host and parasite characteristics are not taken into account. The Markov Random Fields model provided evidence for possible competitive within‐host parasite interactions, providing a mechanism for the observed infracommunity modularity. 5. An integrative approach that examines factors at multiple scales is necessary to understand the composition of ecological communities. Furthermore, patterns at one level can alter the interpretation of ecologically important drivers at another if variation at higher scales is not accounted for.