Quantifying spatial variation in the size and structure of ecologically stratified communities

Summary Including ecological specialization (e.g. functional guild) in analyses performed across regions can help to study how size and structure of communities vary across environmental gradients. Multi‐species occupancy models, and their extension to a multi‐region framework, represent useful tools for such gradient analysis based on functional traits. However, in these models species richness is only a derived parameter and therefore explicit relationships cannot be inferred. We provide a novel hierarchical multi‐region community model that allows for direct modelling of trait‐based patterns of species richness along environmental gradients by partitioning communities into ecologically relevant strata (e.g. guilds). We illustrate the flexibility of the model by simulations, where we estimate guild richness and community composition using both categorical and continuous species traits. In addition, we apply our model to data from eight avian communities to explore how guild richness varies across elevational gradients. Simulations indicate that the model is able to estimate relationships between guild richness and environmental gradients even when the number of regions is low. Applying the model to the bird community data set, we show how the number of species in four feeding guilds varies in different ways across an elevational gradient. Understanding large scale variation in species richness and how it relates to environmental gradients requires an explicit treatment of community structure. Our modelling approach allows the testing of hypotheses directly and simultaneously on strata‐ and community‐specific species richness while accounting for the issues of rarity and detectability, and can be used to investigate the mechanisms which shape large scale spatial variation in species richness.