Integrating biotic interactions in niche analyses unravels patterns of community composition in clownfishes

Mutualistic interactions play a fundamental role in shaping species distributions, driving niche differentiation, and structuring communities. Yet their influence on realized niches and patterns of coexistence remains poorly understood. In clownfishes, mutualism with sea anemones underpins their biogeography and ecological success, with species classified as generalists or specialists according to their host specificity. However, the extent to which host availability constrains or expands clownfish niches has remained unclear. Here we used ecological niche models (ENMs) across the Indo-Pacific to examine how host sea anemones shape clownfish realized niches and community composition. We integrated occurrence data with climatic and habitat predictors and refined estimates by incorporating host niches, quantifying changes in niche breadth, position, and overlap. We further developed a multilayered framework to account for host use within niche quantification, allowing us to assess patterns of resource overlap in communities spanning generalist–specialist dynamics. Our results reveal that mutualistic associations strongly shape clownfish realized niches, with specialists experiencing greater niche constraints than generalists due to their reliance on a limited set of hosts. Host availability emerges as a key driver of community structure, producing high ecological niche overlap among species that is modulated by host partitioning. This host-mediated differentiation facilitates coexistence by reducing resource overlap, with generalist–specialist contrasts playing a central role in sustaining clownfish biodiversity. Our study highlights how biotic interactions mediate species ecological niches and shape community assembly in an iconic mutualistic system. Beyond clownfishes, our framework offers a transferable approach to incorporate interacting species into ENMs, improving ecological interpretations and informing conservation efforts in biodiversity hotspots and other mutualistic systems.

Methods
Occurrences, environmental variables and all input data for the analyses have been collected from online databases and open-source datasets.