We examined the spatial and seasonal drivers of Macrobrachium shrimp community structure in the freshwater reaches of the Yutsun River, northern Iriomote Island, Japan. From January to December 2019, we conducted monthly visual censuses at seven stations spanning 300 m intervals, including a 44 m waterfall barrier. In total, 5963 individuals of eight Macrobrachium species were recorded. Generalised linear mixed models, non-metric multidimensional scaling, hierarchical clustering, and permutational multivariate analysis of variance (PERMANOVA) revealed that station position, rather than season, strongly determined community composition. Three distinct assemblages were identified: the lowermost reach characterised by low abundance and predation-sensitive taxa; the mid-stream below the waterfall dominated by amphidromous species (eg M. lar); and the upstream above the waterfall overwhelmingly dominated by the endemic landlocked species M. shokitai, whichi is endemic to Iriomote Island. These findings highlight how life-history strategies and physical barriers shape riverine shrimp communities and provide essential baseline data for the conservation of island stream ecosystems.
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