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Microhabitat preferences of fish assemblages in the Udzungwa Mountains (Eastern Africa)

Environmental flow assessment (EFA) involving microhabitat preference models is a common approach to set ecologically friendly flow regimes in territories with ongoing or planned projects to develop river basins, such as many rivers of Eastern Africa. However, habitat requirements of many African fish species are poorly studied, which may impair EFAs. This study investigated habitat preferences of fish assemblages, based on species presence–absence data from 300 microhabitats collected in two tributaries of the Kilombero River (Tanzania), aiming to disentangle differences in habitat preferences of African species at two levels: assemblage (i.e. between tributaries) and species (i.e. species‐specific habitat preferences). Overall, flow velocity, which implies coarser substrates and shallower microhabitats, emerged as the most important driver responsible of the changes in stream‐dwelling assemblages at the microhabitat scale. At the assemblage level, we identified two important groups of species according to habitat preferences: (a) cover‐orientated and limnophilic species, including Barbus spp., Mormyridae and Chiloglanis deckenii, and (b) rheophilic species, including Labeo cylindricus, Amphilius uranoscopus and Parakneria spekii. Rheophilic species preferred boulders, fast flow velocity and deeper microhabitats. At the species level, we identified species‐specific habitat preferences. For instance, Barbus spp. preferred low flow velocity shallow depth and fine‐to‐medium substratum, whereas L. cylindricus and P. spekii mainly selected shallow microhabitats with coarse substrata. Knowledge of habitat preferences of these assemblages and species should enhance the implementation of ongoing and future EFA studies of the region.