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  1. The Pyrenean desman (Galemys pyrenaicus) is an endangered stream-dwelling insectivore endemic to the Iberian Peninsula and the north of the Pyrenees. It favours riffles over slow habitats such as runs or pools, yet it is still unclear whether habitat preference is based on prey availability or on other factors, such as mechanical constraints on its hunting habits.
  2. Desman diet and prey selection were analysed along the pristine Elama Stream and the slightly modified Leitzaran Stream in the Basque Country, Spain.
  3. In each stream the prey consumed were identified by metabarcoding 94 desman faeces, and prey availability characterized from 10 Surber samples taken in each habitat type (riffles, runs and pools). Invertebrates were sorted and identified, the biomass of each taxon was calculated, and their DNA was also extracted, amplified using PCR, and sequenced to build a reference database.
  4. Prey availability and diet varied between streams. Desmans positively selected shredders and invertebrates that live on the substrate, and selected against taxa that live in fine sediment, taxa with hard shells or those that are highly mobile. The diet of desmans was more selective in the Elama, the stream with better ecological status. Food availability did not differ among habitats, and therefore does not explain the preference of desmans for riffles; rather, mechanical constraints to deal with buoyancy and physical habitat heterogeneity were hypothesized to be the reason behind the habitat preference.
  5. The results suggest that promoting the formation of riffles in streams can improve the situation of some desman populations living in degraded habitats.
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