Freshwater ecosystems harbour a disproportionately high biodiversity relative to their area, being also one of the most threatened ecosystem types worldwide. However, our capacity to design evidence-based conservation plans for this realm is restricted by all biodiversity shortfalls that have been recognized so far. In this context, the paucity of comparable field data and information on traits and phylogenies of freshwater organisms should be emphasized. Here, we highlight how increased knowledge could be gained and where we should aim at in research on the functional and phylogenetic features of freshwater communities. First, attempts to combine datasets from different sources should pay careful attention to data harmonization. Second, more effort should be focused on natural history observations on species habitats and life histories, providing the backbone of information for multi-trait databases. Third, fully resolved phylogenies would be required for deciphering the evolutionary relationships of freshwater organisms. Provided that these three hurdles can be overcome, conducting studies of local freshwater communities across continental spatial extents would pave the way for mapping functionally important ecosystems and evolutionarily valuable areas for the conservation of freshwater organisms and their habitats.
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