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Table S1 Assessment metrics used in this article and their expected response to minimum flow increases in the by-passed reaches. Assessment metrics Predicted Rationale response Macroinvertebrates Taxonomic richness or Alterations of flow often result in a decrease of taxonomic richness (see e.g. references in Table 3 of Dewson et al., 2007) and minimum flow increases are expected to have an opposite effect. However, decrease in taxonomic richness after minimum flow increases was also observed (Poff & Zimmermann, 2010). EPT richness and % EPT Ephemeroptera, Plecoptera and Trichoptera are more diversified in lotic environment (e.g. Usseglio-Polatera 1994) and can be limited by the stream flow magnitude (Konrad et al., 2008). Minimum flow increases are expected to have an opposite effect. Simpson index Flow restoration should involve a more balanced distribution of abundance across taxa. Dominance by the most abundant taxa may be limited by stream flow (Konrad et al., 2008). In addition, reduced flows have been shown to alter invertebrate diversity (Martinez et al., 2013). Minimum flow increases are expected to have an opposite effect. French biotic index (IBGN) IBGN is based on family richness and their sensitivity to habitat impairment (AFNOR, 2004a). Both metrics are expected to increase with flow restoration. Potamon Type index (PTI) In PTI, taxa are rated according to their occurrence in large rivers (Potamon). Flow restoration in bypassed sections should make communities more similar to those of large rivers (Schöll et al., 2005). River channel Minimum flow increases should favour lotic species that preferentially colonise the main river channel (Usseglio-Polatera et al., 2000). High current velocity Decreased stream flows are known to cause a decrease in water velocities and depths, which often results in Coarse substrate increased sedimentation (Dewson et al., 2007). Minimum flow increases are expected to have an opposite Silt and mud substrate effect. 1 of 3 Proportion of grazers or Higher water velocities, as induced by minimum flow increases, may involve a shift from a higher biomass of filamentous algae towards a low diatom biomass, which may affect grazing efficiency. Herbivores should dominate lower courses of rivers (Vannote et al., 1980). However, the effect of water velocity on grazing efficiency has been shown to vary from one species to another (Dewson et al., 2007). Proportion of shredders Shredder abundance generally decreases with flow increases (as measured by different hydraulic parameters, see e.g. Statzner & Bêche, 2010). In addition, shredders are known to dominate upper courses of streams whereas by collectors progressively replace them further downstream (Vannote et al., 1980). Proportion of sprawlers Invertebrates inhabiting the surface of floating leaves of hydrophytes or fine sediment are expected to be affected by higher velocities resulting from minimum flow increases thus decreasing benthic food availability (Merritt et al., 2002). In contrast, invertebrates firmly attached to substrate should be favoured (e.g. Statzner & Bêche, 2010). Proportion of predators Expansion of wetted area can decrease invertebrate densities and cause a decrease in predation (e.g. Dewson et al., 2007; Statzner & Bêche, 2010). Proportion of passive filter feeders Water velocity influences the provision of food to filter feeders (see Dewson et al., 2007; Statzner & Bêche, 2010). Filter feeders require coarse sediments for a stable attachment (Merritt et al., 2002). Ecological specialisation Flow affects the amount of habitat available to invertebrates (see Dewson et al., 2007). Minimum flow increases are expected to enhance habitats. Fish French fish index (IPR) Minimum flow increases should make communities more similar to those of reference conditions (Oberdorff et al., 2002). Number of rheophilic species Minimum flow increases should increase the proportion of lotic habitat and favour rheophilic species (Oberdorff et al., 2002). Number of lithophilic species Lithophilic spawners require gravel substrates for reproductive success and are sensitive to siltation (Oberdorff et al., 2002). Minimum flow increases are expected to enhance their habitat. Total number of species or 2 of 3 Minimum flow increases should enhance fish species richness (Iwasaki et al., 2012). However, the potential reduction of eutrophication produced by minimum flow increases may decrease productivity and lead to a decrease in species richness (Oberdorff et al., 2002). Density of tolerant species Oberdorff et al. (2002) defined species as tolerant those habitat generalists that are flexible in their water quality requirement. Minimum flow increases are expected to reduce the abundance of tolerant species. Density of omnivorous species Minimum flow increases are expected to restore the food balance in communities and to result in more specialised diets (Oberdorff et al., 2002). Density of invertivorous species Minimum flow increases should favour EPT invertebrates (see above) and a potential consequence for fish communities could be an increase in invertivorous species (Oberdorff et al., 2002). Total density or This metric is used as a surrogate of ecosystem productivity. As for richness, minimum flow increases may enhance the availability of high quality habitat. A potential reduction of eutrophication produced by minimum flow increases may decrease productivity and lead to a decrease in density (Oberdorff et al., 2002). In addition, flow magnitude influences fish population recruitment (Freeman et al., 2001). Midstream guild Minimum flow increases are expected to favour midstream fish species (Lamouroux et al., 2006). High current velocity Minimum flow increases should increase the proportion of lotic habitat and should favour species adapted to High depth the fast-flowing and deep conditions of large rivers that have suffered from a reduction in discharge Coarse substrate (Lamouroux et al., 1999). Decrease in stream flows may result in increased sedimentation (Dewson et al., 2007) whereas minimum flow increases are expected to have an opposite effect and should select species preferring coarse substrates (Oberdorff et al., 2002). Ecological specialisation Habitat homogenisation is facilitated by river regulation (Poff et al., 2007) and affects fish communities (e.g. Schneider & Winemiller, 2008). Minimum flow increases are expected to have an opposite effect. 3 of 3