| Cottus gobio “Rhone lineage” | Chalain, Annecy. Assumed to be this lineage but needs genetic confirmation. Known to occur in Switzerland only in the Doubs river |
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| Sabanejewia larvata | Mezzola. Recorded in a different Eawag project in Switzerland in an inflow to Lake Maggiore |
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| Phoxinus lumaireul | Garda. Recorded by Progetto Fiumi as non-native in an inflow to Lake Geneva, but is the expected native Phoxinus in all southern perialpine lakes |
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| Telestes souffia souffia | Chalain |
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| Coregonus lavaretus | Endemic to Bourget |
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| Chondrostoma soetta | Mezzola. Known in Switzerland from Lugano and Maggiore, but is extremely rare or extinct in these lakes |
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| Salmo cf. carpio | Endemic to Garda |
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| Non-native species recorded by Projet Lac only in lakes outside of Switzerland |
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| Gambusia holbrooki | Varese. Native to North America |
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| Carassius auratus | Garda. Known to occur throughout Switzerland. Native to Asia |
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| Pseudorasbora parva | Garda. Known to occur in lakes Biel, Sempach and other parts of the Rhine catchment. Native to Asia |
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