taxonID	type	description	language	source
039187D59B5CBB24FE5E769571C58A20.taxon	discussion	Prior to Projet Lac, only one species of gudgeon, Gobio gobio was known to occur in Switzerland. Gobio gobio is native to much of Europe north of the Alps and was recorded by Projet Lac in most lakes in the Rhine catchment (not recorded in Brienz and Lower Constance and naturally absent from Rousses, Joux and Brenet), as well as Annecy, Bourget and Bret in the Rhone catchment. Although the endangered Romanogobio benacensis is the native gudgeon in the Adriatic drainage, and its geographic distribution in Italy touches the borders to Switzerland [140, 141], it has not yet been recorded in Switzerland. And even though G. gobio is known to be invasive in much of the Italian Po drainage, no Gobio were recorded by Projet Lac in the lakes south of the Alps. In Upper Lake Constance, genetic barcoding of ten Gobio caught in Projet Lac, revealed five specimens of the blunt-snout gudgeon, Gobio obtusirostris and five Gobio gobio. The former species is native to the Danube river catchment and had not been previously recorded in Lake Constance nor in Switzerland. External phenotypic differences between the G. gobio and G. obtusirostris caught in Lake Constance were small (Figure 31). All Gobio in caught in Lake Constance were from fishing actions in the southern corner of the lake between Romanshorn and the mouth of the Rheintaler Binnenkanal. Individuals of both G. gobio and G. obtusirostris (according to barcoding) were caught together in two fishing actions. One individual of G. obtusirostris was also caught by Progetto Fiumi in the nearby Salmsacher Aach, which enters Lake Constance near Romanshorn. The present-day Alpine Rhine originally flowed into the Danube River (until the end of the last ice-age) and Lake Constance is known as a natural contact zone between Danubian and Rhine lineages of several other fish genera (Barbatula [142], Chondrostoma [143], Lota). Projet Lac provided the first such evidence for the two Gobio species [9].	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B5DBB24FFE57674769E8C60.taxon	discussion	Three species of Carassius are considered to occur in the perialpine region: Carassius carassius (Crucian carp), C. gibelio (Prussian carp) and C. auratus (goldfish). According to the Ordinance of the Swiss Fisheries Act none of these species are native to Switzerland. C. auratus is native to East Asia and has been introduced throughout Europe and most of the world. The native distributions of C. carassius and C. gibelio are uncertain. C. carassius is believed to be native to eastern and central Europe, as far west as the Rhine [9]. C. gibelio may be native to the central European lowlands or introduced from Asia [9]. C. carassius can be identified by a convex rear edge of the dorsal fin and 31 - 36 scales along the lateral line, while the rear edge of the dorsal fin in the other two species is concave or straight and they have fewer scales along the lateral line (26 - 33). C. auratus and C. gibelio are distinguished by colour (golden-bronze and silvery brown, respectively). The three species are however often confused with one another. [9] [9] All Carassius caught in Projet Lac except some from Lake Garda, were C. gibelio. This species was recorded in all southern perialpine lakes, as well as lakes Rousses, Constance Upper and Morat in the north. In most cases, DNA barcoding was not able to distinguish whether these fish were C. gibelio or C. auratus (3 from Maggiore, 1 from Lugano, 2 from Constance Upper and 1 from Morat), but clearly ruled out any C. carassius. Barcoding did however confirm the presence of two individuals of Carassius auratus in Lake Garda.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B5ABB23FE5D74F576218B60.taxon	discussion	The two cyprinid species Abramis brama and Blicca bjoerkna appear superficially similar and often hybridise across much of their overlapping distributions. Many fish identified in the field in Projet Lac as Blicca bjoerkna, were revealed by genetic barcoding to be Abramis brama in their mitochondrial genome. In the other direction, two individuals identified as A. brama were B. bjoerkna in their barcode. A. brama grows to a larger size of 70 cm compared to maximum standard length of 33 cm in B. bjoerkna [9]. The species can also usually be distinguished based on the number of lateral line scales (51 – 60 in A. brama versus 43 – 46 in B. bjoerkna) and branched rays in the anal fin (23 – 30.5 inA. brama versus 19 – 23.5 in B. bjoerkna [9]), but all these meristic traits are difficult to evaluate in juveniles and small subadults. Both species were only recorded in the northern perialpine lakes in Projet Lac. A. brama was generally more common, recorded in 15 lakes, compared to nine lakes for B. bjoerkna. Indeed, B. bjoerkna was not recorded in any lakes that did not also have A. brama. A. brama was recorded in particularly high numbers in Geneva (220 fish) and Lower Constance (69 fish). B. bjoerkna, on the other hand, was particularly abundant in Bret (234 fish) and Upper Constance (143 fish). Both species were similarly abundant in Lake Morat (38 A. brama and 37 B. bjoerkna). In future monitoring efforts great attention has to be paid to carefully distinguish these species. Genetic work to establish the extent of genetic mixing between the species in Switzerland and the perialpine region would also be worthwhile. Both species are also known to hybridize with Rutilus and we recorded several Abramis brama x Rutilus rutilus hybrids. Monitoring of this in the future would help understand the drivers and consequences of hybridization among cyprinid species.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B5BBB22FFE6715776D58FE0.taxon	discussion	the other Rutilus species native to the southern lakes, was recorded in fewer lakes than R. aula (Como, Mezzola, and Maggiore), and was everywhere less abundant than R. aula. R. pigus was recorded in highest numbers in lakes Como and Mezzola where R. rutilus had not become abundant (yet). In Lake Maggiore, only six juvenile fish phenotypically resembling R. pigus were recorded. Three of these were confirmed as R. pigus by genetic barcoding, while two had the mitochondrial barcode of R. rutilus and one had that of R. aula (Figure 34). In Lake Lugano, no fish phenotypically matched R. pigus, however one adult fish that was phenotypically mostly R. rutilus had the mitochondrial barcode and also the lateral line scale count of R. pigus (Figure 34). Several other fish also had meristic traits of R. pigus (> 43 / 44 lateral line scales), yet otherwise resembled R. rutilus. The mismatch between general appearance, meristic traits and mitochondrial barcode again indicates hybridisation and backcrossing between R. pigus and R. rutilus, and in Lake Maggiore also between the two native species R. aula and R. pigus.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B5BBB22FFE6715776D58FE0.taxon	discussion	To our knowledge, this is the first genetic data that show that the dramatic decline of native R. pigus and R. aula in Lakes Lugano and Maggiore was associated with introgression into the abundant invasive northern R. rutilus (as predicted in [92]), but also with introgression between the two native species. It is possibly that the breakdown of reproductive isolation between the native species was mediated by the hyperabundant invasive species. Such complex species interactions deserve further attention by researchers. Another important line of research for the conservation of the native southern Rutilus species would address the reasons for the dominance of the invasive Rutilus rutilus in Lakes Lugano, Maggiore and Varese, but not in Lakes Como and Mezzola. There was no evidence for translocation of either of the southern Rutilus species to the lakes in the Rhine or Rhone catchments (several thousand phenotypes inspected, 70 fish barcoded).	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B5BBB22FFE476B7774E8CC0.taxon	discussion	has been introduced into several southern perialpine lakes and was recorded by Projet Lac in lakes Lugano, Maggiore, Varese, Como and Mezzola. R. rutilus strongly numerically dominated the native Rutilus spp in lakes Lugano and Maggiore, and this northern species was the only Rutilus species recorded in Lake Varese. Interestingly, the introduced R. rutilus was less abundant than the two native Rutilus species in Lakes Como and Mezzola, and it was not recorded in lakes Idro, Iseo and Garda.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B5BBB22FFE476B7774E8CC0.taxon	discussion	The presence of native triotto (R. aula) was recorded in all southern perialpine lakes, except Lugano and Varese. R. aula was particularly abundant in lakes Garda and Iseo, and was the only Rutilus species recorded in Lakes Garda, Iseo and Idro. In Lake Lugano, on the other hand, the only trace of R. aula among the many non-native R. rutilus were three individuals with meristic traits of R. aula (9.5 branched rays in dorsal and anal fins, versus 10.5 in R. rutilus), that though otherwise looked more like R. rutilus. R. aula was very rare in Lake Maggiore, with only four individuals phenotypically identified as this species (versus more than one thousand R. rutilus). Three of these fish were confirmed as R. aula by mitochondrial barcoding (the fourth was not barcoded). On the other hand, one fish from Maggiore that phenotypically matched R. rutilus (out of four barcoded R. rutilus), had the mitochondrial barcode of R. aula. This suggests that hybridisation and backcrossing of hybrids between native R. aula and invasive R. rutilus is occurring.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B5BBB22FFE674F574548AE0.taxon	discussion	Three species of Rutilus were recorded by Projet Lac in the perialpine lakes: common roach (Rutilus rutilus) is native to the Rhine and Rhone catchments and most of Europe (excluding Italian and Iberian peninsulas and Mediterranean drainages of the Balkan peninsula), while triotto (R. aula) and pigo (R. pigus) are native and endemic to the northern Adriatic basin, mainly the Po catchment (Figure 34). Rutilus rutilus was one of the most common species in Projet Lac, recorded in all northern perialpine lakes. This species was also recorded in a large number of fishing actions within each lake. Usually restricted to the littoral zone, R. rutilus also dominated the open water, pelagic zone of some smaller lakes: Remoray, Hallwil, Morat and Brenet. R. rutilus populations in the two most pristine oligotrophic lakes, Lake Brienz and Lake Walen, are genetically and – in the case of Lake Brienz – also phenotypically distinct from Rutilus in the other northern pre-alpine lakes [145]. Additionally, within Lake Brienz, fish from rocky boulder and cobble habitats are phenotypically distinct from those living over any other substrate type (; Figure 35). We consider these to be different roach populations of high conservation priority. That Rutilus from more heavily impacted lakes geographically as distant as Lakes Geneva, Neuchatel and Hallwill are genetically more similar to each other than to those from Lakes Brienz and Walen may imply that Rutilus populations have lost parts of their distinctiveness in the course of ecosystem perturbation and stock transfer. In several Rhine lakes we also recorded intergeneric hybrids between Rutilus rutilus and Abramis brama (Figure 34).	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B59BB20FFE5717577E08E60.taxon	discussion	Two species are known from the region: Chondrostoma soetta from lakes in the Po catchment and C. nasus from lakes and streams north of the Alps (Figure 36). Unfortunately, both species have declined dramatically in recent years. We observed C. soetta only in Lake Mezzola, and C. nasus only in Lake Sarnen. Both species are likely exterminated in several of the lakes in the Po and Rhine drainage where they were previously recorded respectively. It is possible that Protochondrostoma genei occurs or occurred in some of the lakes in the Po catchment, but we did not record it. However, it is noteworthy here to point out that two distinct lineages of C. nasus occur in the region, the Danubian lineage confined to the Lake Constance catchment and the Atlantic lineage in the rest of the Atlantic drainage of Switzerland (Figure 37) [143].	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B57BB2EFFE475F777E28A40.taxon	discussion	was recorded in almost all northern perialpine lakes, except Thun, Brienz, Walen, Upper Zurich and Joux. S. hesperidicus was recorded in all southern perialpine lakes. Despite being previously reported in the region, no phenotypes of S. erythrophthalmus were recorded in the southern lakes, and all genetically barcoded Scardinius from the southern lakes were S. hesperidicus. We note that subadult S. hesperidicus can have bright orange-red fins, which can lead to confusion with S. erythrophthalmus. The presence of the latter species south of the Alps hence remains to be confirmed.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B57BB2EFFFB76D771458BA0.taxon	discussion	north of the Alps was first revealed by Projet Lac in the first lake sampled by the project (Lake Morat). In the course of the further surveys, the southern species was recorded in a total of 12 northern perialpine lakes, as well as in Lake Sils (Table 16). It was also reported to us with photographic documentation from Lake Poschiavo (Marcel Michel, personal communication). In most lakes, the presence of S. hesperidicus was evident from the phenotype, including by the distinct colouration of the fins in adult fish. However, there were also two northern lakes (Thun and Zurich) where the presence of the southern species was revealed only by barcoding of the mitochondrial gene COI. Mismatches between phenotype and barcode were observed in several lakes suggesting some level of hybridization and backcrossing.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B57BB2EFFE674F574BB89A0.taxon	discussion	Two different species of Scardinius occur in the region of this report [9]. Scardinius erythrophthalmus is native north of the Alps with a wide distribution across most of Europe except the peninsulas of Mediterranean Europe. Scardinius hesperidicus is native south of the Alps, and probably only to the Po river catchment and Adriatic rivers east of the Po (Kottelat & Freyhof). Among other differences, the two species can usually be distinguished as adults by the colour of the fins: red in S. erythrophthalmus (particularly the pelvic fins) and dark grey / brown in S. hesperidicus (Figure 38).	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B55BB2CFFE4765771998BE0.taxon	discussion	has unfortunately become very rare in Lake Lugano. Only two individuals were caught in Projet Lac (Figure 38). One was a large (115 mm TL) individual of typical appearance with the high count of lateral line scales that Buj et al. [146] describe for A. maxima. The second was of very different appearance, and could not be assigned to A. arborella, A. maxima or A. alburnus. The COI gene (barcode) was sequenced for both fish. They were separated by several mutations, falling into two distinct subclades within samples currently considered A. arborella. The identity and diversity of Alburnus from Lake Lugano should urgently be investigated. Our unquantified impression is that the phenotype that corresponds to A. maxima is shared with Lake Maggiore whereas the other kind seems to resemble Alburnus from Lake Garda.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B55BB2CFFE4765771998BE0.taxon	discussion	A second unusual observation in Alburnus requires reporting here: we noticed a previously undocumented phenotypic and ecological polymorphism of Alburnus alburnus in Lake Brienz. In this lake, we observed considerable variation in shape: on one hand fish with very long snouts, and on the other hand, blunt-snouted fish that resemble Alburnus alburnus from other lakes (Figure 39). The long-snouted type was commonly caught near the surface whereas the blunt-snouted type could be caught near the surface or in considerable depths down to 20 m.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B55BB2CFFE474F577C189C0.taxon	discussion	Two species of Alburnus are known from the perialpine region investigated in Projet Lac: Alburnus alburnus from Rhine and Rhone catchments, and Alburnus arborella from the Adriatic catchment. It is noteworthy that both species were recorded exclusively within their expected native range. The population of Alburnus arborella from Lake Lugano was originally described as Alborella maxima, Fatio 1882, considered distinctively larger than A. arborella, Bonaparte 1841. Buj et al. [146] found that the Lugano population grew indeed much larger than other A. arborella and was also meristically distinct. However, because those authors studied East Adriatic Alburnus populations plus the Lugano population, but did not include populations from the lakes between these regions, it is difficult to interprete their findings with regard to the status of the Lugano population. Currently, Alborella maxima is considered a synonym of Alburnus arborella.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B52BB2BFE5C779777EE8C80.taxon	discussion	The Phoxinus of all lakes and streams of the Aare system correspond to	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B52BB2BFE5C779777EE8C80.taxon	discussion	This extension of the previously known distribution range is complimentary to the data of Palandačić et al, filling the gap between the previous records in Bavaria and those in Lake Geneva that were previously appearing isolated. The new distribution range data is consistent with the expansion out of a Danubian refugium and into the Swiss midlands via the old postglacial Danubian connections of Lakes Walen and Constance that were subsequently captured by the Rhine catchment. P. csikii is hence, likely the native minnow of the Swiss Rhine and Aare catchments, possibly including Lake Geneva.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B52BB2BFE5F725770E78F80.taxon	discussion	South of the Alps, the expected Italian minnow,	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B52BB2BFE5F725770E78F80.taxon	discussion	was recorded by Projet Lac only in Lake Garda. No Phoxinus were recorded in the other northern Italian and Ticino lakes. Barcoding of some individuals caught in Progetto Fiumi in the Ticino River near Breggia and La Spiagetta did confirm the presence of P. lumaireul in the Swiss Po drainage, but other Progetto Fiumi samples from theTicino River near Breggia, turned out to be a northcentral European taxon, informally referred to as Phoxinus sp. “ morella ” [147]. These are almost certainly due to translocation from northern central Europe to Ticino. The true remaining distribution of P. lumaireul in Ticino and its interaction with other Phoxinus taxa will need to be addressed in future projects. Surprisingly too, some samples from a tributary of Lake Geneva (Stockalper Canal; Rhone drainage) were identified as P. lumaireul, implying that three different lineages currently co-occur in the Lake Geneva region (P. csikii, P. septimaniae, P. lumaireul). P. lumaireul has most likely been translocated to Lake Geneva from the southern Alps by humans. It is important to emphasize that Phoxinus phoxinus, previously thought to be the common minnow in the northern prealpine region, was not recorded at all in Projet Lac (nor in Progetto Fiumi).	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B52BB2BFE5C709771838DC0.taxon	discussion	The Phoxinus of Lake Chalain in the Jura region of the Rhone drainage, as well as those from tributaries of the Doubs (sampled in Progetto Fiumi), were revealed to be	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B52BB2BFE5C709771838DC0.taxon	discussion	This is consistent with the known range of this taxon that was recently extended from the Pyrennees to the Jura Rhone [147]. More surprisingly, Progetto Fiumi data revealed that P. septimaniae, nearly completely absent from the lakes in the region, does occur in most streams of northern Switzerland, often together with P. csikii. The exception is the Alpine Rhine (and Lake Constance) where the species seems absent. Interestingly, of all our northern Swiss lake samples, only one individual from Lake Thun was barcoded as P. septimaniae whereas 45 were P. csikii. This is in contrast to Lake Chalain in the Rhone drainage, where P. septimaniae lives in the lake in the absence of P. csikii, and also in contrast to the two alpine lakes, Sils and Poschiavo, where both species co-occur.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B52BB2BFE5F74F570628B80.taxon	discussion	Until a recent systematic and taxonomic revision of the European minnows (genus Phoxinus), two species were thought to occur in the region sampled by Projet Lac. The species native and widespread in the northern perialpine region was thought to be the central European Phoxinus phoxinus, and the species native and widespread in the region south of the Alps was thought to be Phoxinus lumaireul. Five other species were known with small distributions in southeastern and southwestern Europe but none of these was thought to occur in the region around the Alps. In 2017, the Phoxinus from around Europe were investigated using molecular markers, resulting in a revision of known species and their distribution ranges and the restoration from synonymy and delineation of several additional species that had been considered synonyms of, mostly, P. phoxinus [147]. The only samples from Switzerland included in the study were from Lake Geneva and the Ticino. The Ticino sample was identified as P. lumaireul as expected. Surprisingly however, the Lake Geneva samples were identified as P. septimaniae and P. csikii. The former was a known and valid species believed to be restricted to Mediterranean coastal streams in southern France [9]. The latter is one of the species restored from synonymy, and otherwise having a wide distribution covering most of the southern and northern Danube basin. Prior to Projet Lac and the genetic analyses of the samples, it was therefore entirely unclear which Phoxinus species occurred in the other lakes of Switzerland north of the Alps. Phoxinus was not common in Projet Lac catches, despite being previously documented in most lakes across the northern perialpine region. Indeed, among the northern lakes, Phoxinus was recorded only in the cool and oligotrophic lakes Walen, Lucerne, Thun, Brienz, as well as in Neuchatel and Chalain. Additionally, Phoxinus were collected from lakes Sils (Danube catchment) and Poschaivo (Po catchment). Barcoding of Phoxinus collected from these lakes and from several streams sampled by Progetto Fiumi in all major catchments revealed the existence of four deeply divergent mitochondrial lineages of Phoxinus that conform to three of the described and valid species plus one lineage that was defined by Palandačić et al [147] but remains undescribed.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B50BB29FE5E74B571DC8C80.taxon	discussion	Two species of spined loach (Cobitis) are often considered to be native around the central Alps: Cobitis bilineata is native to the Po river catchment, while C. taenia has a wide geographic range north of the Alps [9]. In Switzerland, the spined loach of the northern perialpine and midland region was often assumed to be C. taenia (Fish atlas), but Kottelat & Freyhof reported C. bilineata as introduced to northwstern Switzerland [9]. All Cobitis recorded by Projet Lac phenotypically resembled C. bilineata (Figure 41). This included those in the northern perialpine lakes Neuchatel, Morat and Biel (excluding one distinct phenotype in Lake Biel, see below), and all lakes south of the Alps that had Cobitis (Como, Mezzola, Iseo, Garda, Maggiore and Varese). Similarly, all Cobitis recorded by Progetto Fiumi on both sides of the Alps resembled C. bilineata. Among other distinguishing features, C. bilineata has two black spots on the base of the tail and C. taenia has only one spot on the upper section of the tail. The identity of Projet Lac and Progetto Fiumi samples as C. bilineata was confirmed by DNA barcoding, which revealed identical barcodes in the fish analysed from north and south of the Alps, consistent with reason range expansion. Thus, no C. taenia were recorded in Swiss lakes and rivers north of the Alps and it is unclear whether C. taenia ever occurred in the northern perialpine region, or whether C. bilineata has recently invaded and displaced a putatively native species. We inspected Cobitis samples from the Lake Biel region from the 1930 s in the Natural History Museum of Bern. Many of these fish were so strongly bleached that their melanin pattern was reduced to invisibility, but the few that could be identified were clearly C. bilineata. In this regard it is also important to note, that C. taenia seems absent from the entire upper Rhone catchment in France northwest of Switzerland [149] and has only isolated occurrences in southwestern Germany (Baden Württemberg south of Karlsruhe), mostly confined to the Rhine valley. Populations from the Seine catchment (Yonne, Figure 41) and the Karlsruhe region are very clearly C. taenia [150]. [9] Cobitis species are often diagnosed based on distinctive features in the shape and arrangement of melanic blotches and stripes. Among our samples from Lake Biel was one fish with a pattern very different from C. bilineata and C. taenia (Figure 41). Instead of dark blotches that are squared or longer than high, and separated by gaps about as wide or wider than the blotch itself, this fish had blotches that were higher than long and were separated by gaps clearly narrower than the blotch. It also had more vertical lines of black spots on the caudal fish than most C. bilineata. It seems most likely that this fish is a deviant phenotype of C. bilineata but it could be a different species, especially since the taxonomy of the Cobitis in eastern Europe is very poorly resolved. More samples will be needed from Lake Biel to answer this question.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59B51BBD7FFE67115704E8BA0.taxon	discussion	Six species of Barbatula (stone loach) are currently known from Europe: Barbartula quignardi from northern Spain and southern France; B. leoparda from a tiny Mediterranean drainage in French Catalonia; B. sturanyi, B. zetensis and B. vardarensis all have small distribution ranges on the Balkan region; and B. barbatula from the rest of Europe. Large morphological variation within B. barbatula has long been suspected to indicate the presence of several additional, undescribed species [9]. Indeed, a phylogeographic study by Sediva et al [151] revealed that B. barbatula consisted of many, deeply divergent mitochondrial lineages, with some originating in the Pleistocene (2.6 million – 12 thousand years ago) and even the Miocene (23 – 5 million years ago). The three described Balkanian species are phylogenetically all nested within this large group of lineages commonly referred to collectively as B. barbatula. Prior to Projet Lac, it was not known which of these lineages occurred in Switzerland and around the perialpine region. Barbatula were recorded in Projet Lac in lakes Chalain, Geneva, Constance, Walen, Zurich, Zug, Lucerne, Biel and Neuchatel. Large variation in colour pattern and head shape were evident among the collected fish, both within and among lakes. Sequencing the COI mitochondrial gene (barcode) and comparison with sequences on GenBank (an online database of genetic sequences) revealed the presence of Barbatula quignardi in the Rhone catchment in lakes Chalain and Geneva, as well as in the fish collected by Progetto Fiumi from the Allaine River. Morphologically, populations of B. quignardi tended to differ from the others by having a deeper caudal peduncle. The remaining barcoded Barbatula consisted of two distinct lineages. One lineage was recorded by Projet Lac in the lakes of the Aare-Rhine (including Limat and Reuss river subcatchments; Neuchatel, Biel, Walen, Zurich, Lucerne, Zug), while in Progetto Fiumi, the only river that this lineage was recorded from was the Sense River. Populations of this lineage are referred to in this report as Barbatula sp. Lineage I. Fish of this lineage seem to be mostly composed of smaller fish with blunt snouts and high-contrast, large, dark blotches (although those in Lucerne were somewhat paler and larger). The second lineage was widespread among the streams and rivers of the Aare-Rhine (including the River Sense; based on Progetto Fiumi), but was recorded in Projet Lac in only one lake of this catchment (Lake Zürich Obersee). On the other hand this was the loach recorded in lakes Geneva and Constance outside the Aare-Rhine catchment. This lineage is referred to in this report as Barbatula sp Lineage II. These fish appeared to grow larger than most fish we collected of the populations of Barbatula sp. Lineage I. The fish of Lake Constance were particularly variable, with enormous differences in colour pattern and head shape. Barluenga et al [142] had previously described the unusually large genetic variation and very high genetic differentiation between some populations of Barbatula in Lake Constance. It is not impossible that there are two different species in Lake Constance and this situation requires attention in the future. Barbatula sp. “ Lineage II ” and B. quignardi turned out to be sister taxa in the barcode tree, whereas B. sp. “ Lineage I ” was the sister lineage of both of these together and all three belonged to the Western clade of Sediva et al. The most surprising finding here is that B. sp. “ Lineage I ” and B. sp. “ Lineage II ” are geographically fully sympatric in the Aare-Rhine, but seem to partition the macrohabitat between them with Lineage I mostly confined to the streams (only exception Lake Zürich Obersee) and Lineage II mostly confined to the lakes (only exception the Sense River). This situation requires further investigation in the future.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BAFBBD6FFE67737742E8CE0.taxon	discussion	Considerable genetic divergence emerged among the barcoded	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BAFBBD6FFE67737742E8CE0.taxon	discussion	from the northern lakes, between the fish of the western lakes of the sampled region (Chalain, Annecy) compared to other northern lakes. Despite evidence suggesting the additional presence of E. cisalpinus in Lake Geneva in the first half of the 19 th century (barcoding of historic samples from a museum collection) [154], all ten Esox barcoded from Lake Geneva in Projet Lac were genetically E. lucius. Two lineages were apparent among the Geneva pike however, with five of the fish sharing the lineage of a historically sampled E. lucius (also collected in the first half of the 19 th century) [154] 4. This lineage was also shared with two pike from Lake Joux. The five other E. lucius from Lake Geneva shared a lineage with fish of other northern perialpine lakes (including also one fish from Lake Joux). Another distinct lineage of E. lucius contained all barcoded pike from Chalain (3 fish) and one from Annecy. This lineage clustered with GenBank reference samples mostly from Canada (as well as other parts of Europe) and may reflect the translocation of fish for stocking.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BAFBBD6FFE674B4715D8B60.taxon	discussion	Two species of pike in the genus Esox are considered native to Switzerland. The northern pike Esox lucius is widespread in cooler fresh and brackish water across the northern hemisphere. The second species Esox cisalpinus was described from lakes south of the Alps in 2011 based on genetic and phenotypic evidence [152, 153]. It was described under two different names by two author teams in the same year, with the name E. cisalpinus considered to have precedence over E. flaviae. The formal description suggested that adult E. lucius exhibit only the round-spotted phenotype, while E. cisalpinus shows mostly diagonal bars or stellate spots, with some fish showing vertical or horizontal bars. The number of scales along the lateral line also seems to distinguish the two species, with E. cisalpinus ranging from 101 – 115 scales and E. lucius generally from 125 – 148 scales [153]. Figure 43 shows the phenotypic variability of Esox caught in Projet Lac. Indeed, all very large E. lucius (> 60 cm) exhibited the round-spotted pattern. Intermediate-sized adults were more variable, for example the fish from Lake Walen with stripes and spots arranged in diagonal bars. Multiple round-spotted phenotypes, matchingEsox lucius, were also recorded in Projet Lac in some southern lakes (Maggiore and Lugano), corresponding with previous reports of the northern species in these lakes as a result of stocking [153]. Among the DNA-barcoded Esox from the southern lakes, one fish from Lugano was genetically identified as E. lucius (corresponding with its northern phenotype; Figure 43). All other pike from the southern lakes were E. cisalpinus in their mitochondrial sequence (5 from Lugano, 3 from Maggiore, 3 from Garda, 1 from Como, 1 from Mezzola), despite some having the northern, round-spot pattern (Figure 43). Interbreeding between E. cisalpinus and stocked E. lucius may have caused this disconnection between phenotype and mitochondrial genotype (barcode).	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BACBBD5FE5E757471AF8EC0.taxon	discussion	Since recolonization of the lakes after the retreat of the ice-sheets across Europe around 15,000 years ago, whitefish (Coregonus) have diversified into different ecological niches within each larger lake or set of connected lakes [155]. This has resulted in up to six ecologically differentiated species within a lake. At least 25 perialpine lakes were known to support native Coregonus species, the majority of which were endemic. The ecosystem changes resulting from eutrophication in the second half of the 19 th century led to extinction and speciation reversal of Coregonus species in many lakes. Almost 40 % of Coregonus species went extinct across the region. Detailed information on the diversity of perialpine Coregonus species and the effects of human activities is available in Vonlanthen et al [42], with two key figures provided in Figure 24. [24, 48] [42] [42] Coregonus spp can occupy many different spatial habitats, from the shallow benthic to open pelagic and the profundal zone down to 300 m of depth. No other group of fish occupies such a wide range of habitats in these lakes. Known ecologically relevant differences among Coregonus species include body size and growth rate, number, length and shape of gill rakers, eye size and visual pigments, diet and spawning habitat. The most distinct ecological types are the following: 1. large, fast growing, sparsely gill rakered, benthivorous species, which spawn in shallow water, referred to as “ Balchen ” - type whitefish (e. g. Coregonus duplex in Zurich / Walen, C. alpinus in Thun / Brienz, Coregonus litora - lis in Lucerne, C. arenicolus in Constance, C. suidteri in midland lakes and C. palaea in Neuchatel). 2. small sized, slow growing, densely rakered, zooplanktivorous species that live in the pelagic zone and spawn in deeper water, referred to as “ Albeli ” - type whitefish (e. g. Coregonus heglingus in Zurich / Walen, C. albellus in Thun / Brienz, C. muelleri in Lucerne). 3. small or medium sized, slow growing, sparsely rakered, benthivorous species that live and spawn in the deep profundal zone of lakes (e. g. Coregonus gutturosus in Constance, C. profundus in Thun). Species with other combinations of these or other characteristics occur in lakes with more than three Coregonus species. For instance a type that is in many regards intermediate between the “ Balchen ” - type and “ Albeli ” - type whitefish, referred to as “ Felchen ” - type (e. g. Coregonus fatio in Thun, C. zuerichensis in Zürich, Walen, C. macrophthalmus in Constance), or large-bodied, fast growing, densely rakered pelagic zooplanktivores such as the Blaufelchen, C. wartmanni of Lake Constance. Reproductive isolation among members of lake radiations is maintained by differences in spawning depth, spawning season, possibly mate choice [39, 156] and possibly natural selection against intermediate phenotypes resulting from hybridisation. [157, 158] Coregonus spp were recorded in Projet Lac in all northern perialpine lakes, except Bret. The highest number of Coregonus species recorded in the same lake was in LakeThun, where all six species known to occur in the lake were recovered. All four species known from Lake Brienz were also recorded in Projet Lac [24, 160]. Three Coregonus species were recorded in Upper Constance, Upper Zurich, Lucerne and Biel. Coregonus spp were most commonly caught between 10 and 40 meters and dominated the biomass in the open water of many lakes. One species of Coregonus presumed to be extirpated in one lake was re-discovered in that lake in Projet Lac. In upper Lake Zurich, genetic analyses of samples collected in Projet Lac revealed the presence of three species, C. duplex, C. zuerichensis and C. heglingus [161], whereas C. heglingus was previously thought believed to have been extirpated in Lake Zurich. In Lake Lucerne, one individual resembling the deep-water adapted Coregonus nobilis (Edelfisch) was also recovered in Projet Lac. This species had also almost gone extinct (and was at some point believed to be extinct) during eutrophication, but was rediscovered in 2004 [162]. None of the other believed extinct Coregonus species, such as the profundal C. gutturosus in Lake Constance, C. fera and C. hiemalis in Lake Geneva, or C. restrictus in Lake Morat were recorded by Projet Lac.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BAABBD3FE5F74B577BD89C0.taxon	discussion	Species of trout (Salmo spp) were recorded in most lakes surveyed by Projet Lac. Salmo spp dominated the fish biomass in the littoral and benthic zones of the alpine lakes Sils and Poschiavo. In the perialpine lakes, trout were most frequently caught in the inflowing streams and rivers. In Zug, Hallwil, Lower Constance, Chalain and Lucerne trout were only caught in adjacent streams and rivers, and not in the lake itself. Large, silvery lake forms of Salmo trutta caught in the pelagic zone (“ lake trout ” sometimes called S. trutta forma lacustris) were most common in Lake Geneva, with some also caught in lakes Walen, Upper Constance, Brienz, Sarnen, Neuchatel, Morat, Saint-Point and Joux.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BAABBD3FE5E765771888E80.taxon	discussion	are native in the northern perialpine lakes and probably also in Lake Sils in the alpine section of the Inn-Danube catchment. Atlantic trout were recorded in all lakes in the Rhine catchment except Upper Zurich, Biel and Rousses. In the Rhone catchment, Atlantic S. trutta have been widely introduced, any may be native only in Lake Geneva. In the Rhone lakes this species was missing from Projet Lac catches of only the smallest lakes: Remoray, Bonlieu and Bret. It is not known which of these lakes may have hosted the native Rhone or zebra tout Salmo rhodanensis in the past, and what happened to these populations. Atlantic trout S. trutta has also been introduced into all surveyed southern perialpine lakes, as well as Lake Poschiavo. Indeed, S. trutta were recorded in every lake of the Po catchment, except Varese (which did not have any trout). Salmo trutta is known to hybridize with southern Salmo species in some water bodies where they have been introduced, and remain distinct in others. The massive stocking of S. trutta into southern drainages is thought to have led to nearly complete displacement of the native species in some drainages [164]. This makes the proper assessment of trout diversity in southern drainage systems very important, but also complicated. Projet Lac recorded Atlantic trout Salmo trutta and three Adriatic-endemic Salmo species in the southern lakes: Salmo marmoratus (marbled trout) in lakes Maggiore, Lugano and Poschiavo, Salmo cenerinus (northern Italian brook trout) only in Lake Poschiavo, and three individuals resembling Salmo carpio (carpione) in Lake Garda. “ Engadiner trout ” were also identified in Lake Sils, characterized by very few large black spots and genetically belonging to the Danubian Salmo labrax. This taxon coexists with Salmo trutta in Lake Sils as two genomically distinct species (Figure 46). Finally, a local lake trout type was documented in Lake Poschiavo, with an unusual pattern of very dense large black spots. This taxa genetically resembled S. marmorata in the mitochondrial barcode, but Salmo cenerinus at microsatellite markers, with considerable introgression from Salmo trutta (Figure 47). This likely native form of lake trout in Poschiavo and is referred to in this report as Salmo sp. “ Blackspot ”. Based on information from local fisheries authorities, this trout form spawns in the lake, where an annual spawn fishery takes place. This makes it ecologically unique in Switzerland. The only other known lake-spawning trout in the perialpine region is S. carpio of Lake Garda, which is interestingly of similar hybrid origins (mitochondrially S. marmoratus, otherwise mostly S. cenerinus). [165] It is noteworthy that Projet Lac recorded lake trout forms of S. marmorata in Lake Maggiore. The highest abundance and diversity of trout was recorded in the alpine lakes Sils (Danube catchment) with two native species, and Poschiavo (Po catchment) with three native and two non-native species. The Salmo labrax (Danube trout) phenotype was recorded in both lakes. This lineage is native to the Danube catchment, and has been introduced into Lake Poschiavo. Salmo sp. “ Blackspot ” was recorded also in Lake Sils where it was possibly introduced from Lake Poschiavo. In Poschiavo, the two species native to the Po river catchment, Salmo cenerinus and Salmo marmoratus were confirmed as genetically distinct from one another and from S. trutta, but with strong signs of hybridization (Figure 47), possibly associated with the arrival of S. trutta and S. labrax in the lake. Some genetic differences remain that correspond to the different phenotypes (Figure 47).	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA8BBDFFE5F7715771E8AA0.taxon	discussion	The perialpine lakes of Switzerland form the southern geographic range limit of the genus Salvelinus (lake char). Officially, one species of Salvelinus is currently native to Switzerland according to federal law (VBGF): Salvelinus umbla. This species naturally occurs in all deep perialpine lakes north of the Alps, and was introduced into many alpine and southern perialpine lakes, beginning in medieval times and extensively in the 19 th – 20 th century. Two additional endemic species of Salvelinus once occurred in Switzerland: a deep-water adapted (profundal) species in each of lakes Constance (Salvelinus profundus) and Neuchatel (Salvelinus neocomensis). These species were considered to have been driven extinct by the negative effects of lake eutrophication. [9] The genus Salvelinus is renowned for its diversity of ecologically distinct forms in northern latitude lakes, for example Iceland, Scandinavia and Siberia, often with multiple forms occurring within the same lake. In several cases, these forms have been shown to be genetically distinct sympatric species. A considerable diversity of forms also occurs in some deep perialpine lakes in Switzerland. The Swiss naturalist Konrad Gessner already described three forms of Salvelinus in 1575 (Figure 48). Gessner mostly focused on the strong size differences between the forms, and named them accordingly: Umbla minor, Umbla major, and Umbla maxima. However, with the exception of the two profundal species of lakes Constance and Neuchatel, the diversity of Salvelinus has not been studied since the birth of modern taxonomy. [80] [80] [13] A large variety of forms can still be found among Salvelinus in some Swiss lakes (Figure 49). A widespread “ generalist ” form lives in many smaller lakes, as well as in some larger lakes as the single known surviving form (such as Geneva, Zug and Zurich; Figure 50), and often has a bright red belly. Four other ecologically specialized forms 5 can be distinguished in several lakes: limnetic (living in open water), benthic (near the lake floor), profundal (deepwater) and piscivorous giant (fish feeding). Limnetic forms are characterized by a slender body and a rather small head, and often exhibit an orange belly during the spawning period. Benthic forms of Salvelinus have a bulkier body shape with a long, wide head. Profundal forms are adapted to live in the deep zones of the lake, with especially large eyes, pale body coloration, and often have inflated bellies when brought to the surface. Piscivorous giant forms are mainly characterized by their large body size and often by large jaws. All four specialized forms can co-occur in the one lake, as is the case in Lake Thun 6 (Figure 49). Lake Thun has several additional forms that are currently being investigated using morphological and genetic methods (Doenz, Seehausen et al, in prep [25]). It is currently unclear whether and which of the Salvelinus forms are different species. It is also unknown how many different species there used to be in Switzerland. In lakes where Salvelinus has been extensively studied and where many individuals of each of the different forms are available, genetic differentiation has been shown between coexisting forms. For example, such studies show that S. profundus is clearly a distinct species from S. umbla, and also suggest that there are several species in Lake Thun [25]. In Projet Lac, native Salvelinus were caught in lakes Thun, Brienz, Walen, Upper Constance, Upper Zurich, Lucerne and Zug in the Rhine catchment, and Geneva and Annecy in the Rhone. Salvelinus was also recorded as a non-native species in the two alpine (Sils and Poschiavo) and several southern perialpine lakes (Iseo, Lugano, Como, Mezzola). The highest diversity of Salvelinus was observed in lakes Thun, Lucerne and Walen, each with three forms (Figure 49). At least two other distinct forms are known from lakes Thun and Brienz, with at least one other disctinct form known from Lake Lucerne [25]. The rediscovery of the presumed extinct S. profundus in Upper Lake Constance was particularly remarkable. It was caught in nets set at the location where this species was last documented in 1974 [166]. Several samples of Salvelinus from Projet Lac have been used for genetic investigations (i. e. lakes Thun, Walen, Lucerne, Constance, Geneva, Sils and Poschiavo). While these analyses are not yet complete, it can already be said that the data show that several genetically differentiated forms coexist in some lakes. The results also show that biogeographical context, ecological adaptation, as well as past stocking practices must be considered in order to understand the origins of the sympatric forms, and the wider phylogenetic relationships among the Salvelinus species and forms in the region. Salvelinus introduced into lakes Sils and Poschiavo from Austrian populations (Figure 51) are genetically very different from the native Salvelinus in Swiss perialpine lakes. Genetic data also indicate that each lake originally harbored its own char populations, and that individuals of different forms from the same lake were often more closely related to each other than the same forms in other lakes [25, 167]. However, analyses of the same genetic data also showed clear traces of stock transfer among lakes (Figure 51). For example, the original Salvelinus populations of lakes Constance, Thun and Brienz have been strongly mixed with introduced populations from other lakes. The native population in Lake Neuchatel, seems to have been completely replaced by a population introduced from Lake Geneva ([25]; no Salvelinus were caught by Projet Lac in Neuchatel). Detailed analyses are underway to characterize what remains of the native populations in these lakes.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA7BBDEFFE5701476888D00.taxon	discussion	Three-spined stickleback (Gasterosteus spp) were recorded in six lakes in Projet Lac (Table 11). Gasterosteus gymnurus is native to Switzerland in Lake Maggiore and in the Rhine near Basel. Although currently included in G. gymnurus, the native populations in lakes Maggiore and Garda 7 belong to the northern Adriatic lineage. This lineage is morphologically and genetically distinct and should be recognised as a separate species [168, 169, 170]. G. gymnurus recorded by Projet Lac in Lake Geneva were not native to the lake. This species was first documented in the lake in 1872 [171] and belongs to a West-European (middle Rhone) lineage [172].	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA7BBDDFFE5711770B989A0.taxon	discussion	was recorded in lakes Constance (Upper and Lower lakes), Biel and Lucerne. G. aculeatus was first recorded in the Lake Constance catchment in 1870 in streams on the Austrian side of the lake (see and references in [174]). Genetic analyses suggest that the G. aculeatus in Lake Constance derive mostly from a genetic lineage found in the Baltic drainage (Poland) [172]. Gasterosteus across the middle of Switzerland, such as those caught in lake Biel, are a hybrid mixture of the native upper Rhine and non-native Baltic lineages of G. aculeatus, as well as the non-native middle Rhone lineage of G. gymnurus [175]. [173] The Gasterosteus aculeatus of Lake Constance, and especially those of Upper Lake Constance, were far more abundant, larger and were found in a wider range of lake habitats than stickleback caught in the other lakes sampled by Projet Lac (Table 11, Figure 52). More than 2,500 G. aculeatus were recorded in the littoral zone, benthic zone and pelagic zones of Upper Lake Constance, to around 45 meters deep. This species formed 96 % of the number of fish and 30 % of the biomass caught in the CEN pelagic nets in Upper Lake Constance and formed around 50 % of the fish caught in the vertical gillnets (volume-weighted, whole-lake NPUE). The G. aculeatus of Upper Lake Constance have many and large bony plates covering the entire side of their body and thereby resemble both their freshwater-Baltic and marine ancestors. Most other lineages of G. aculeatus reduced their number of bony plates as they adapted to freshwater habitats, such as streams, rivers, small lakes or the littoral zone of larger lakes [177]. However, freshwater lineages of G. aculeatus in the Baltic [176], as well as several other lineages around the world have maintained the full set of bony plates. This may provide them with an adaptive advantage in the habitats of large lakes where piscivorous fish are the dominant predators [180]. The strong and highly developed armour of the Upper Lake Constance G. aculeatus, inherited from their marine ancestors, may be part of the reason why they are able to colonise the pelagic zone of such a large waterbody. [176] [178, 179] Gasterosteus aculeatus were also abundant in the pelagic zone of Lower Lake Constance, constituting almost 65 % of fish caught in the CEN pelagic nets. G. aculeatus caught in Lower Lake Constance were on average 2 cm smaller than those caught in the Upper Lake (average total length 47 mm compared to 67 mm). The smaller body size of G. aculeatus in Lower Lake Constance meant that very few were caught in the vertical nets in this lake. Analyses of gillnet mesh size selectivity show that the smallest mesh size of the vertical nets (10 mm) only starts to become efficient at catching stickleback over 60 mm in length. The smaller size of the stickleback in the Lower Lake therefore resulted in very few of this species being caught in this vertical net protocol.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA5BBDBFFE47297714F8DA0.taxon	discussion	The sculpin,	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA5BBDBFFE47297714F8DA0.taxon	discussion	is a taxon with wide and irregular distribution across Europe and considerable phenotypic and genetic variation between populations that may well comprise of several species. Cottus was caught in the benthic zone of many lakes across a wide range of depths from the littoral zone to the deepest point. Along the depth gradient, two peaks in abundance were evident in many lakes, in the shallow littoral and in the profundal, with a gap at intermediate depths. Cottus were common in the Rhine catchment, naturally absent only from the higher-altitude Jura lakes Brenet, Joux and Rousses, and were notably missing from Projet Lac catches in the lakes Zug, Morat and Constance Untersee. In the Po catchment, Cottus were caught in Poschiavo, Como, Mezzola, Garda and Maggiore, while in the Rhone catchment, this species was only caught in Geneva, Annecy and Chalain. [9, 183] Genetic differences among catchments, and between lake and stream populations in the Aare-Rhine Analysis of Cottus gobio collected in Projet Lac and an earlier Eawag project “ BioChange ” identified that the populations of Cottus gobio in the Rhine (Aare, but also including Geneva), Rhone (Doubs, but not Geneva) and Po catchments showed substantial genetic differentiation (Figure 55) [41]. The similarity of the C. gobio in Lake Geneva to populations in the Rhine catchment had already been shown in earlier work [184] and is attributed to fish crossing from the Upper Rhine to Rhone through ephemeral waterways formed at the retreating edge of the Rhone glacier in the early Holocene (c. 11,000 years ago). In addition, lake populations of Cottus within the Aare-Rhine catchment were genetically distinct from stream populations, whereas lake populations were more similar to each other than to geographically intervening stream populations. Lake and stream Cottus in the Aare catchment thus seem to belong to two distinct evolutionary lineages, possibly representing two separate colonisations (with lakes Constance and Geneva belonging to the stream lineage). This suggested that recolonization of Switzerland after deglaciation occurred in two waves, with the stream lineage representing the first wave of colonization. The lake lineage only arrived in the Aare after lakes Constance and Geneva had become inaccessible for colonisation of fish from the Aare; respectively by the Rhine falls in Constance and the retreat of the Rhone glacier further into the Alps for Geneva [41].	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA5BBDBFFE47297714F8DA0.taxon	description	Phenotypic and genetic differences between littoral and profundal forms	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA5BBDBFFE47297714F8DA0.taxon	discussion	Phenotypically distinct forms of Cottus were recorded in the profundal zone of lakes in the Aare and Po-Adriatic catchments to almost the deepest point of several lakes. In the Aare catchment, Cottus were caught to 209 m deep in Lake Thun (lake max depth Zmax = 217 m), to 214 m deep in Lake Lucerne (Zmax = 214 m) and to 145 m in Lake Walen (Zmax = 151 m). Also in the Po-Adriatic catchment, Cottus were caught to 125 m deep in Lake Maggiore (Zmax = 372 m) and to 290 m deep in Lake Garda (Zmax = 350 m). The deep-caught fish were paler in colour and tended to have flatter heads compared to the fish caught in the littoral zone of the same lakes (Figure 53). In the Po-Adriatic lakes the profundal fish corresponded to Cottus ferrugineus (described by Heckel & Kner in 1858), currently considered a synonym of C. gobio (Figure 54). Parts of the genomes of profundal and littoral individuals from lakes Thun, Walen and Lucerne were analysed in detail. Significant genomic differentiation between littoral and profundal Cottus existed in Lake Walen, but not in lakes Lucerne or Thun. However, several genetic loci showed substantial genetic differentiation between the profundal and littoral populations, especially in Lake Thun, suggesting that the very small number of profundal fish that were available for analysis (e. g. n = 5 in Lake Thun) may have limited the ability to detect genomewide differentiation. Alternatively, it is possible that the phenotypic differences are the result of plasticity (i. e. the ability of one genotype to produce different phenotypes when exposed to different environments) and further research with a greater number profundal fish is required to properly understand the situation. Sufficient numbers of profundal fish from lakes Maggiore and Garda were not available to test for genomic differentiation. However, DNA barcoding revealed that three profundal fish from Maggiore and Garda belonged to a different mitochondrial lineage than the one barcoded littoral fish from Lake Maggiore and two stream fish from the Maggia (collected by Progetto Fiumi).	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA0BBD9FE5F755777238000.taxon	vernacular_names	European perch	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA0BBD9FE5F755777238000.taxon	discussion	were recorded in all except the alpine lakes (Sils and Poschiavo) and was the most abundant species caught in Projet Lac. Across most of central Europe, P. fluviatilis typically have red fins and four to six vertical bars (some of which are often V-shaped). Perch populations in lakes across Switzerland exhibited unusually large variation in fin colour (common and extremes of fin coloration), as well as in the number of vertical bars within and among lakes. Most lakes were dominated by fish with yellow-orange or yellow fins, but highly distinct red-finned forms were found along with the yellow-finned forms in Lugano, St-Point, Geneva, Walen and Constance (Figure 56, Figure 57). Many Perca fluviatilis recorded in Projet Lac also exhibited unusually large variation in the vertical striping, ranging from four bars to eight or more. In Lake Constance, yellow-finned perch with many vertical bars was the more common phenotype caught in Projet Lac, whereas red-finned fish with few vertical bars, resembling classical central European perch, were much rarer. DNA-barcoding of Constance perch as part of Projet Lac showed that yellow-orange finned perch were genetically distinct from red-finned fish. This corresponded with previous genetic analysis of perch in Lake Constance using microsatellite DNA, which also revealed significant genetic variation between yellow-finned and red-finned individuals [187]. The earlier study also showed that the yellow-finned perch were more vulnerable to infection by several parasites (tapeworm Triaenophorus nodulosus and gill worm Ancyrocephalus percae), which do not generally cause damage to the red-finned perch and populations elsewhere. The combination of the significant genetic differentiation and different immune responses between the red-finned and yellow-finned perch in Lake Constance suggest that these are two genetically distinct species with different evolutionary histories. An additional level of genetic and taxonomic variation among perch in Switzerland is again best demonstrated by earlier work in Lake Constance. This work revealed strong genetic differentiation between the populations of Perca fluviatilis living in Lower and Upper parts of Lake Constance (Untersee and Obersee) [188]. The two populations most likely originate from different glacial refugia that met in Lake Constance during range expansion after the last glacial period, and persist as two distinct species with little hybridisation [189]. Experimental evidence suggests that divergence between the two populations may be maintained by postzygotic isolation through genetic incompatibility. It is not yet clear whether and how the variation and differentiation between fin colour types is related to this historical differentiation of lineages. Further work is needed to clarify the status and species diversity in Lake Constance perch.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BA0BBD9FE5F755777238000.taxon	description	Fin coloration was recorded for most perch collected in Projet Lac and lakes were determined to contain only the common yellow / orange-finned form, or both yellow / orange- and red-finned forms. The assignment as such is not meant to imply that yellow- and red-finned perch are distinct species in every lake. However, the phenotypic diversity in many lakes and in the region overall, is unusual compared to places elsewhere in Europe, and the situation requires careful genetic, ecological and phenotypic analysis. Until the situation is properly understood, a precautionary approach to conservation should treat red- and yellow-finned perch as two different management units. The likely outcome will be that red- and yellow-finned perch are distinct species in some lakes, but not in others.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BBEBBC7FE5D755771B98B40.taxon	discussion	The freshwater blenny	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
039187D59BBEBBC7FE5D755771B98B40.taxon	discussion	is native to the lakes and streams south of the Alps. Salaria were recorded by Projet Lac in lakes Garda, Maggiore, Lugano and Como. Salaria were also recorded in the northern perialpine lakes Geneva and Annecy. The population in Lake Geneva is phenotypically distinct from the southern perialpine populations in several key traits, including features that are used to distinguish between the species in this genus [191] (Figure 58). For instance, males of the populations of the southern perialpine lakes have blue cephalic pores on the lower part of the cheek, while those from Lake Geneva lack these pores. Barcoding of Salaria from all Projet Lac sampling sites revealed that the Lake Geneva population is genetically distinct from the populations of the southern perialpine lakes. This indicates that Lake Geneva was not colonised from southern Swiss or northern Italian populations of Salaria, but most likely from populations further down the Rhone in France. Following the identification key of Doadrio et al [191], the Lake Geneva population would be diagnosed as typical Salaria fluviatilis, whereas the populations from the lakes south of the Alps would not (given the presence of blue cephalic pores on the lower cheek, which they share with S. atlantica). Projet Lac sampling in Lake Maggiore revealed, besides the common phenotype of Salaria, a rare and previously unknown phenotype that is highly distinct in its colour pattern. Three individuals were documented by underwater photography and one of these was collected by hand net. The new phenotype has marbling on the head instead of the diagnostic head stripes of S. fluviatilis and has a broad, dark midlateral band instead of vertical bars on the flank (Figure 59). S. economidisi from LakeTrichonis in Greece has a similar midlateral stripe pattern. Further work with additional collections is required to understand this situation.	en	Alexander, Timothy, Seehausen, Ole (2021): Diversity, distribution and community composition of fish in perialpine lakes – “ Projet Lac ” synthesis report. Eawag: Swiss Federal Institute of Aquatic Science and Technology, ISBN: 978-3-906484-76-1, DOI: http://doi.org/10.5281/zenodo.5779569, URL: https://www.dora.lib4ri.ch/eawag/islandora/object/eawag:24051
