, Gewässerabschnittsbasierte Einzugsgebietsgliederung der Schweiz, Bundesamt für Umwelt (BAFU), 2014.

M. T. Barbour, J. Gerritsen, B. D. Snyder, and J. B. Stribling, Rapid bioassessment protocols for use in streams and wadeable rivers, 1999.

M. A. Barnes and C. R. Turner, The ecology of environmental DNA and implications for conservation genetics, Conservation Genetics, vol.17, issue.1, pp.1-17, 2016.

K. Barton, Retrieved from http://R-Forge.r-Proje ct.Org/Proje cts/Mumin/ Baselga, A. (2010). Partitioning the turnover and nestedness components of beta diversity, Global Ecology and Biogeography, vol.19, issue.1, pp.134-143, 2009.

A. Baselga, D. Orme, S. Villeger, J. De-bortoli, and F. Leprieur, Partitioning beta diversity into turnover and nestedness components, Package Betapart, Version, vol.1, pp.4-5, 2017.

R. Blackman, E. Mächler, F. Altermatt, A. Arnold, P. Beja et al., Advancing the use of molecular methods for routine freshwater macroinvertebrate biomonitoring-the need for calibration experiments, Metabarcoding and Metagenomics, vol.3, 2019.

K. Bohmann, A. Evans, M. T. Gilbert, G. R. Carvalho, S. Creer et al., Environmental DNA for wildlife biology and biodiversity monitoring, Trends in Ecology & Evolution, vol.29, issue.6, pp.358-367, 2014.

A. Borja, A. Miles, A. Occhipinti-ambrogi, and T. Berg, Current status of macroinvertebrate methods used for assessing the quality of European marine waters: Implementing the Water Framework Directive, LB-Borja2009), vol.633, pp.181-196, 2009.

J. Bylemans, E. M. Furlan, C. M. Hardy, P. Mcguffie, M. Lintermans et al., An environmental DNA-based method for monitoring spawning activity: A case study, using the endangered Macquarie perch (Macquaria australasica), Methods in Ecology and Evolution, vol.8, issue.5, pp.646-655, 2017.

J. Bylemans, D. M. Gleeson, M. Lintermans, C. M. Hardy, M. Beitzel et al., Monitoring riverine fish communities through eDNA metabarcoding: Determining optimal sampling strategies along an altitudinal and biodiversity gradient, Metabarcoding and Metagenomics, vol.2, 2018.

B. J. Cardinale, J. E. Duffy, A. Gonzalez, D. U. Hooper, C. Perrings et al., Biodiversity loss and its impact on humanity, Nature, vol.486, issue.7401, pp.59-67, 2012.

F. Carrara, F. Altermatt, I. Rodriguez-iturbe, and A. Rinaldo, Dendritic connectivity controls biodiversity patterns in experimental metacommunities, Proceedings of the National Academy of Sciences, vol.109, issue.15, pp.5761-5766, 2012.

S. A. Chamberlain and E. Szöcs, taxize: taxonomic search and retrieval in R, 1000.

,. Chapin, F. S. Sala, O. E. Burke, I. C. Grime, J. P. Hooper et al., Ecosystem consequences of changing biodiversity, BioScience, vol.48, issue.1, pp.45-52, 1998.

R. Civade, T. Dejean, A. Valentini, N. Roset, J. Raymond et al., Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system, PLoS One, vol.11, issue.6, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01470192

G. Csardi and T. Nepusz, The igraph software package for complex network research, InterJournal, Complex Systems, issue.5, pp.1-9, 2006.

L. S. De-souza, J. C. Godwin, M. A. Renshaw, and E. Larson, Environmental DNA (eDNA) detection probability is influenced by seasonal activity of organisms, PLoS One, vol.11, issue.10, 2016.

K. Deiner and F. Altermatt, Transport distance of invertebrate environmental DNA in a natural river, PLoS One, vol.9, issue.2, 2014.

K. Deiner, H. M. Bik, E. Mächler, M. Seymour, A. Lacoursiere-roussel et al., Environmental DNA metabarcoding: Transforming how we survey animal and plant communities, Molecular Ecology, vol.26, issue.21, pp.5872-5895, 2017.

K. Deiner, E. A. Fronhofer, E. Mächler, J. C. Walser, and F. Altermatt, Environmental DNA reveals that rivers are conveyer belts of biodiversity information, Nat Commun, vol.7, 2016.

M. Dornelas, A. E. Magurran, S. T. Buckland, A. Chao, R. L. Chazdon et al., Quantifying temporal change in biodiversity: Challenges and opportunities, Proceedings of the Royal Society B: Biological Sciences, vol.280, 1750.

D. Dudgeon, A. H. Arthington, M. O. Gessner, Z. Kawabata, D. J. Knowler et al., Freshwater biodiversity: Importance, threats, status and conservation challenges, Biological Reviews, vol.81, issue.2, pp.163-182, 2006.

R. C. Edgar, UNOISE2: Improved error-correction for Illumina 16S and ITS amplicon sequencing, 2016.

V. Elbrecht and F. Leese, Validation and development of COI metabarcoding primers for freshwater macroinvertebrate bioassessment, Frontiers in Environmental Science, vol.5, p.11, 2017.

G. F. Ficetola, C. Miaud, F. Pompanon, and P. Taberlet, Species detection using environmental DNA from water samples, Biology Letters, vol.4, issue.4, pp.423-425, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00308650

D. S. Finn, N. Bonada, C. Múrria, and J. M. Hughes, Small but mighty: Headwaters are vital to stream network biodiversity at two levels of organization, Journal of the North American Benthological Society, vol.30, issue.4, pp.963-980, 2011.

K. J. Gaston, Global patterns in biodiversity, Nature, vol.405, pp.220-227, 2000.

J. Geller, C. Meyer, M. Parker, and H. Hawk, Redesign of PCR primers for mitochondrial cytochrome c oxidase subunit I for marine invertebrates and application in all-taxa biotic surveys, Molecular Ecology Resources, vol.13, issue.5, pp.851-861, 2013.

P. Giraudoux, pgirmess: Spatial analysis and data mining for field ecologists. R Package Version, vol.361, p.9, 2018.

N. J. Gotelli and R. K. Colwell, Estimating species richness, Biological Diversity: Frontiers in Measurement and Assessment, vol.12, pp.39-54, 2011.

M. Hajibabaei, S. Shokralla, X. Zhou, G. A. Singer, and D. J. Baird, Environmental barcoding: A next-generation sequencing approach for biomonitoring applications using river benthos, PLoS One, vol.6, issue.4, 2011.

B. Hänfling, L. Lawson-handley, D. S. Read, C. Hahn, J. Li et al., Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods, Molecular Ecology, vol.25, issue.13, pp.3101-3119, 2016.

E. Harvey and F. Altermatt, Regulation of the functional structure of aquatic communities across spatial scales in a major river network, Ecology, vol.100, issue.4, 2019.

E. Harvey, I. Gounand, E. A. Fronhofer, and F. Altermatt, Disturbance reverses classic biodiversity predictions in river-like landscapes, Proceedings of the Royal Society B: Biological Sciences, vol.285, 1893.
URL : https://hal.archives-ouvertes.fr/hal-01970519

M. Holyoak, M. A. Leibold, and R. D. Holt, Metacommunities: Spatial dynamics and ecological communities, 2005.

F. Isbell, A. Gonzalez, M. Loreau, J. Cowles, S. Díaz et al., Linking the influence and dependence of people on biodiversity across scales, Nature, vol.546, pp.65-72, 2017.

C. L. Jerde, B. P. Olds, A. J. Shogren, E. A. Andruszkiewicz, A. R. Mahon et al., Influence of stream bottom substrate on retention and transport of vertebrate environmental DNA, Environmental Science & Technology, vol.50, issue.16, pp.8770-8779, 2016.

P. Koleff, K. J. Gaston, and J. J. Lennon, Measuring beta diversity for presence-absence data, Journal of Animal Ecology, vol.72, issue.3, pp.367-382, 2003.

B. J. Laforest, A. K. Winegardner, O. A. Zaheer, N. W. Jeffery, E. E. Boyle et al., Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding, BMC Ecology, vol.13, issue.1, p.13, 2013.

L. Handley and L. , How will the 'molecular revolution' contribute to biological recording?, Biological Journal of the Linnean Society, vol.115, issue.3, pp.750-766, 2015.

M. Leray and N. Knowlton, Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding, PeerJ, vol.5, 2017.

M. Leray, J. Y. Yang, C. P. Meyer, S. C. Mills, N. Agudelo et al., A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: Application for characterizing coral reef fish gut contents, Frontiers in Zoology, vol.10, issue.1, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268031

Y. Li, N. T. Evans, M. A. Renshaw, C. L. Jerde, B. P. Olds et al., Estimating fish alpha-and beta-diversity along a small stream with environmental DNA metabarcoding, Metabarcoding and Metagenomics, vol.2, 2018.

C. Lundmark, BioBlitz: Getting into backyard biodiversity, BioScience, vol.53, issue.4, 2003.

J. Macher and F. Leese, Environmental DNA metabarcoding of rivers: Not all eDNA is everywhere, and not all the time, 2017.

R. J. Machida, M. Leray, S. Ho, and N. Knowlton, Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples. Scientific Data, 4, 170027, 2017.

E. Mächler, M. Osathanunkul, and F. Altermatt, Shedding light on eDNA: Neither natural levels of UV radiation nor the presence of a filter feeder affect eDNA-based detection of aquatic organisms, PloS One, vol.13, issue.4, 2018.

P. J. Mcmurdie and S. Holmes, phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data, PloS One, vol.8, issue.4, 2013.

J. Oksanen, F. G. Blanchet, R. Kindt, P. Legendre, P. R. Minchin et al., vegan: Community ecology package. R Package Version, pp.117-118, 2011.

B. P. Olds, C. L. Jerde, M. A. Renshaw, Y. Li, N. T. Evans et al., Estimating species richness using environmental DNA, Ecology and Evolution, vol.6, issue.12, pp.4214-4226, 2016.

F. Pennekamp, M. Pontarp, A. Tabi, F. Altermatt, R. Alther et al., Biodiversity increases and decreases ecosystem stability, Nature, vol.563, issue.7729, pp.109-112, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01944370

M. Pfaundler and U. Schoenenberger, Datensatz MQ-GWN-CH, modellierte mittlere natürliche Abflüsse für das Gewässernetz der Schweiz, Bundesamt für Umwelt (BAFU), 2013.

D. Pont, M. Rocle, A. Valentini, R. Civade, P. Jean et al., Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation, Scientific Reports, vol.8, issue.1, p.10361, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01834958

S. Postel and S. Carpenter, Freshwater ecosystem services. Nature's Services: Societal Dependence on Natural Ecosystems, 0195.

A. Purvis and A. Hector, Getting the measure of biodiversity, Nature, vol.405, 2000.

, R: A language and environment for statistical computing, 2008.

V. H. Resh and D. M. Rosenberg, Freshwater biomonitoring and benthic macroinvertebrates, 1993.

T. B. Reynoldson, C. Logan, T. Pascoe, and S. P. Thompson, CABIN (Canadian Aquatic Biomonitoring Network) invertebrate biomonitoring field and laboratory manual, Environment Canada, 2003.

L. M. Sassoubre, K. M. Yamahara, L. D. Gardner, B. A. Block, and A. B. Boehm, Quantification of environmental DNA (eDNA) shedding and decay rates for three marine fish, Environ Sci Technol, vol.50, issue.19, pp.10456-10464, 2016.

A. Schmidt-kloiber and D. Hering, www. freshwaterecology. info-An online tool that unifies, standardises and codifies more than 20,000 European freshwater organisms and their ecological preferences, Ecological Indicators, vol.53, pp.271-282, 2015.

M. Seymour, E. A. Fronhofer, and F. Altermatt, Dendritic network structure and dispersal affect temporal dynamics of diversity and species persistence, Oikos, vol.124, issue.7, pp.908-916, 2015.

A. J. Shogren, J. L. Tank, E. A. Andruszkiewicz, B. Olds, C. Jerde et al., Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments, Journal of the Royal Society Interface, vol.13, issue.119, 2016.

A. J. Shogren, J. L. Tank, E. Andruszkiewicz, B. Olds, A. R. Mahon et al., Controls on eDNA movement in streams: Transport, retention, and resuspension, Scientific Reports, vol.7, issue.1, 2017.

S. Shokralla, J. L. Spall, J. F. Gibson, and M. Hajibabaei, Nextgeneration sequencing technologies for environmental DNA research, Molecular Ecology, vol.21, issue.8, pp.1794-1805, 2012.

J. D. Tonkin, F. Altermatt, D. S. Finn, J. Heino, J. D. Olden et al., The role of dispersal in river network metacommunities: Patterns, processes, and pathways, Freshwater Biology, vol.63, issue.1, pp.141-163, 2018.

A. Valentini, P. Taberlet, C. Miaud, R. Civade, J. Herder et al., Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding, Molecular Ecology, vol.25, issue.4, pp.929-942, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01419572

R. H. Whittaker, Evolution and measurement of species diversity, Taxon, pp.213-251, 1972.

L. Wilkinson and S. Urbanek, venneuler: Venn and Euler diagrams. R Package Version, p.1, 2011.

D. J. Winter, rentrez: An R package for the NCBI eUtils API, The R Journal, vol.9, issue.2, p.520, 2017.