References
Alberdi, A., Aizpurua, O., Gilbert, M. T. P., & Bohmann, K. (2018).
Scrutinizing key steps for reliable metabarcoding of environmental
samples. Methods in Ecology and Evolution , 9, 134–147. doi:
10.1111/2041-210X.12849
Balasingham, K. D., Walter, R. P., Mandrak, N. E., & Heath, D. D.
(2017). Environmental DNA detection of rare and invasive fish species in
two Great Lakes tributaries. Molecular Ecology , 27, 112–127.
doi: 10.1111/mec.14395
Baran, R., Jůza, T., Tušer, M., Balk, H., Blabolil, P., Čech, M.,
… Kubečka, J. (2017). A novel upward-looking hydroacoustic method
for improving pelagic fish surveys. Scientific Reports , 7, 4823.
doi: 10.1038/s41598-017-04953-6
Barnes, M. A., Turner, C. R., Jerde, C. L., Renshaw, M. A., Lindsay
Chadderton, W., & Lodge, D. M. (2014). Environmental Conditions
Influence eDNA Persistence in Aquatic Systems. Environmental
Science & Technology , 48, 1819−1827. doi: 10.1021/es404734p
Baron, J. S., LeRoy Poff, N., Angermeier, P. L., Dahm, C. N., Gleick, P.
H., Hairston, N. G., … Steinman, A. D. (2002). Meeting ecological
and societal needs for freshwater. Ecological Applications , 12,
1242–1260. doi: 10.1890/1051-0761(2002)012[1247:MEASNF]2.0.CO;2
Blabolil, P., Logez, M., Ricard, D., Prchalová, M., Říha, M., Sagouis,
A., … Argillier, C. (2016). An assessment of the ecological
potential of Central and Western European reservoirs based on fish
communities. Fisheries Research , 173, 80–87. doi:
10.1016/j.fishres.2015.05.022
Blabolil, P., Boukal, D.S., Ricard, D., Kubečka, J., Říha, M., Vašek,
M., … Peterka, J. (2017a). Optimal gillnet sampling design for
the estimation of fish community indicators in heterogeneous freshwater
ecosystems. Ecological Indicators , 77, 368–376. doi:
10.1016/j.ecolind.2017.02.036
Blabolil, P., Říha, M., Ricard, D., Peterka, J., Prchalová, M., Vašek,
M., … Kubečka, J. (2017b). A simple fish-based approach to assess
the ecological quality of freshwater reservoirs in Central Europe.Knowledge and Management of Aquatic Ecosystems , 2017-1, 418. doi:
10.1051/kmae/2017043
Blabolil, P., Duras, J., Jůza, T., Kočvara, L., Matěna, J., Muška, M.,
… Peterka, J. (2018). Assessment of burbot (Lota lota )
population sustainability in temperate reservoir. Journal of Fish
Biology , 92: 1545–1559. doi: 10.1111/jfb.13610
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible
trimmer for Illumina sequence data. Bioinformatics . 30,
2114–2120. doi: 10.1093/bioinformatics/btu170
Boukal, D. S., Jankovský, M., Kubečka, J., & Heino, M. (2012).
Stock-catch analysis of carp recreational fisheries in Czech reservoirs:
insights into fish survival, water body productivity and impact of
extreme events. Fisheries Research , 119–120: 23–32. doi:
10.1016/j.fishres.2011.12.003
Bronner, I. F., Quail, M. A., Turner, D. J., & Swerdlow, H. (2014).
Improved Protocols for Illumina Sequencing. Current Protocols in
Human Genetics , 18.2.1-18.2.42. doi: 10.1002/0471142905.hg1802s80
Bylemans, J., Gleeson, D. M., Duncan, R. P., Hardy, C. M., & Furlan, E.
M. (2019). A performance evaluation of targeted eDNA and eDNA
metabarcoding analyses for freshwater fishes. Environmental DNA ,
1, 402–414. doi: 10.1002/edn3.41
Collins, R.A., Wangensteen, O.S., O’Gorman, E.J., Mariani, S., Sims,
D.W. & Genner, M.J. (2018). Persistence of environmental DNA in marine
systems. Communications biology , 1, 185.
doi:
10.1038/s42003-018-0192-6
de Souza, L. S., Godwin, J. C., Renshaw, M. A., & Larson, E. (2016).
Environmental DNA (eDNA) detection probability is influenced by seasonal
activity of organisms. PLoS One 11, e0165273. doi:
10.1371/journal.pone.0165273
Deiner, K., Fronhofer, E. A., Mächler, E., Walser, J.-C., & Altermatt,
F. (2016). Environmental DNA reveals that rivers are conveyor belts of
biodiversity information. Nature Communications , 7, 12544. doi:
10.1038/ncomms12544.
Deiner, K., Bik, H. M., Mächler, E., Seymour, M., Lacoursière-Roussel,
A., Altermatt, F., … Bernatchez, L. (2017). Environmental DNA
metabarcoding: Transforming how we survey animal and plant communities.Molecular Ecology , 26, 5872–5895. doi: 10.1111/mec.14350
Delrieu-Trottin, E., Williams, J. T., Pitassy, D., Driskell, A., Hubert,
N., Viviani, J., … Planes, S. (2019). A DNA barcode reference
library of French Polynesian shore fishes. Scientific data , 6,
114. doi: 10.1038/s41597-019-0123-5
Djurhuus, A., Closek, C. J., Kelly, R. P., Pitz, K. J., Michisaki, R.
P., Starks, H. A., … Breitbart, M. (2020). Environmental DNA
reveals seasonal shifts and potential interactions in a marine
community. Nature Communications , 11, 254. doi:
10.1038/s41467-019-14105-1
EC, 2000. European Commision: Directive 2000/60/EC of the European
Parliament and of the Council of 23 October 2000 establishing a
framework for Community action in the field of water policy.Official Journal of the European Parliament , L327, 1–82.
Ford, D. E. (1990). Reservoir inflow processes. In: K. W. Thornton, B.
Kimmel & F. E. Pazne (Eds.), Reservoir Limnology: Ecological
Perspectives (pp. 15–42), Wiley, New York.
Furlan, E. M., Gleeson, D., Wisniewski, C., Yick, J., & Duncan, R. P.
(2019). eDNA surveys to detect species at very low densities: A case
study of European carp eradication in Tasmania, Australia. Journal
of Applied Ecology . 56, 2505–2517. doi: 10.1111/1365-2664.13485
Hänfling, B., Lawson Handley, L., Read, D. S., Hahn, C., Li, J.,
Nichols, P., … Winfield, I. J. (2016). Environmental DNA
metabarcoding of lake fish communities reflects long-term data from
established survey methods. Molecular Ecology , 25, 3101–3119.
doi: 10.1111/mec.13660
Harper, L. R., Griffiths, N. P., Lawson Handley, L., Sayer, C. D., Read,
D. S., Harper, K. J., … Hänfling, B. (2019a). Development and
application of environmental DNA surveillance for the threatened crucian
carp (Carassius carassius ). Freshwater Biology , 64,
93–107. doi: 10.1111/fwb.13197
Harper, L. R., Lawson Handley, L., Hahn, C., Boonham, N., Rees, H. C.,
Lewis, E., … Hänfling, B. (2019b). Generating and testing
ecological hypotheses at the pondscape with environmental DNA
metabarcoding: A case study on a threatened amphibian.Environmental DNA , 00, 1-16. doi: 10.1002/edn3.57
Hering, D., Borja, A., Jones, J. I., Pont, D., Boets, P., Bouchez, A.,
… Kelly, M. (2018). Implementation options for DNA-based
identification into ecological status assessment under the European
Water Framework Directive. Water Research , 138, 192–205. doi:
10.1016/j.watres.2018.03.003
Holubová, M., Čech, M., Vašek, M., & Peterka, J. (2019). On the use of
a visual census in surveying fish communities in lentic water bodies.Ecological Indicators . 105, 1–5. doi:
10.1016/j.ecolind.2019.05.042
Huson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007). MEGAN
analysis of metagenomic data. Genome Research , 17(3), 377–386.
doi: 10.1101/gr.5969107
Jane, S. F., Wilcox, T. M., McKelvey, K. S., Young, M. K., Schwartz, M.
K., Lowe, W. H., … Whiteley, A. R. (2015). Distance, flow and PCR
inhibition: eDNA dynamics in two headwater streams. Molecular
Ecology Resources , 15, 216–227. doi: 10.1111/1755-0998.12285
Jonsson, B., & Gravem, F. R. (1985). Use of space and food by resident
and migrant brown trout, Salmo trutta . Environmental
Biology of Fishes, 14, 281–293. doi: 10.1007/BF00002633
Jeunen, G. J., Knapp, M., Spencer, H. G., Lamare, M. D., Taylor, H. R.,
Stat, M., … Gemmell, M. J. (2019). Environmental DNA (eDNA)
metabarcoding reveals strong discrimination among diverse marine
habitats connected by water movement. Molecular Ecology
Resources , 19, 426–438. doi: 10.1111/1755-0998.12982
Jo, T., Murakami, H., Yamamoto, S., Masuda, R. & Minamoto, T. (2019)
Effect of water temperature and fish biomass on environmental DNA
shedding, degradation, and size distribution. Ecology and
evolution , 9, 1135–1146. doi:
10.1002/ece3.4802
Jůza, T., Ricard, D., Blabolil, P., Čech, M., Draštík, V., Frouzová, J.,
… Kubečka, J. (2015). Species-specific gradients of juvenile fish
density and size in pelagic areas of temperate reservoirs.Hydrobiologia , 762: 169-181. doi: 10.1007/s10750-015-2346-6
Kelly, R. P., Shelton, A. O., & Gallego, R. (2019). Understanding PCR
processes to draw meaningful conclusions from environmental DNA studies.Scientific Reports , 9, 1–14. doi: 10.1038/s41598-019-48546-x
Kottelat, M., & Freyhof, J. (2007) Handbook of European freshwater
fishes. Kottelat, Cornol. doi: 10.1007/s10228-007-0012-3
Kubečka, J., Hohausová, E., Matěna, J., Peterka, J., Amarasinghe, U. S.,
Bonar, S. A., … Winfield, I. J. (2009). The true picture of a
lake or reservoir fish stock: A review of needs and progress.Fisheries Research , 96, 1–5. doi: 10.1016/j.fishres.2008.09.021
Labadie, J. W. (2004). Optimal Operation of Multireservoir Systems:
State-of-the-Art Review. Journal of Water Resources Planning and
Management , 130, 93–111. doi: 10.1061/(ASCE)0733-9496(2004)130:2(93)
Lacoursière-Roussel, A., Côté, G., Leclerc, V., & Bernatchez, L.
(2016). Quantifying relative fish abundance with eDNA: a promising tool
for fisheries management. Journal of Applied Ecology , 53,
1148–1157. doi: 10.1111/1365-2664.12598
Lawson Handley, L. (2015). How will the ‘molecular revolution’
contribute to biological recording? Biological Journal of the
Linnean Society , 115, 750–766. doi: 10.1111/bij.12516
Lawson Handley, L., Read, D. S., Winfield, I. J., Kimbell, H., Johnson,
H., Li, J., … Hänfling, B. (2019). Temporal and spatial variation
in distribution of fish environmental DNA in England’s largest lake.Environmental DNA , 1, 26–39. doi: 10.1002/edn3.5
Li, J., Hatton‐Ellis, T. W., Lawson Handley, L., Kimbell, H. S.,
Benucci, M., Peirson, G., & Hänfling, B. (2019a). Ground‐truthing of a
fish‐based environmental DNA metabarcoding method for assessing the
quality of lakes. Journal of Applied Ecology , 56, 1232–1244.
doi: 10.1111/1365-2664.13352
Li, J., Lawson Handley, L., Harper, L. R., Brys, R., Watson, H. V., Di
Muri, C., … Hänfling, B. (2019b). Limited dispersion and quick
degradation of environmental DNA in fish ponds inferred by
metabarcoding. Environmental DNA . 1, 238–250. doi:
10.1002/edn3.24
Lusk, S., Hanel, L., Lojkásek, B., Lusková, V., & Muška, M. (2017). The
Red List of lampreys and fishes of the Czech Republic. In: Chobot, K.,
& Němec, M. (Eds.), Red List of threatened species of the Czech
Republic vertebrates. Příroda, 34, (pp. 51–82), Nature Conservation
Agency of the Czech Republic, Prague.
Magoč, T., & Salzberg, S. L. (2011). FLASH: fast length adjustment of
short reads to improve genome assemblies. Bioinformatics , 27,
2957–2963. doi: 10.1093/bioinformatics/btr507
McDevitt, A. D., Sales, N. G., Browett, S. S., Sparnenn, A. O., Mariani,
S., Wangensteen, O. S., … Benvenuto C. (2019). Environmental DNA
metabarcoding as an effective and rapid tool for fish monitoring in
canals. Journal of Fish Biology , 95, 679–682. doi:
10.1111/jfb.14053
Mehner, T., Diekmann, M., Brämick, U., & Lemcke, R. (2005). Composition
of fish communities in German lakes as related to lake morphology,
trophic state, shore structure and human-use intensity. Freshwater
Biology , 50, 70–85. doi: 10.1111/j.1365-2427.2004.01294.x
Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K.,
… Iwasaki, W. (2015). MiFish, a set of universal PCR primers for
metabarcoding environmental DNA from fishes: detection of more than 230
subtropical marine species. Royal Society Open Science , 2,
150088. doi: 10.1098/rsos.150088
Monsen, N. E., Cloern, J. E., Lucas, L. V., & Monismith, S. G. (2002).
The use of flushing time, residence time, and age as transport time
scales. Limnology and Oceanography , 47, 1545–1553. doi:
10.4319/lo.2002.47.5.1545
Moyer, G. R.,, Díaz-Ferguson, E., Hill, J. E., & Shea, C. (2014).
Assessing environmental DNA detection in controlled lentic systems.PLoS One 9, e103767. doi: 10.1371/journal.pone.0103767
Naylor, R. L., Williams, S. L., Strong, D. R. (2001). Aquaculture–A
gateway for exotic species. Science . 294, 1655-1656. doi:
10.1126/science.1064875
Nicholson, A., McIsaac, D., MacDonald, C., Gec, P., Mason, B. E., Rein,
W., … Hanner, R. H. (2020) An analysis of metadata reporting in
freshwater environmental DNA research calls for the development of best
practice guidelines. Environmental DNA .
doi: 10.1002/edn3.81
Oksanen, J., Blanchet, F. G., Friendly, M., Kindt, R., Legendre, P.,
McGlinn, D., … Wagner, H. (2019). vegan: Community Ecology
Package. R package version 2.5-6 .
Olds, B. P., Jerde, C. L., Renshaw, M. A., Li, Y., Evans, N. T., Turner,
C. R., … Lamberti, G. A. (2016). Estimating species richness
using environmental DNA. Ecology and Evolution , 16, 4214–4226.
doi: 10.1002/ece3.2186
Pergl, J., Sádlo, J., Petrusek, A., Laštůvka, Z., Musil, J., Perglová,
I., … Pyšek, P. (2016). Black, Grey and Watch Lists of alien
species in the Czech Republic based on environmental impacts and
management strategy. NeoBiota , 28, 1–37. doi:
10.3897/neobiota.28.4824
Pont, D., Rocle, M., Valentini, A., Civade, R., Jean, P., Maire, A.,
… Dejean, T. (2018). Environmental DNA reveals quantitative
patterns of fish biodiversity in large rivers despite its downstream
transportation. Scientific Reports , 8, 10361. doi:
10.1038/s41598-018-28424-8
Prchalová, M., Kubečka, J., Čech, M., Frouzová, J., Draštík, V.,
Hohausová, E., … Vašek, M. (2009a). The effect of depth, distance
from dam and habitat on spatial distribution of fish in an artificial
reservoir. Ecology of Freshwater Fish , 18, 247–260. doi:
10.1111/j.1600-0633.2008.00342.x
Prchalová, M., Kubečka, J., Říha, M., Mrkvička, T., Vašek, M., Jůza, T.,
… Křížek, J. (2009b). Size selectivity of standardized multimesh
gillnets in sampling coarse Europen species. Fisheries Research ,
96, 51–57. doi: 10.1016/j.fishres.2008.09.017
R Development Core Team, 2020. R: A Language and Environment for
Statistical Computing. R Foundation for Statistical Computing.
Riaz, T, Shehzad W, Viari, A, Pompanon, F., Taberlet, P., & Coissac, P.
(2011). ecoPrimers: inference of new DNA barcode markers from whole
genome sequence analysis. Nucleic Acids Research , 39, e145. doi:
10.1093/nar/gkr732
Říha, M., Kubečka, J., Mrkvička, T., Prchalová, M., Čech, M., Draštík,
V., … Vašek M. (2008). Dependence of beach seine net efficiency
on net length and diel period. Aquatic Living Resources , 21,
411–418. doi: 10.1051/alr:2008061
Říha, M., Ricard, D., Vašek, M., Prchalová, M., Mrkvička, T., Jůza, T.,
… Kubečka, J. (2015). Patterns in diel habitat use of fish
covering the littoral and pelagic zones in a reservoir.Hydrobiologia , 747, 111–131. doi: 10.1007/s10750-014-2124-x
Robinson, V. C., Garcia de Leaniz, C., Rolla, M., & Consuegra, S.
(2019). Monitoring the eradication of the highly invasive topmouth
gudgeon (Pseudorasbora parva ) using a novel eDNA assay.Environmental DNA . 1, 74–85. doi: 10.1002/edn3.12
Robson, H. L. A., Noble, T. H., Saunders, R. J., Robson, S. K. A.,
Burrows, D. W., & Jerry, D. R. (2016). Fine‐tuning for the tropics:
application of eDNA technology for invasive fish detection in tropical
freshwater ecosystems. Molecular Ecology Resources . 16. 922–932.
doi: 10.1111/1755-0998.12505
Ruppert, K. M., Kline, R. J., & Rahman, M. S. (2019). Past, present,
and future perspectives of environmental DNA (eDNA) metabarcoding: A
systematic review in methods, monitoring, and applications of global
eDNA. Global Ecology and Conservation , 17, e00547. doi:
10.1016/j.gecco.2019.e00547
Rychtecký, P., & Znachor, P. (2011). Spatial heterogeneity and seasonal
succession of phytoplankton along the longitudinal gradient in a
eutrophic reservoir. Hydrobiologia , 663, 175–186. doi:
10.1007/s10750-010-0571-6
Scharfenberger, U., Jeppesen, E., Beklioğlu, M., Søndergaard, M.,
Angeler, D. G., Çakıroğlu, A. İ., … Adrian, R. (2019). Effects of
trophic status, water level, and temperature on shallow lake metabolism
and metabolic balance: A standardized pan-European mesocosm experiment.Limnology and Oceanography , 64, 616–631. doi: 10.1002/lno.11064
Sellers, G. S., Di Muri, C., Gómez, A., & Hänfling, B. (2018). Mu-DNA:
a modular universal DNA extraction method adaptable for a wide range of
sample types. Metabarcoding and Metagenomics , 2, e24556. doi:
10.17605/OSF.IO/VRB4A
Šmejkal, M., Prchalová, M., Čech, M., Vašek, M., Říha, M., Jůza, T.,
… Kubečka, J. (2014). Associations of fish with various types of
littoral habitats in reservoirs. Ecology of Freshwater Fish , 23,
405–413. doi: 10.1071/MF15361
Šmilauer, P., & Lepš, J. (2014). Multivariate Analysis of
Ecological Data Using CANOCO 5 . Cambridge University Press. doi:
10.1017/CBO9781139627061
Stoner, A. W. (2004). Effects of environmental variables on fish feeding
ecology: Implications for the performance of baited fishing gear and
stock assessment. Journal of Fish Biology , 65, 1445–1471. doi:
10.1111/j.0022-1112.2004.00593.x
Straškraba, M. (2005). Reservoirs and Other Artificial Water Bodies. In:
P. OSullivan & C. Reynolds, (Eds.). The Lakes Handbook, Volume 2 (pp.
300–327). Oxford, UK: Blackwell Science Ltd.
Straškrabová, V., Hejzlar, J., Procházková, L., & Vyhnálek, V. (1994).
Eutrophication in stratified deep reservoirs. Water Science and
Technology , 30, 273–279. doi: 10.2166/wst.1994.0537
Straškrabová V., & Pivnička K. (2001). The Klíčava Reservoir –
Hydrobiological and Ichthyological studies (1965-2000) . Acta
Universitatis Carolinae, Environmentalica.
Taberlet, P., Bonin, A., Zinger, L., & Coissac, E. (2018).Environmental DNA . 1st ed. Oxford: Oxford University Press. doi:
10.1093/oso/9780198767220.001.0001
Thornton, K. W., Kimmel, B. L., & Payne F. E. (1990). Reservoir
Limnology: Ecological Perspectives . Willey, New York.
Trancart, T., Carpentier, A., Acou, A., Danet, V., Elliott, S., &
Feunteun E. (2019). Behaviour of endangered European eels in proximity
to a dam during downstream migration: Novel insights using high accuracy
3D acoustic telemetry. Ecology of Freshwater Fish . 29, 266–279.
doi: 10.1111/eff.12512
Tsuji, S., Ushio, M., Sakurai, S., Minamoto, T. & Yamanaka, H. (2017)
Water temperature-dependent degradation of environmental DNA and its
relation to bacterial abundance. PloS One , 12, e0176608.
doi:
10.1371/journal.pone.0176608
Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen,
P. F., … Dejean, T. (2016). Next-generation monitoring of aquatic
biodiversity using environmental DNA metabarcoding. Molecular
Ecology , 25, 929–942. doi: 10.1111/mec.13428
Vašek, M., Prchalová, M., Peterka, J., Ketelaars, H. A. M., Wagenvoort,
A. J., Čech, M., … Kubečka, J. (2013). The utility of predatory
fish in biomanipulation of deep reservoirs. Ecological
Engineering , 52: 104-111. doi: 10.1016/j.ecoleng.2012.12.100
Vejřík, L., Vejříková, I., Kočvara, L., Blabolil, P., Peterka, J.,
Sajdlová, Z., … Čech M. (2019). The pros and cons of the invasive
freshwater apex predator, European catfish Silurus glanis , and
powerful angling technique for its population control. Journal of
Environmental Management , 241, 374–382. doi:
10.1016/j.jenvman.2019.04.005
Wells, S. A. (2019). CE-QUAL-W2: A two-dimensional, laterally
averaged, hydro-dynamic and water quality model, version 4.2 .:User manual. Department of Civil and Environmental Engineering,
Portland State University, Portland, OR.
Wetzel, R. G. (2001). Limnology: Lake and River Ecosystems . 3rd
Edition. Academic Press . doi: 10.1016/C2009-0-02112-6
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000). A greedy
algorithm for aligning DNA sequences. Journal of Computational
Biology , 7, 203–214. doi: 10.1089/10665270050081478
Zhang, S., Lu, Q., Wang, Y., Wang, X., Zhao, J., & Yao, M. (2019).
Assessment of fish communities using environmental DNA: Effect of
spatial sampling design in lentic systems of different sizes.Molecular Ecology Resources . 20, 242–255. doi:
10.1111/1755-0998.13105
Znachor, P., Nedoma, J., Hejzlar, J., Seďa, J., Komárková, J., Kolář,
V., … Boukal, D. S. (2020). Changing environmental conditions
underpin long-term patterns of phytoplankton in a freshwater reservoirScience of the Total Environment , 710, 135626. doi:
10.1016/j.scitotenv.2019.135626