Evans N T, Lamberti G A. Freshwater fisheries assessment using environmental DNA: a primer on the method, its potential, and shortcomings as a conservation tool. Fisheries Research, 2018, 197: 60-66. DOI:10.1016/j.fishres.2017.09.013
[2]Dodds W K, Perkin J S, Gerken J E. Human impact on freshwater ecosystem services: a global perspective. Environmental Science & Technology, 2013, 47(16): 9061-9068.
[3] [4]Irfan S, Alatawi A M M. Aquatic ecosystem and biodiversity: a review. Open Journal of Ecology, 2019, 9(1): 1-13. DOI:10.4236/oje.2019.91001
[5]Holmlund C M, Hammer M. Ecosystem services generated by fish populations. Ecological Economics, 1999, 29(2): 253-268. DOI:10.1016/S0921-8009(99)00015-4
[6]Reid A J, Carlson A K, Creed I F, Eliason E J, Gell P A, Johnson P T J, Kidd K A, MacCormack T J, Olden J D, Ormerod S J, Smol J P, Taylor W W, Tockner K, Vermaire J C, Dudgeon D, Cooke S J. Emerging threats and persistent conservation challenges for freshwater biodiversity. Biological Reviews, 2019, 94(3): 849-873. DOI:10.1111/brv.12480
[7]Almond R E, Grooten M, Peterson T. Living Planet Report 2020-Bending the curve of biodiversity loss. World Wildlife Fund, 2020.
[8]FAO. The state of world fisheries and aquaculture 2020. Sustainability in action. The Food and Agriculture Organization of the United Nations, 2020.
[9]Schenekar T. The Current state of eDNA research in freshwater ecosystems: are we shifting from the developmental phase to standard application in biomonitoring?. Hydrobiologia, 2022, 1-20.
[10]Nagler M, Podmirseg S M, Ascher-Jenull J, Sint D, Traugott M. Why eDNA fractions need consideration in biomonitoring. Molecular Ecology Resources, 2022, 22(7): 2458-2470. DOI:10.1111/1755-0998.13658
[11]Pawlowski J, Apothéloz-Perret-Gentil L, Altermatt F. Environmental DNA: what's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring. Molecular Ecology, 2020, 29(22): 4258-4264. DOI:10.1111/mec.15643
[12]Taberlet P, Coissac E, Hajibabaei M, Rieseberg L H. Environmental DNA. Molecular Ecology, 2012, 21(8): 1789-1793. DOI:10.1111/j.1365-294X.2012.05542.x
[13]王萌, 金小伟, 林晓龙, 杜丽娜, 崔永德, 吴小平, 孙红英, 谢志才, 王新华, 王备新. 基于环境DNA-宏条形码技术的底栖动物监测及水质评价研究进展. 生态学报, 2021, 41(18): 7440-7453.
[14]Thomsen P F, Willerslev E. Environmental DNA-An emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation, 2015, 183: 4-18. DOI:10.1016/j.biocon.2014.11.019
[15]Strickler K M, Fremier A K, Goldberg C S. Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms. Biological Conservation, 2015, 183: 85-92. DOI:10.1016/j.biocon.2014.11.038
[16]Bohmann K, Evans A, Gilbert M T P, Carvalho G R, Creer S, Knapp M, Yu D W, de Bruyn M. Environmental DNA for wildlife biology and biodiversity monitoring. Trends in Ecology & Evolution, 2014, 29(6): 358-367.
[17] [18] [19]Nakao R, Miyata R, Nakamura N, Muramatsu M, Okamura H, Imamura F, Akamatsu Y. Development of environmental DNA chip for monitoring the invasive alien fishes in dam reservoirs. Landscape and Ecological Engineering, 2022, 1-9. DOI:10.1007/s11355-022-00522-w?utm_content=meta
[20]Pascher K, Švara V, Jungmeier M. Environmental DNA-based methods in biodiversity monitoring of protected areas: application range, limitations, and needs. Diversity, 2022, 14(6): 463. DOI:10.3390/d14060463
[21]Minamoto T, Miya M, Sado T, Seino S, Doi H, Kondoh M, Nakamura K, Takahara T, Yamamoto S, Yamanaka H, Araki H, Iwasaki W, Kasai A, Masuda R, Uchii K. An illustrated manual for environmental DNA research: water sampling guidelines and experimental protocols. Environmental DNA, 2021, 3(1): 8-13. DOI:10.1002/edn3.121
[22]Miya M. Environmental DNA metabarcoding: a novel method for biodiversity monitoring of marine fish communities. Annual Review of Marine Science, 2022, 14: 161-185. DOI:10.1146/annurev-marine-041421-082251
[23]Wang S P, Yan Z G, Hänfling B, Zheng X, Wang P X, Fan J T, Li J L. Methodology of fish eDNA and its applications in ecology and environment. Science of the Total Environment, 2021, 755: 142622. DOI:10.1016/j.scitotenv.2020.142622
[24]Ogram A, Sayler G S, Barkay T. The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods, 1987, 7(2/3): 57-66.
[25]Rondon M R, August P R, Bettermann A D, Brady S F, Grossman T H, Liles M R, Loiacono K A, Lynch B A, MacNeil I A, Minor C, Tiong C L, Gilman M, Osburne M S, Clardy J, Handelsman J, Goodman R M. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Applied and Environmental Microbiology, 2000, 66(6): 2541-2547. DOI:10.1128/AEM.66.6.2541-2547.2000
[26]Ficetola G F, Miaud C, Pompanon F, Taberlet P. Species detection using environmental DNA from water samples. Biology Letters, 2008, 4(4): 423-425. DOI:10.1098/rsbl.2008.0118
[27]Kawato M, Yoshida T, Miya M, Tsuchida S, Nagano Y, Nomura M, Yabuki A, Fujiwara Y, Fujikura K. Optimization of environmental DNA extraction and amplification methods for metabarcoding of deep-sea fish. MethodsX, 2021, 8: 101238. DOI:10.1016/j.mex.2021.101238
[28]Rivera S F, Rimet F, Vasselon V, Vautier M, Domaizon I, Bouchez A. Fish eDNA metabarcoding from aquatic biofilm samples: methodological aspects. Molecular Ecology Resources, 2022, 22(4): 1440-1453. DOI:10.1111/1755-0998.13568
[29] [30]Everts T, Halfmaerten D, Neyrinck S, De Regge N, Jacquemyn H, Brys R. Accurate detection and quantification of seasonal abundance of American bullfrog (Lithobates catesbeianus) using ddPCR eDNA assays. Scientific Reports, 2021, 11(1): 11282. DOI:10.1038/s41598-021-90771-w
[31]Valdivia-Carrillo T, Rocha-Olivares A, Reyes-Bonilla H, Domínguez-Contreras J F, Munguia-Vega A. Integrating eDNA metabarcoding and simultaneous underwater visual surveys to describe complex fish communities in a marine biodiversity hotspot. Molecular Ecology Resources, 2021, 21(5): 1558-1574. DOI:10.1111/1755-0998.13375
[32]Andruszkiewicz E A, Yamahara K M, Closek C J, Boehm A B. Quantitative PCR assays to detect whales, rockfish, and common murre environmental DNA in marine water samples of the Northeastern Pacific. PLoS One, 2020, 15(12): e0242689. DOI:10.1371/journal.pone.0242689
[33]Dugal L, Thomas L, Jensen M R, Sigsgaard E E, Simpson T, Jarman S, Thomsen P F, Meekan M. Individual haplotyping of whale sharks from seawater environmental DNA. Molecular Ecology Resources, 2022, 22(1): 56-65. DOI:10.1111/1755-0998.13451
[34]Gold Z, Wall A R, Curd E E, Kelly R P, Pentcheff N D, Ripma L, Barber P H, Wetzer R. eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.). Conservation Genetics Resources, 2020, 12(4): 685-690. DOI:10.1007/s12686-020-01161-9
[35]Li M, Shan X J, Wang W J, Ding X S, Dai F Q, Lv D, Wu H H. Qualitative and quantitative detection using eDNA technology: a case study of Fenneropenaeus chinensis in the Bohai Sea. Aquaculture and Fisheries, 2020, 5(3): 148-155. DOI:10.1016/j.aaf.2020.03.012
[36]Maggioni D, Assandri G, Ramazzotti F, Magnani D, Pellegrino I, Valsecchi E, Galimberti A. Differential genetic variability at two mtDNA COI regions does not imply mismatches in Odonata molecular identification performances. The European Zoological Journal, 2021, 88(1): 425-435. DOI:10.1080/24750263.2021.1896795
[37]Schmidt K J, Soluk D A, Maestas S E M, Britten H B. Persistence and accumulation of environmental DNA from an endangered dragonfly. Scientific Reports, 2021, 11: 18987. DOI:10.1038/s41598-021-98099-1
[38]Aldeguer-Riquelme B, Ramos-Barbero M D, Santos F, Antón J. Environmental dissolved DNA harbours meaningful biological information on microbial community structure. Environmental Microbiology, 2021, 23(5): 2669-2682. DOI:10.1111/1462-2920.15510
[39]Balasubramanian V K, Joseph Maran M I, Ramteke D, Vijaykumar D S, Kottarathail Rajendran A, Ramachandran P, Ramachandran R. Environmental DNA reveals aquatic biodiversity of an urban backwater area, southeast coast of India. Marine Pollution Bulletin, 2021, 171: 112786. DOI:10.1016/j.marpolbul.2021.112786
[40]Hanžek N, Gligora Udovič M, Kajan K, Borics G, Várbíró G, Stoeck T, Žutinić P, Orlić S, Stanković I. Assessing ecological status in karstic lakes through the integration of phytoplankton functional groups, morphological approach and environmental DNA metabarcoding. Ecological Indicators, 2021, 131: 108166. DOI:10.1016/j.ecolind.2021.108166
[41]Suter L, Polanowski A M, Clarke L J, Kitchener J A, Deagle B E. Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder. Molecular Ecology, 2021, 30(13): 3140-3157. DOI:10.1111/mec.15587
[42]Xie R L, Zhao G F, Yang J H, Wang Z H, Xu Y P, Zhang X W, Wang Z J. eDNA metabarcoding revealed differential structures of aquatic communities in a dynamic freshwater ecosystem shaped by habitat heterogeneity. Environmental Research, 2021, 201: 111602. DOI:10.1016/j.envres.2021.111602
[43]Carvalho C S, De Oliveira M E, Rodriguez-Castro K G, Saranholi B H, Galetti P M Jr. Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance. Molecular Ecology Resources, 2022, 22(4): 1262-1273. DOI:10.1111/1755-0998.13543
[44]Gargan L M, Brooks P R, Vye S R, Ironside J E, Jenkins S R, Crowe T P, Carlsson J. The use of environmental DNA metabarcoding and quantitative PCR for molecular detection of marine invasive non-native species associated with artificial structures. Biological Invasions, 2022, 24(3): 635-648. DOI:10.1007/s10530-021-02672-8
[45]Rees H C, Maddison B C, Middleditch D J, Patmore J R M, Gough K C. REVIEW: The detection of aquatic animal species using environmental DNA: a review of eDNA as a survey tool in ecology. Journal of Applied Ecology, 2014, 51(5): 1450-1459. DOI:10.1111/1365-2664.12306
[46]Deiner K, Walser J C, Mächler E, Altermatt F. Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biological Conservation, 2015, 183: 53-63. DOI:10.1016/j.biocon.2014.11.018
[47]Thomsen P F, Kielgast J, Iversen L L, Møller P R, Rasmussen M, Willerslev E. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One, 2012, 7(8): e41732. DOI:10.1371/journal.pone.0041732
[48] [49]Pawlowski J, Bruce K, Panksep K, Aguirre F I, Amalfitano S, Apothéloz-Perret-Gentil L, Baussant T, Bouchez A, Carugati L, Cermakova K, Cordier T, Corinaldesi C, Costa F O, Danovaro R, Dell'anno A, Duarte S, Eisendle U, Ferrari B J D, Frontalini F, Frühe L, Haegerbaeumer A, Kisand V, Krolicka A, Lanzén A, Leese F, Lejzerowicz F, Lyautey E, Maček I, Sagova-Marečková M, Pearman J K, Pochon X, Stoeck T, Vivien R, Weigand A, Fazi S. Environmental DNA metabarcoding for benthic monitoring: a review of sediment sampling and DNA extraction methods. Science of the Total Environment, 2022, 818: 151783. DOI:10.1016/j.scitotenv.2021.151783
[50]Thomson-Laing G, Howarth J D, Vandergoes M J, Wood S A. Optimised protocol for the extraction of fish DNA from freshwater sediments. Freshwater Biology, 2022, 67(9): 1584-1603. DOI:10.1111/fwb.13962
[51]Xie Y W, Wang J Z, Yang J H, Giesy J P, Yu H X, Zhang X W. Environmental DNA metabarcoding reveals primary chemical contaminants in freshwater sediments from different land-use types. Chemosphere, 2017, 172: 201-209. DOI:10.1016/j.chemosphere.2016.12.117
[52]Stoeck T, Frühe L, Forster D, Cordier T, Martins C I M, Pawlowski J. Environmental DNA metabarcoding of benthic bacterial communities indicates the benthic footprint of salmon aquaculture. Marine Pollution Bulletin, 2018, 127: 139-149. DOI:10.1016/j.marpolbul.2017.11.065
[53]Brannock P M, Learman D R, Mahon A R, Santos S R, Halanych K M. Meiobenthic community composition and biodiversity along a 5500 km transect of Western Antarctica: a metabarcoding analysis. Marine Ecology Progress Series, 2018, 603: 47-60. DOI:10.3354/meps12717
[54]Lejzerowicz F, Gooday A J, Angeles I B, Cordier T, Morard R, Apothéloz-Perret-Gentil L, Lins L, Menot L, Brandt A, Levin L, Arbizu P M, Smith C, Pawłowski J. Eukaryotic biodiversity and spatial patterns in the clarion-clipperton zone and other abyssal regions: insights from sediment DNA and RNA metabarcoding. Frontiers in Marine Science, 2021, 8: 671033. DOI:10.3389/fmars.2021.671033
[55]Bruce K, Blackman R C, Bourlat S J, Hellström M, Bakker J, Bista I, Bohmann K, Bouchez A, Brys R, Clark K, Elbrecht V, Fazi S, Fonseca V G, Hänfling B, Leese F, Mächler E, Mahon A R, Meissner K, Panksep K, Pawlowski J, Yáñez P L S, Seymour M, Thalinger B, Valentini A, Woodcock P, Traugott M, Vasselon V, Deiner K. A practical guide to DNA-based methods for biodiversity assessment, 2021.
[56]Mariani S, Baillie C, Colosimo G, Riesgo A. Sponges as natural environmental DNA samplers. Current Biology, 2019, 29(11): R401-R402. DOI:10.1016/j.cub.2019.04.031
[57]Turon M, Angulo-Preckler C, Antich A, Praebel K, Wangensteen O S. More than expected from old sponge samples: a natural sampler DNA metabarcoding assessment of marine fish diversity in nha trang bay (Vietnam). Frontiers in Marine Science, 2020, 7: 605148. DOI:10.3389/fmars.2020.605148
[58]Cai W, Harper L R, Neave E F, Shum P, Craggs J, Arias M B, Riesgo A, Mariani S. Environmental DNA persistence and fish detection in captive sponges. Molecular Ecology Resources, 2022, 22(8): 2956-2966. DOI:10.1111/1755-0998.13677
[59]Verdier H, Konecny-Dupre L, Marquette C, Reveron H, Tadier S, Grémillard L, Barthès A, Datry T, Bouchez A, Lefébure T. Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers. Molecular Ecology Resources, 2022, 22(6): 2158-2170. DOI:10.1111/1755-0998.13604
[60]Xing Y C, Gao W R, Shen Z X, Zhang Y Y, Bai J, Cai X W, Ouyang J L, Zhao Y H. A review of environmental DNA field and laboratory protocols applied in fish ecology and environmental health. Frontiers in Environmental Science, 2022, 10: 725360. DOI:10.3389/fenvs.2022.725360
[61]Dougherty M M, Larson E R, Renshaw M A, Gantz C A, Egan S P, Erickson D M, Lodge D M. Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances. The Journal of Applied Ecology, 2016, 53(3): 722-732. DOI:10.1111/1365-2664.12621
[62]Agersnap S, Larsen W B, Knudsen S W, Strand D, Thomsen P F, Hesselsøe M, Mortensen P B, Vrålstad T, Møller P R. Monitoring of noble, signal and narrow-clawed crayfish using environmental DNA from freshwater samples. PLoS One, 2017, 12(6): e0179261. DOI:10.1371/journal.pone.0179261
[63]Andújar C, Arribas P, Yu D W, Vogler A P, Emerson B C. Why the COI barcode should be the community DNA metabarcode for the Metazoa. Molecular Ecology, 2018, 27(20): 3968-3975. DOI:10.1111/mec.14844
[64]Kelly R P, Port J A, Yamahara K M, Crowder L B. Using environmental DNA to census marine fishes in a large mesocosm. PLoS One, 2014, 9(1): e86175. DOI:10.1371/journal.pone.0086175
[65]Miya M, Sato Y, Fukunaga T, Sado T, Poulsen J Y, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W. 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, 2015, 2(7): 150088. DOI:10.1098/rsos.150088
[66]Evans N T, Olds B P, Renshaw M A, Turner C R, Li Y Y, Jerde C L, Mahon A R, Pfrender M E, Lamberti G A, Lodge D M. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resources, 2016, 16(1): 29-41. DOI:10.1111/1755-0998.12433
[67]Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen P F, Bellemain E, Besnard A, Coissac E, Boyer F, Gaboriaud C, Jean P, Poulet N, Roset N, Copp G H, Geniez P, Pont D, Argillier C, Baudoin J M, Peroux T, Crivelli A J, Olivier A, Acqueberge M, Le Brun M, Møller P R, Willerslev E, Dejean T. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 2016, 25(4): 929-942. DOI:10.1111/mec.13428
[68]Taberlet P, Bonin A, Zinger L, Coissac E. Environmental DNA: for biodiversity research and monitoring. First edition.
[69]Bylemans J. Monitoring Freshwater Fish Communities with Environmental DNA (eDNA) Metabarcoding. University of Canberra, 2018.
[70]Kitano T, Umetsu K, Tian W, Osawa M. Two universal primer sets for species identification among vertebrates. International Journal of Legal Medicine, 2007, 121(5): 423-427. DOI:10.1007/s00414-006-0113-y
[71]Shaw J L A, Clarke L J, Wedderburn S D, Barnes T C, Weyrich L S, Cooper A. Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biological Conservation, 2016, 197: 131-138. DOI:10.1016/j.biocon.2016.03.010
[72]Vences M, Lyra M L, Perl R G B, Bletz M C, Stanković D, Lopes C M, Jarek M, Bhuju S, Geffers R, Haddad C F B, Steinfartz S. Freshwater vertebrate metabarcoding on Illumina platforms using double-indexed primers of the mitochondrial 16S rRNA gene. Conservation Genetics Resources, 2016, 8(3): 323-327. DOI:10.1007/s12686-016-0550-y
[73]Stat M, John J, DiBattista J D, Newman S J, Bunce M, Harvey E S. Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity. Conservation Biology, 2019, 33(1): 196-205. DOI:10.1111/cobi.13183
[74]Balasingham K D, Walter R P, Mandrak N E, Heath D D. Environmental DNA detection of rare and invasive fish species in two Great Lakes tributaries. Molecular Ecology, 2018, 27(1): 112-127. DOI:10.1111/mec.14395
[75]Kocher T D, Thomas W K, Meyer A, Edwards S V, Pääbo S, Villablanca F X, Wilson A C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America, 1989, 86(16): 6196-6200.
[76]Burgener M, Hübner P. Mitochondrial DNA enrichment for species identification and evolutionary analysis. Zeitschrift für Lebensmitteluntersuchung Und-Forschung A, 1998, 207(4): 261-263. DOI:10.1007/s002170050329
[77]Gillet B, Cottet M, Destanque T, Kue K, Descloux S, Chanudet V, Hughes S. Direct fishing and eDNA metabarcoding for biomonitoring during a 3-year survey significantly improves number of fish detected around a South East Asian Reservoir. PLoS One, 2018, 13(12): e0208592. DOI:10.1371/journal.pone.0208592
[78]Thomsen P F, Kielgast J, Iversen L L, Wiuf C, Rasmussen M, Gilbert M T P, Orlando L, Willerslev E. Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 2012, 21(11): 2565-2573. DOI:10.1111/j.1365-294X.2011.05418.x
[79]Deiner K, Renshaw M A, Li Y Y, Olds B P, Lodge D M, Pfrender M E. Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods in Ecology and Evolution, 2017, 8(12): 1888-1898. DOI:10.1111/2041-210X.12836
[80]Clarke L J, Suter L, Deagle B E, Polanowski A M, Terauds A, Johnstone G J, Stark J S. Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ, 2021, 9: e12458. DOI:10.7717/peerj.12458
[81]Christianson L M, Johnson S B, Schultz D T, Haddock S H D. Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences. Molecular Ecology Resources, 2022, 22(1): 283-294. DOI:10.1111/1755-0998.13459
[82]Osathanunkul M, Minamoto T. A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment. PeerJ, 2020, 8: e10338. DOI:10.7717/peerj.10338
[83]Soh E Y C, Smith F, Gimenez M R, Yang L, Vejborg R M, Fletcher M, Halliday N, Bleves S, Heeb S, Cámara M, Givskov M, Hardie K R, Tolker-Nielsen T, Ize B, Williams P. Disruption of the Pseudomonas aeruginosa Tat system perturbs PQS-dependent quorum sensing and biofilm maturation through lack of the Rieske cytochrome bc1 sub-unit. PLoS Pathogens, 2021, 17(8): e1009425. DOI:10.1371/journal.ppat.1009425
[84]Polanco F A, Mutis Martinezguerra M, Marques V, Villa-Navarro F, Borrero Perez G H, Cheutin M C, Dejean T, Hocdé R, Juhel J B, Maire E. Detecting aquatic and terrestrial biodiversity in a tropical estuary using environmental DNA. Biotropica, 2021, 53(6): 1606-1619. DOI:10.1111/btp.13009
[85]Charvoz L, Apothéloz-Perret-Gentil L, Reo E, Thiébaud J, Pawlowski J. Monitoring newt communities in urban area using eDNA metabarcoding. PeerJ, 2021, 9: e12357. DOI:10.7717/peerj.12357
[86]Mullin K E, Barata I M, Dawson J, Orozco-terWengel P. First extraction of eDNA from tree hole water to detect tree frogs: a simple field method piloted in Madagascar. Conservation Genetics Resources, 2022, 14(1): 99-107. DOI:10.1007/s12686-021-01245-0
[87]Zhang S, Zhao J D, Yao M. A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish. Methods in Ecology and Evolution, 2020, 11(12): 1609-1625. DOI:10.1111/2041-210X.13485
[88]Shu L, Ludwig A, Peng Z G. Environmental DNA metabarcoding primers for freshwater fish detection and quantification: in silico and in tanks. Ecology and Evolution, 2021, 11(12): 8281-8294. DOI:10.1002/ece3.7658
[89]Deiner K, Bik H M, Mächler E, Seymour M, Lacoursière-Roussel A, Altermatt F, Creer S, Bista I, Lodge D M, De Vere N, Pfrender M E, Bernatchez L. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 2017, 26(21): 5872-5895. DOI:10.1111/mec.14350
[90]Jo T, Murakami H, Masuda R, Sakata M K, Yamamoto S, Minamoto T. Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA. Molecular Ecology Resources, 2017, 17(6): e25-e33.
[91]Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research, 2011, 39(21): e145-e145. DOI:10.1093/nar/gkr732
[92]Bylemans J, Gleeson D M, Hardy C M, Furlan E. Toward an ecoregion scale evaluation of eDNA metabarcoding primers: a case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia). Ecology and Evolution, 2018, 8(17): 8697-8712. DOI:10.1002/ece3.4387
[93]Collins R A, Bakker J, Wangensteen O S, Soto A Z, Corrigan L, Sims D W, Genner M J, Mariani S. Non-specific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution, 2019, 10(11): 1985-2001. DOI:10.1111/2041-210X.13276
[94]Hänfling B, Lawson Handley L, Read D S, Hahn C, Li J L, Nichols P, Blackman R C, Oliver A, Winfield I J. Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Molecular Ecology, 2016, 25(13): 3101-3119. DOI:10.1111/mec.13660
[95]Banerji A, Bagley M, Elk M, Pilgrim E, Martinson J, Domingo J S. Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding. Hydrobiologia, 2018, 818(1): 71-86. DOI:10.1007/s10750-018-3593-0
[96]Valdez-Moreno M, Ivanova N V, Elías-Gutiérrez M, Pedersen S L, Bessonov K, Hebert P D N. Using eDNA to biomonitor the fish community in a tropical oligotrophic lake. PLoS One, 2019, 14(4): e0215505. DOI:10.1371/journal.pone.0215505
[97]Schloss P D, Westcott S L, Ryabin T, Hall J R, Hartmann M, Hollister E B, Lesniewski R A, Oakley B B, Parks D H, Robinson C J, Sahl J W, Stres B, Thallinger G G, Van Horn D J, Weber C F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 2009, 75(23): 7537-7541. DOI:10.1128/AEM.01541-09
[98]Edgar R C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 2010, 26(19): 2460-2461. DOI:10.1093/bioinformatics/btq461
[99]Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ, 2016, 4: e2584. DOI:10.7717/peerj.2584
[100]Kalyuzhnaya M G, Lapidus A, Ivanova N, Copeland A C, McHardy A C, Szeto E, Salamov A, Grigoriev I V, Suciu D, Levine S R, Markowitz V M, Rigoutsos I, Tringe S G, Bruce D C, Richardson P M, Lidstrom M E, Chistoserdova L. High-resolution metagenomics targets specific functional types in complex microbial communities. Nature Biotechnology, 2008, 26(9): 1029-1034. DOI:10.1038/nbt.1488
[101]Kuczynski J, Stombaugh J, Walters W A, González A, Caporaso J G, Knight R. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Current Protocols in Microbiology, 2012, 27(1): 1-30.
[102]Fung C, Rusling M, Lampeter T, Love C, Karim A, Bongiorno C, Yuan L L. Automation of QIIME2 metagenomic analysis platform. Current Protocols, 2021, 1(9): e254. DOI:10.1002/cpz1.254
[103]Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W. MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Molecular Biology and Evolution, 2018, 35(6): 1553-1555. DOI:10.1093/molbev/msy074
[104]Yao M, Zhang S, Lu Q, Chen X Y, Zhang S-Y, Kong Y Q, Zhao J D. Fishing for fish environmental DNA: ecological applications, methodological considerations, surveying designs, and ways forward. Molecular Ecology, 2022, 31(20): 5132-5164. DOI:10.1111/mec.16659
[105]Plough L V, Ogburn M B, Fitzgerald C L, Geranio R, Marafino G A, Richie K D. Environmental DNA analysis of river herring in Chesapeake Bay: a powerful tool for monitoring threatened keystone species. PLoS One, 2018, 13(11): e0205578. DOI:10.1371/journal.pone.0205578
[106]Dejean T, Valentini A, Duparc A, Pellier-Cuit S, Pompanon F, Taberlet P, Miaud C. Persistence of environmental DNA in freshwater ecosystems. PLoS One, 2011, 6(8): e23398. DOI:10.1371/journal.pone.0023398
[107] [108]Sepulveda A J, Nelson N M, Jerde C L, Luikart G. Are environmental DNA methods ready for aquatic invasive species management?. Trends in Ecology & Evolution, 2020, 35(8): 668-678.
[109]Bonfil R, Palacios-Barreto P, Vargas O U M, Ricaño-Soriano M, Díaz-Jaimes P. Correction to: detection of critically endangered marine species with dwindling populations in the wild using eDNA gives hope for sawfishes. Marine Biology, 2021, 168(5): 60. DOI:10.1007/s00227-021-03862-7
[110]Burgoa Cardás J, Deconinck D, Márquez I, Peón Torre P, Garcia-Vazquez E, Machado-Schiaffino G. New eDNA based tool applied to the specific detection and monitoring of the endangered European eel. Biological Conservation, 2020, 250: 108750. DOI:10.1016/j.biocon.2020.108750
[111]Budd A M, Cooper M K, Le Port A L, Schils T, Mills M S, Deinhart M E, Huerlimann R, Strugnell J M. First detection of critically endangered scalloped hammerhead sharks (Sphyrna lewini) in Guam, Micronesia, in five decades using environmental DNA. Ecological Indicators, 2021, 127: 107649. DOI:10.1016/j.ecolind.2021.107649
[112]Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z I. Estimation of fish biomass using environmental DNA. PLoS One, 2012, 7(4): e35868. DOI:10.1371/journal.pone.0035868
[113]Jamieson I G, Allendorf F W. How does the 50/500 rule apply to MVPs?. Trends in Ecology & Evolution, 2012, 27(10): 578-584.
[114]Begon M, Townsend C R. Ecology: from individuals to ecosystems. John Wiley & Sons, 2020.
[115]Luikart G, Ryman N, Tallmon D A, Schwartz M K, Allendorf F W. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics, 2010, 11(2): 355-373. DOI:10.1007/s10592-010-0050-7
[116]Immell D, Anthony R G. Estimation of black bear abundance using a discrete DNA sampling device. The Journal of Wildlife Management, 2008, 72(1): 324-330. DOI:10.2193/2006-297
[117]Krebs C. Ecology: the experimental analysis of distribution and abundance, Harper & Row, 1973.
[118]Schwarz C J, Seber G A F. Estimating animal abundance: review Ⅲ. Statistical Science, 1999, 14(4): 427-456.
[119]Yates M C, Glaser D M, Post J R, Cristescu M E, Fraser D J, Derry A M. The relationship between eDNA particle concentration and organism abundance in nature is strengthened by allometric scaling. Molecular Ecology, 2021, 30(13): 3068-3082. DOI:10.1111/mec.15543
[120]Yates M C, Bernos T A, Fraser D J. A critical assessment of estimating census population size from genetic population size (or vice versa) in three fishes. Evolutionary Applications, 2017, 10(9): 935-945. DOI:10.1111/eva.12496
[121]Mizumoto H, Urabe H, Kanbe T, Fukushima M, Araki H. Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin Taimen, a critically endangered Asian salmonid. Limnology, 2018, 19(2): 219-227. DOI:10.1007/s10201-017-0535-x
[122]Fukaya K, Murakami H, Yoon S, Minami K, Osada Y, Yamamoto S, Masuda R, Kasai A, Miyashita K, Minamoto T, Kondoh M. Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling. Molecular Ecology, 2021, 30(13): 3057-3067. DOI:10.1111/mec.15530
[123]Stoeckle M Y, Soboleva L, Charlop-Powers Z. Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary. PLoS One, 2017, 12(4): e0175186. DOI:10.1371/journal.pone.0175186
[124]Pont D, Rocle M, Valentini A, Civade R, Jean P, Maire A, Roset N, Schabuss M, Zornig H, Dejean T. Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation. Scientific Reports, 2018, 8: 10361. DOI:10.1038/s41598-018-28424-8
[125]Thomsen P F, Møller P R, Sigsgaard E E, Knudsen S W, Jørgensen O A, Willerslev E. Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes. PLoS One, 2016, 11(11): e0165252. DOI:10.1371/journal.pone.0165252
[126]Marques V, Castagné P, Fernández A P, Borrero-Pérez G H, Hocdé R, Guérin P É, Juhel J B, Velez L, Loiseau N, Letessier T B, Bessudo S, Valentini A, Dejean T, Mouillot D, Pellissier L, Villéger S. Use of environmental DNA in assessment of fish functional and phylogenetic diversity. Conservation Biology: the Journal of the Society for Conservation Biology, 2021, 35(6): 1944-1956. DOI:10.1111/cobi.13802
[127]Aglieri G, Baillie C, Mariani S, Cattano C, Calò A, Turco G, Spatafora D, Di Franco A, Di Lorenzo M, Guidetti P, Milazzo M. Environmental DNA effectively captures functional diversity of coastal fish communities. Molecular Ecology, 2021, 30(13): 3127-3139. DOI:10.1111/mec.15661
[128]Zhong W J, Zhang J Y, Wang Z H, Lin J Q, Huang X Y, Liu W H, Li H J, Pellissier L, Zhang X W. Holistic impact evaluation of human activities on the coastal fish biodiversity in the Chinese coastal environment. Environmental Science & Technology, 2022, 56(10): 6574-6583.
[129] [130]曾志新, 罗军, 颜立红, 邹建文, 肖绿田. 生物多样性的评价指标和评价标准. 湖南林业科技, 1999, 26(2): 26-29.
[131]Blancher P, Lefrançois E, Rimet F, Vasselon V, Argillier C, Arle J, Beja P, Boets P, Boughaba J, Chauvin C, Deacon M, Duncan W, Ejdung G, Erba S, Ferrari B, Fischer H, Hänfling B, Haldin M, Hering D, Hette-Tronquart N, Hiley A, Järvinen M, Jeannot B, Kahlert M, Kelly M, Kleinteich J, Koyuncuoǧlu S, Krenek S, Langhein-Winther S, Leese F, Mann D, Marcel R, Marcheggiani S, Meissner K, Mergen P, Monnier O, Narendja F, Neu D, Onofre Pinto V, Pawlowska A, Pawlowski J, Petersen M, Poikane S, Pont D, Renevier M S, Sandoy S, Svensson J, Trobajo R, Tünde Zagyva A, Tziortzis I, van der Hoorn B, Vasquez M I, Walsh K, Weigand A, Bouchez A. A strategy for successful integration of DNA-based methods in aquatic monitoring. Metabarcoding and Metagenomics, 2022, 6: 215-226.
[132]Bracken F S A, Rooney S M, Kelly-Quinn M, King J J, Carlsson J. Identifying spawning sites and other critical habitat in lotic systems using eDNA "snapshots": a case study using the sea lamprey Petromyzon marinus L. Ecology and Evolution, 2018, 9(1): 553-567.
[133]Tillotson M D, Kelly R P, Duda J J, Hoy M, Kralj J, Quinn T P. Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales. Biological Conservation, 2018, 220: 1-11. DOI:10.1016/j.biocon.2018.01.030
[134]Takeuchi A, Iijima T, Kakuzen W, Watanabe S, Yamada Y, Okamura A, Horie N, Mikawa N, Miller M J, Kojima T, Tsukamoto K. Release of eDNA by different life history stages and during spawning activities of laboratory-reared Japanese eels for interpretation of oceanic survey data. Scientific Reports, 2019, 9(1): 6074. DOI:10.1038/s41598-019-42641-9
[135]Hayer C A, Bayless M F, George A, Thompson N, Richter C A, Chapman D C. Use of environmental DNA to detect grass carp spawning events. Fishes, 2020, 5(3): 27. DOI:10.3390/fishes5030027
[136]Cristescu M E, Hebert P D N. Uses and misuses of environmental DNA in biodiversity science and conservation. Annual Review of Ecology, Evolution, and Systematics, 2018, 49(1): 209-230. DOI:10.1146/annurev-ecolsys-110617-062306
[137]赵彦伟, 陈家琪, 董丽, 麻晓梅, 白洁, 田凯. 环境DNA技术在水生态领域应用研究进展. 农业环境科学学报, 2021, 40(10): 2057-2065. DOI:10.11654/jaes.2021-0666
[138] [139]Geerts A N, Boets P, van den Heede S, Goethals P, van der heyden C. A search for standardized protocols to detect alien invasive crayfish based on environmental DNA (eDNA): a lab and field evaluation. Ecological Indicators, 2018, 84: 564-572. DOI:10.1016/j.ecolind.2017.08.068
[140]Leese F, Bouchez A, Abarenkov K, Altermatt F, Borja Á, Bruce K, Ekrem T, Čiampor Jr F, Čiamporová-Zatovičová Z, Costa F O, Duarte S, Elbrecht V, Fontaneto D, Franc A, Geiger M F, Hering D, Kahlert M, Kalamujić Stroil B, Kelly M, Keskin E, Liska I, Mergen P, Meissner K, Pawlowski J, Penev L, Reyjol Y, Rotter A, Steinke D, van der Wal B, Vitecek S, Zimmermann J, Weigand A M. Why we need sustainable networks bridging countries, disciplines, cultures and generations for aquatic biomonitoring 2.0: a perspective derived from the DNAqua-net COST action. Next Generation Biomonitoring: Part 1. Amsterdam: Elsevier, 2018: 63-99.
[141]Miya M, Sado T. Environmental DNA sampling and experimental manual version 2.1. Ed. by eDNA Methods Standardization Committee, The eDNA Society, 2019.
[142]De Brauwer M, Chariton A, Clarke L, Cooper M, Dibattista J, Furlan E, Giblot-Ducray D, Gleeson D, Harford A, Herbert S, MacDonald A J, Miller A, Montgomery K, Mooney T, Noble L M, Rourke M, Sherman C D H, Stat M, Suter L, West K M, White N, Villacorta-Rath C, Zaiko A, Trujillo-Gonzalez A. Environmental DNA protocol development guide for biomonitoring. National eDNA Reference Centre, Canberra, 2022.
[143]Muha T P, Robinson C V, Garcia de Leaniz C, Consuegra S. An optimised eDNA protocol for detecting fish in lentic and lotic freshwaters using a small water volume. PLoS One, 2019, 14(7): e0219218. DOI:10.1371/journal.pone.0219218
[144]Xiong F, Shu L, Zeng H H, Gan X N, He S P, Peng Z G. Methodology for fish biodiversity monitoring with environmental DNA metabarcoding: the primers, databases and bioinformatic pipelines. Water Biology and Security, 2022, 1(1): 100007. DOI:10.1016/j.watbs.2022.100007
[145]Gold Z, Curd E E, Goodwin K D, Choi E S, Frable B W, Thompson A R, Walker H J Jr, Burton R S, Kacev D, Martz L D, Barber P H. Improving metabarcoding taxonomic assignment: a case study of fishes in a large marine ecosystem. Molecular Ecology Resources, 2021, 21(7): 2546-2564. DOI:10.1111/1755-0998.13450
[146]Barnes M A, Turner C R. The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics, 2016, 17(1): 1-17. DOI:10.1007/s10592-015-0775-4
[147]Maruyama A, Nakamura K, Yamanaka H, Kondoh M, Minamoto T. The release rate of environmental DNA from juvenile and adult fish. PLoS One, 2014, 9(12): e114639. DOI:10.1371/journal.pone.0114639
[148]Jo T, Murakami H, Yamamoto S, Masuda R, Minamoto T. Effect of water temperature and fish biomass on environmental DNA shedding, degradation, and size distribution. Ecology and Evolution, 2019, 9(3): 1135-1146. DOI:10.1002/ece3.4802
[149]Díaz-Ferguson E E, Moyer G R. History, applications, methodological issues and perspectives for the use of environmental DNA (eDNA) in marine and freshwater environments. Revista De Biologia Tropical, 2014, 62(4): 1273-1284. DOI:10.15517/rbt.v62i4.13231
相关知识
Advances in the application of environmental DNA technology in fish ecology
Advances and prospects in behavioral ecology of aquatic an
Functional ecology of freshwater fish: research progress and prospects
Preliminary exploration of marine pollution evolutionary ecology: From behavior, adaptation to evolution
鱼类生态学(fish ecology).ppt
Advances of application of optogenetics in animal behavioral research
Characteristics of spatial and temporal ecological niches of the dominant species of fish assemblages in the saltmarsh wetlands of the Yangtze Estuary
植物源一词的由来|绿植源Plantary
Application of RS, GIS and GPS Techniques in Study of Avian Habitat
回顾水族新品展示区——第一弹!
网址: Advances in the application of environmental DNA technology in fish ecology https://m.mcbbbk.com/newsview636987.html
上一篇: 基于水声学方法的天目湖鱼类季节和 |
下一篇: 海洋鱼类摄食生态与食物网研究进展 |