과제정보
본 논문은 환경부의 재원으로 국립생태원의 지원을 받아 수행하였습니다(NIE-기반연구-2021-45).
참고문헌
- Akamatsu, Y., G. Kume, M. Gotou, T. Kono, T. Fujii, R. Inui and Y. Kurita. 2020. Using environmental DNA analyses to assess the occurrence and abundance of the endangered amphidromous fish Plecoglossus altivelis ryukyuensis. Biodiversity Data Journal 8: e39679. https://doi.org/10.3897/bdj.8.e39679
- Akre, T.S., L.D. Parker, E. Ruther, J.E. Maldonado, L. Lemmon and N.R. McInerney. 2019. Concurrent visual encounter sampling validates eDNA selectivity and sensitivity for the endangered wood turtle (Glyptemys insculpta). PLoS ONE 14: e0215586. https://doi.org/10.1371/journal.pone.0215586
- Altschul, S.F., W. Gish, W. Miller, E.W. Myers and D.J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
- Anderson, M.J. 2005. PERMANOVA: a FORTRAN Computer Program for Permutational Multivariate Analysis of Aariance. Department of Statistics, University of Auckland, Auckland.
- Bergman, P.S., G. Schumer, S. Blankenship and E. Campbell. 2016. Detection of adult green sturgeon using environmental DNA analysis. PLoS ONE 11: e0153500. https://doi.org/10.1371/journal.pone.0153500
- Bolyen, E., J.R. Rideout, M.R. Dillon, N.A. Bokulich, C.C. Abnet, G.A. Al-Ghalith, H. Alexander, E.J. Alm, M. Arumugam, F. Asnicar, Y. Bai, J.E. Bisanz, K. Bittinger, A. Brejnrod, C.J. Brislawn, C.T. Brown, B.J. Callahan, A.M. Caraballo-Rodriguez, J. Chase, E.K. Cope, R. Da Silva, C. Diener, P.C. Dorrestein, G.M. Douglas, D.M. Durall, C. Duvallet, C.F. Edwardson, M. Ernst, M. Estaki, J. Fouquier, J.M. Gauglitz, S.M. Gibbons, D.L. Gibson, A. Gonzalez, K. Gorlick, J. Guo, B. Hillmann, S. Holmes, H. Holste, C. Huttenhower, G.A. Huttley, S. Janssen, A.K. Jarmusch, L. Jiang, B.D. Kaehler, K.B. Kang, C.R. Keefe, P. Keim, S.T. Kelley, D. Knights, I. Koester, T. Kosciolek, J. Kreps, M.G.I. Langille, J. Lee, R. Ley, Y.-X. Liu, E. Loftfield, C. Lozupone, M. Maher, C. Marotz, B.D. Martin, D. McDonald, L.J. McIver, A.V. Melnik, J.L. Metcalf, S.C. Morgan, J.T. Morton, A.T. Naimey, J.A. Navas-Molina, L.F. Nothias, S.B. Orchanian, T. Pearson, S.L. Peoples, D. Petras, M.L. Preuss, E. Pruesse, L.B. Rasmussen, A. Rivers, M.S. Robeson II, P. Rosenthal, N. Segata, M. Shaffer, A. Shiffer, R. Sinha, S.J. Song, J.R. Spear, A.D. Swafford, L.R. Thompson, P.J. Torres, P. Trinh, A. Tripathi, P.J. Turnbaugh, S. UlHasan, J.J.J. van der Hooft, F. Vargas, Y. Vazquez-Baeza, E. Vogtmann, M. von Hippel, W. Walters, Y. Wan, M. Wang, J. Warren, K.C. Weber, C.H.D. Williamson, A.D. Willis, Z.Z. Xu, J.R. Zaneveld, Y. Zhang, Q. Zhu, R. Knight and J.G. Caporaso. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology 37: 852-857. https://doi.org/10.1038/s41587-019-0209-9(2019)
- Bylemans, J., E.M. Furlan, D.M. Gleeson, C.M. Hardy and R.P. Duncan. 2018. Does size matter? An experimental evaluation of the relative abundance and decay rates of aquatic environmental DNA. Environmental Science & Technology 52: 6408-6416. https://doi.org/10.1021/acs.est.8b01071
- Carim, K., T. Wilcox, M. Young, K. McKelvey, M. Schwartz. 2015. Protocol for collecting eDNA samples from streams [Version 2.1]. Missoula, MT: U.S. Department of Agriculture Forest Service, Conservation NGCfWaF; 2015 July 2015.
- Clarke, K.R. and W.M. Warwick. 1994. Similarity-based testing for community pattern: the 2-way layout with no replication. Marine Biology 118: 167-176. https://doi.org/10.1007/BF00699231
- Clarke, K.R. and R.N. Gorley. 2006. PRIMER v6: User Manual/Tutorial(Plymouth Routines in Multivariate Ecological Research). PRIMER-E, Plymouth.
- Clarke, L.J., J.M. Beard, K.M. Swadling and B.E. Deagle. 2017. Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies. Ecology and Evolution 7: 873-883. https://doi.org/10.1002/ece3.2667
- Collins, R.A., J. Bakker, O.S. Wangensteen, A.Z. Soto, L. Corrigan, D.W. Sims, M.J. Genner and S. Mariani. 2019. Nonspecific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution 10: 1985-2001. https://doi.org/10.1111/2041-210x.13276
- Day, K., H. Campbell, A. Fisher, K. Gibb, B. Hill, A. Rose and S.N. Jarman. 2019. Development and validation of an environmental DNA test for the endangered Gouldian finch. Endangered Species Research 40: 171-182. https://doi.org/10.3354/ESR00987
- Deiner, K., J.C. Walser, E. Machler and F. Altermatt. 2015. Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biological Conservation 183: 53-63. https://doi.org/10.1016/j.biocon.2014.11.018
- Deiner, K., M.A. Renshaw, Y. Li, B.P. Olds, D.M. Lodge and M.E. Pfrender. 2017. Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods in Ecology and Evolution 8: 1888-1898. https://doi.org/10.1111/2041-210X.12836
- Edgar, R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461. https://doi.org/10.1093/bioinformatics/btq461
- Evans, N.T., B.P. Olds, M.A. Renshaw, C.R. Turner, Y. Li, C.L. Jerde, A.R. Mahon, M.E. Pfrender, G.A. Lamberti and D.M. Lodge. 2015. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resources 16: 29-41. https://doi.org/10.1111/1755-0998.12433
- Evans, N.T., Y. Li, M.A. Renshaw, B.P. Olds, K. Deiner, C.R. Turner, C.L. Jerde, D.M. Lodge, G.A. Lamberti and M.E. Pfrender. 2017. Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering. Canadian Journal of Fisheries and Aquatic Sciences 74: 1362-1374. https://doi.org/10.1139/cjfas2016-0306
- Ficetola, G.F., C. Miaud, F. Pompanon and P. Taberlet. 2008. Species detection using environmental DNA from water samples. Biology Letters 4: 423-425. https://doi.org/10.1098/rsbl.2008.0118
- Ficetola, G.F., J. Pansu, A. Bonin, E. Coissac, C. Giguet-Covex, M. De Barba, L. Gielly, C.M. Lopes, F. Boyer, F. Pompanon, G. Raye and P. Taberlet. 2015. Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Molecular Ecology Resources 15: 543-556. https://doi.org/10.1111/1755-0998.12338
- Field, J.G., K.R. Clarke and M. Warwick. 1982. A practical strategy for analyzing multi-species distribution patterns. Marine Ecology Progress Series 8: 37-53. https://doi.org/10.3354/meps008037
- Fitzpatrick, M.C., E.L. Preisser, A.M. Ellison and J.S. Elkinton. 2009. Observer bias and the detection of low-density populations. Ecological Applications 19: 1673-1679. https://doi.org/10.1890/09-0265.1
- Fujii, K., H. Doi, S. Matsuoka, M. Nagano, H. Sato and H. Yamanaka. 2019. Environmental DNA metabarcoding for fish community analysis in backwater lakes: a comparison of capture methods. PLoS ONE 14: e0210357. https://doi.org/10.1371/journal.pone.0210357
- Goldberg, C.S., C.R. Turner, K. Deiner, K.E. Klymus, P.F. Thomsen, M.A. Murphy, S.F. Spear, A. McKee, S.J. Oyler-McCance, R.S. Cornman, M.B. Laramie, A.R. Mahon, R.F. Lance, D.S. Pilliod, K.M. Strickler, L.P. Waits, A.K. Fremier, T. Takahara, J.E. Herder and P. Taberlet. 2016. Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods in Ecology and Evolution 7: 1299-1307. https://doi.org/10.1111/2041-210X.12595
- Grealy, A.C., M.C. McDowell, P. Scofield, D.C. Murray, D.A. Fusco, J. Haile, G.J. Prideaux and M. Bunce. 2015. A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages. Quaternary Science Reviews 128: 37-47. https://doi.org/10.1016/j.quascirev.2015.09.014
- Hinlo, R., D. Gleeson, M. Lintermans and E. Furlan. 2017. Methods to maximise recovery of environmental DNA from water samples. PLoS ONE 12: e0179251. https://doi.org/10.1371/journal.pone.0179251
- Kelly, R.P., J.A. Port, K.M. Yamahara, R.G. Martone, N. Lowell, P.F. Thomsen, M.E. Mach, M. Bennett, E. Prahler, M.R. Caldwell and L.B. Crowder. 2014. Harnessing DNA to improve environmental management. Science 344: 1455-1456. https://doi.org/10.1126/science.1251156
- Knudsen, S.W., R.B. Ebert, M. Hesselsoe, F. Kuntke, J. Hassingboe, P.B. Mortensen, P.F. Thomsen, E.E. Sigsgaard, B.K. Hansen, E.E. Nielsen and P.R. Moller. 2019. Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea. Journal of Experimental Marine Biology and Ecology 510: 31-45. https://doi.org/10.1016/j.jembe.2018.09.004
- Kumar, G., J.E. Eble and M.R. Gaither. 2019. A practical guide to sample preservation and pre-PCR processing of aquatic environmental DNA. Molecular Ecology Resources 20: 29-39. https://doi.org/10.1111/1755-0998.13107
- Martin, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10-12. https://doi.org/10.14806/ej.17.1.200
- Minamoto, T., H. Yamanaka, T. Takahara, M.N. Honjo and Z. Kawabata. 2012. Surveillance of fish species composition using environmental DNA. Limnology 13: 193-197. https://doi.org/10.1007/s10201-011-0362-4
- Minamoto, T., K. Hayami, M.K. Sakata and A. Imamura. 2019. Real-time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: Application to winter surveys. Ecological Research 34: 237-242. https://doi.org/10.1111/1440-1703.1018
- Miya, M., Y. Sato, T. Fukunaga, T. Sado, J.Y. Poulsen, K. Sato, T. Minamoto, S. Yamamoto, H. Yamanaka, H. Araki, M. Kondoh and W. Iwasaki. 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 7: https://doi.org/10.1098/rsos.150088
- Oliver, I. and A.J. Beattie. 1993. A possible method for the rapid assessment of biodiversity. Conservation Biology 7: 562-568. https://doi.org/10.1046/j.1523-1739.1993.07030562.x
- Ruppert, K.M., R.J. Kline and M.S. Rahman. 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. https://doi.org/10.1016/j.gecco.2019.e00547
- Sarmento-Soares, L.M. and R.F. Martins-Pinheiro. 2008. A systematic revision of Tatia (Siluriformes: Auchenipteridae: Centromochlinae). Neotropical Ichthyology 6: 495-542. https://doi.org/10.1590/S1679-62252008000300022
- Schmelzle, M.C. and A.P. Kinziger. 2016. Using occupancy modelling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species. Molecular Ecology Resources 16: 895-908. https://doi.org/10.1111/1755-0998.12501
- Schrader, C., A. Schielke, L. Ellerbroek and R. Johne. 2012. PCR inhibitors-occurrence, properties and removal. Journal of Applied Microbiology 113: 1014-1026. https://doi.org/10.1111/j.1365-2672.2012.05384.x
- Seymour, M., I. Durance, B.J. Cosby, E. Ransom-Jones, K. Deiner, S.J. Ormerod, J.K. Colbourne, G. Wilgar, G.R. Carvalho and M. de Bruyn. 2018. Acidity promotes degradation of multispecies environmental DNA in lotic mesocosms. Communications Biology 1: 4. https://doi.org/10.1038/s42003-017-0005-3
- Shu, L., A. Ludwig and Z. Peng. 2020. Standards for methods utilizing environmental DNA for detection of fish species. Genes 11: 296. https://doi.org/10.3390/genes11030296
- Simpfendorfer, C.A., P.M. Kyne, T.H. Noble, J. Goldsbury, R.K. Basiita, R. Lindsay, A. Shields, C. Perry and D.R. Jerry. 2016. Environmental DNA detects critically endangered largetooth sawfish in the wild. Endangered Species Research 30: 109-116. https://doi.org/10.3354/esr00731
- Stoeckle, B.C., S. Beggel, A.F. Cerwenka, E. Motivans, R. Kuehn R and J. Geist. 2017. A systematic approach to evaluate the influence of environmental conditions on eDNA detection success in aquatic ecosystems. PloS ONE 12: e0189119. https://doi.org/10.1371/journal.pone.0189119
- Taberlet, P., E. Coissac, M. Hajibabaei and L.H. Rieseberg. 2012. Environmental DNA. Molecular Ecology 21: 1789-1793. https://doi.org/10.1111/j.1365-294X.2012.05542.x
- Taberlet, P., A. Bonin, L. Zinger and E. Coissac. 2018. Environmental DNA: For Biodiversity Research and Monitoring. Oxford University Press, Oxford.
- Takahara, T., T. Minamoto, H. Yamanaka, H. Doi and Z. Kawabata. 2012. Estimation of fish biomass using environmental DNA. PLoS ONE 7: e35868. https://doi.org/10.1371/journal.pone.0035868
- Takahara, T., T. Minamoto and H. Doi. 2013. Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS ONE 8: e56584. https://doi.org/10.1371/journal.pone.0056584
- Tsuji, S., M. Ushio, S. Sakurai, T. Minamoto and H. Yamanaka. 2017. Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLoS ONE 12: e0176608. https://doi.org/10.1371/journal.pone.0176608
- Tsuji, S., T. Takahara, H. Doi, N. Shibata and H. Yamanaka. 2019. The detection of aquatic macroorganisms using environmental DNA analysis - A review of methods for collection, extraction, and detection. Environmental DNA 1: 99-108. https://doi.org/10.1002/edn3.21
- Vasselon, V., I. Domaizon, F. Rimet, M. Kahlert and A. Bouchez. 2017. Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter? Freshwater Science 36: 162-177. https://doi.org/10.1086/690649
- Wang, S., Z. Yan, B. Hanfling, X. Zheng, P. Wang, J. Fan and J. Li. 2021. Methodology of fish eDNA and its applications in ecology and environment. Science of the Total Environment 755: 1-17. https://doi.org/10.1016/j.scitotenv.2020.142622
- Weltz, K., J.M. Lyle, J. Ovenden, J.A.T. Morgan and D.A. Moreno. 2017. Application of environmental DNA to detect an endangered marine skate species in the wild. PLoS ONE 12: e0178124. https://doi.org/10.1371/journal.pone.0178124
- Zhang, S., J. Zhao and M. Yao. 2020. A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish. Methods in Ecology and Evolution 11: 1609-1625. https://doi.org/10.1111/2041-210X.13485