Gangloff, M. M., Edgar, G. J. & Wilson, B. Imperilled species in aquatic ecosystems: emerging threats, management and future prognosis. Aquatic Conserv. Mar. Freshw. Ecosyst. 26, 858–871 (2016).
WWF. Living Planet Report—2018: Aiming Higher (eds Grooten, M. & Almond, R.E.A.). WWF, Gland, Switzerland (2018).
Zhou, X. et al. Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater. Nat. Commun. 9, 1276 (2018).
Mei, Z. et al. Accelerating population decline of Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis). Biol. Conserv. 153, 192–200 (2012).
Wang, D., Turvey, S.T., Zhao, X. & Mei, Z. Neophocaena asiaeorientalisssp.asiaeorientalis. The IUCN Red List of Threatened Species 2013 e.T43205774A45893487, http://dx.doi.org/https://doi.org/10.2305/IUCN.UK.2013-1.RLTS.T43205774A45893487.en(2013).
Yang, J. et al. A preliminary study on diet of the Yangtze finless porpoise using next-generation sequencing techniques. Mar. Mammal Sci. 35, 1579–1586 (2019).
Wang, D. Population status, threats and conservation of the Yangtze finless porpoise. Chin. Sci. Bull. 54, 3473–3484 (2009).
Wu, J. et al. Progress in studies on water ecology in Tian’e Zhou Oxbow. Acta Hydrobiol. Sin. 41, 935–946 (2017) (In Chinese).
Nabi, G., Hao, Y., Robeck, T. R., Zheng, J. & Wang, D. Physiological consequences of biologic state and habitat dynamics on the critically endangered Yangtze finless porpoises (Neophocaena asiaeorientalis ssp. asiaeorientalis) dwelling in the wild and semi-natural environment. Conserv. Physiol. 6, coy072 (2018).
Stewart, K., Ma, H., Zheng, J. & Zhao, J. Using environmental DNA to assess population-wide spatiotemporal reserve use. Conserv. Biol. 31, 1173–1182 (2017).
Chen, M. et al. Parentage-based group composition and dispersal pattern studies of the Yangtze Finless Porpoise population in Poyang Lake. Int. J. Mol. Sci. 17, 1268 (2016).
Civade, R. et al. Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS ONE 11, e0157366 (2016).
Evans, N. T. et al. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol. Ecol. Resour. 16, 29–41 (2016).
Hänfling, B. et al. Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Mol. Ecol. 25, 3101–3119 (2016).
Fujii, K. et al. Environmental DNA metabarcoding for fish community analysis in backwater lakes: a comparison of capture methods. PLoS ONE 14, e0210357 (2019).
Andruszkiewicz, E. A. et al. Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding. PLoS ONE 12, e0176343 (2017).
Harper, L. R. et al. Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus). Ecol. Evol. 8, 6330–6341 (2018).
Günther, B., Knebelsberger, T., Neumann, H., Laakmann, S. & Arbizu, P. M. Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes. Sci. Rep. 8, 14822 (2018).
Djurhuus, A. et al. Evaluation of marine zooplankton community structure through environmental DNA metabarcoding. Limnol. Oceanogr. Methods 16, 209–221 (2018).
Ficetola, G. F., Miaud, C., Pompanon, F. & Taberlet, P. Species detection using environmental DNA from water samples. Biol. Lett. 4, 423–425 (2008).
Taberlet, P., Coissac, E., Hajibabaei, M. & Rieseberg, L. H. Environmental DNA. Mol. Ecol. 21, 1789–1793 (2012).
Thomsen, P. F. et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21, 2565–2573 (2012).
Stewart, K. A. Understanding the biotic and abiotic factors on sources of aquatic environmental DNA. Biodivers. Conserv. 28, 983–1001 (2019).
Lopes, C. M. et al. eDNA metabarcoding: a promising method for anuran surveys in highly diverse tropical forests. Mol. Ecol. Resour. 17, 904–914 (2017).
Hobbs, J., Helbing, C. C. & Veldhoen, N. Environmental DNA protocol for freshwater aquatic ecosystems version 2.2. Report for the BC Ministry of Environment, Victoria BC Canada (2017).
Laramie, M.B., Pilliod, D.S., Goldberg, C.S. & Strickler, K.M. Environmental DNA sampling protocol—Filtering water to capture DNA from aquatic organisms.U.S. Geological Survey Techniques and Methods, book 2, chap. A13, 15 p. (2015).
Ma, H. et al. Characterization, optimization, and validation of environmental DNA (eDNA) markers to detect an endangered aquatic mammal. Conserv. Genet. Resour. 8, 561–568 (2016).
Thomsen, P. F. et al. Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE 7, e41732 (2012).
Dougherty, M. M. et al. Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances. J. Appl. Ecol. 53, 722–732 (2016).
Evans, N. T. et al. Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering. Can. J. Fish. Aquat. Sci. 74, 1362–1374 (2017).
Renshaw, M. A., Olds, B. P., Jerde, C. L., Mcveigh, M. M. & Lodge, D. M. The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction. Mol. Ecol. Resour. 15, 168–176 (2015).
Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994).
Hall, T. A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Sym. Ser. 41, 95–98 (1999).
Miya, M. et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R. Soc. Open Sci. 2, 150088 (2015).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Olds, B. P. et al. Estimating species richness using environmental DNA. Ecol. Evol. 6, 4214–4226 (2016).
Deiner, K. et al. Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA. Methods Ecol. Evol. 8, 1888–1898 (2017).
Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahé, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).
Port, J. A. et al. Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA. Mol. Ecol. 25, 527–541 (2016).
Pochon, X., Zaiko, A., Fletcher, L. M., Laroche, O. & Wood, S. A. Wanted dead or alive? Using metabarcoding of environmental DNA and RNA to distinguish living assemblages for biosecurity applications. PLoS ONE 12, e0187636 (2017).
Sato, H., Sogo, Y., Doi, H. & Yamanaka, H. Usefulness and limitations of sample pooling for environmental DNA metabarcoding of freshwater fish communities. Sci. Rep. 7, 14860 (2017).
Yamamoto, S. et al. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci. Rep. 7, 40368 (2017).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
Huson, D. H. et al. MEGAN Community Edition—interactive exploration and analysis of large-scale microbiome sequencing data. PLoS Comput. Biol. 12, e1004957 (2016).
DiBattista, J. D. et al. Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea. Coral Reefs 36, 1245–1252 (2017).
Siegenthaler, A. et al. Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring. Mol. Ecol. Resour. 19, 206–220 (2019).
Racine, J. S. RStudio: a platform-independent IDE for R and Sweave. J. Appl. Econ. 27, 167–172 (2012).
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org (2018).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (eds Gentleman, R., Hornik, K. & Parmigiani, G.) 1–212 (Springer, 2009).
Guevara, M. R., Hartmann, D. & Mendoza, M. diverse: an R package to analyze diversity in complex systems. R J. 8, 60–78 (2016).
Valentini, A. et al. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol. Ecol. 25, 929–942 (2016).
Stoeckle, M. Y., Soboleva, L. & Charlop-Powers, Z. Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary. PLoS ONE 12, e0175186 (2017).
Thomsen, P. F. et al. Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes. PLoS ONE 11, e0165252 (2016).
Huang, L., Wu, Z. & Li, J. Fish fauna, biogeography and conservation of freshwater fish in Poyang Lake Basin China. Environ. Biol. Fish. 96, 1229–1243 (2013).
Gong, J. et al. Interannual variation of the fish community structure in the Tian-e-Zhou Oxbow of Yangtze River. J. Hydroecol. 39, 46–53 (2018) (In Chinese).
Gong, C., Chen, Z. & Cheng, F. The status and management suggestions of the Yangtze finless porpoise prey fish in the Tian-e-Zhou Oxbow of Yangtze River. China Fish. 6, 43–45 (2019) (In Chinese).
Wang, T., Wang, H., Sun, G., Huang, D. & Shen, J. Length–weight and length–length relationships for some Yangtze River fishes in Tian-e-zhou Oxbow China. J. Appl. Ichthyol. 28, 660–662 (2012).
Yang, S., Li, M., Zhu, Q., Wang, M. & Liu, H. Spatial and temporal variations of fish assemblages in Poyanghu Lake. Resour. Environ. Yangtze Basin 24, 54–64 (2015) (In Chinese).
Jin, B. et al. Fish assemblage structure in relation to seasonal environmental variation in sub-lakes of the Poyang Lake floodplain, China. Fish. Manag. Ecol. 26, 131–140 (2019).
Fang, C. et al. Fish resources in Poyang Lake and their utilization. Jiangsu Agric. Sci. 44, 233–243 (2016) (In Chinese).
Zhong, B. et al. Classification of Pelteobagrus fish in Poyang Lake based on mitochondrial COI gene sequence. Mitochondrial DNA A 27, 4635–4637 (2016).
Xiong, G., Zhang, T., Lin, Y., Wang, W. & You, X. Analysis of some characters of fish in the inner Lake of Poyang Lake Wetland. Jiangxi Fish. Sci. Technol. 3, 10–12 (2018) (In Chinese).
Liu, X. et al. Biodiversity pattern of fish assemblages in Poyang Lake Basin: threat and conservation. Ecol. Evol. 9, 11672–11683 (2019).
Liu, M. et al. Species diversity of drifting fish eggs in the Yangtze River using molecular identification. PeerJ 6, e5807 (2018).
Hinlo, R., Furlan, E., Suitor, L. & Gleeson, D. Environmental DNA monitoring and management of invasive fish: comparison of eDNA and fyke netting. Manag. Biol. Invasion 8, 89–100 (2017).
Pilliod, D. S., Goldberg, C. S., Arkle, R. S. & Waits, L. P. Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Can. J. Fish. Aquat. Sci. 70, 1123–1130 (2013).
Lacoursière-Roussel, A., Côté, G., Leclerc, V. & Bernatchez, L. Quantifying relative fish abundance with eDNA: a promising tool for fisheries management. J. Appl. Ecol. 53, 1148–1157 (2016).
Lacoursière-Roussel, A., Rosabal, M. & Bernatchez, L. Estimating fish abundance and biomass from eDNA concentrations: variability among capture methods and environmental conditions. Mol. Ecol. Resour. 16, 1401–1414 (2016).
Ushio, M. et al. Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcod. Metagenom. 2, 1–15 (2018).
Simmons, M., Tucker, A., Chadderton, W. L., Jerde, C. L. & Mahon, A. R. Active and passive environmental DNA surveillance of aquatic invasive species. Can. J. Fish. Aquat. Sci. 73, 76–83 (2016).
Smart, A. S., Tingley, R., Weeks, A. R., vanRooyen, A. R. & McCarthy, M. A. Environmental DNA sampling is more sensitive than a traditional survey technique for detecting an aquatic invader. Ecol. Appl. 25, 1944–1952 (2015).
Eiler, A., Löfgren, A., Hjerne, O., Nordén, S. & Saetre, P. Environmental DNA (eDNA) detects the pool frog (Pelophylax lessonae) at times when traditional monitoring methods are insensitive. Sci. Rep. 8, 5452 (2018).
Lin, Y., Gao, Z. & Zhao, A. Introduction and use of non-native species for aquaculture in China: status, risks and management solutions. Rev. Aquacult. 7, 28–38 (2015).
Xiong, et al. Non-native freshwater fish species in China. Rev. Fish. Biol. Fish. 25, 651–687 (2015).
Pilliod, D. S., Goldberg, C. S., Arkle, R. S. & Waits, L. P. Factors influencing detection of eDNA from a stream-dwelling amphibian. Mol. Ecol. Resour. 14, 109–116 (2014).
Eichmiller, J. J., Best, S. E. & Sorensen, P. W. Effects of temperature and trophic state on degradation of environmental DNA in lake water. Environ. Sci. Technol. 50, 1859–1867 (2016).
Zou, K. et al. eDNA metabarcoding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling. Sci. Total Environ. 702, 134704 (2020).
Fernández, S., Rodríguez-Martínez, S., Martínez, J. L., Garcia-Vazquez, E. & Ardura, A. How can eDNA contribute in riverine macroinvertebrate assessment? A metabarcoding approach in the Nalón River (Asturias, Northern Spain). Environ. DNA 1, 385–401 (2019).
Lacoursière-Roussel, A. et al. eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity. Ecol. Evol. 8, 7763–7777 (2018).
Liu, Y. et al. Application of environmental DNA metabarcoding to spatiotemporal finfish community assessment in a temperate embayment. Front. Mar. Sci. 6, 674 (2019).
Xie, X. et al. Are river protected areas sufficient for fish conservation? Implications from large-scale hydroacoustic surveys in the middle reach of the Yangtze River. BMC Ecol. 19, 42 (2019).
Xinhua. China starts 10-year fishing ban on Yangtze River.China Daily;https://www.chinadaily.com.cn/a/202001/02/WS5e0d4851a310cf3e35581f65.html(2020).
Yang, S., Xu, K., Milliman, J. D. & Wu, C. Decline of Yangtze River water and sediment discharge: Impact from natural and anthropogenic changes. Sci. Rep. 5, 12581 (2015).
Source: Ecology - nature.com
