References
Amann, R., & Fuchs, B. M. (2008). Single-cell identification in microbial communities by improved fluorescence in situhybridization techniques. Nature Reviews Microbiology, 6(5), 339-348.
Barnes, M. A. & Turner, C. R. (2016). The ecology of environmental DNA and implications for conservation genetics. Conservation Genetics, 17(1), 1-17.
Bylemans, J., Furlan, E. M., Gleeson, D. M., Hardy, C. M., & Duncan, R. P. (2018). Does size matter? An experimental evaluation of the relative abundance and decay rates of aquatic environmental DNA. Environmental Science & Technology, 52(11), 6408-6416.
Carraro, L., Hartikainen, H., Jokela, J., Bertuzzo, E., & Rinaldo, A. (2018). Estimating species distribution and abundance in river networks using environmental DNA. Proceedings of the National Academy of Sciences, 115(46), 11724-11729.
Del Re, A. C. & Hoyt, W. T. (2018). MAc: Meta-Analysis with Correlations. R package version 1.1.1. https://CRAN.R-project.org/package=Mac
Eichmiller, J. J., Miller, L. M., & Sorensen, P. W. (2016). Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish. Molecular Ecology Resources, 16(1), 56-68.
Ellison, S. L., English, C. A., Burns, M. J., & Keer, J. T. (2006). Routes to improving the reliability of low level DNA analysis using real-time PCR. BMC Biotechnology, 6(1), 1-11.
Ficetola, G. F., Miaud, C., Pompanon, F., & Taberlet, P. (2008). Species detection using environmental DNA from water samples. Biology Letters, 4(4), 423-425.
Fukaya, K., Murakami, H., Yoon, S., Minami, K., Osada, Y., Yamamoto, S., … & Kondoh, M. (2021). Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling. Molecular Ecology, 30(13), 3057-3067.
Furlan, E. M., Gleeson, D., Hardy, C. M., & Duncan, R. P. (2016). A framework for estimating the sensitivity of eDNA surveys. Molecular Ecology Resources, 16(3), 641-654.
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(13), 3101-3119.
Hansen, B. K., Bekkevold, D., Clausen, L. W., & Nielsen, E. E. (2018). The sceptical optimist: challenges and perspectives for the application of environmental DNA in marine fisheries. Fish and Fisheries, 19(5), 751-768.
Harper, L. R., Buxton, A. S., Rees, H. C., Bruce, K., Brys, R., Halfmaerten, D., … & Hänfling, B. (2019). Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia, 826(1), 25-41.
Harrison, J. B., Sunday, J. M., & Rogers, S. M. (2019). Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proceedings of the Royal Society B, 286(1915), 20191409.
Hirohara, T., Tsuri, K., Miyagawa, K., Paine, R. T., & Yamanaka, H. (2021). The Application of PMA (Propidium Monoazide) to Different Target Sequence Lengths of Zebrafish eDNA: A New Approach Aimed Toward Improving Environmental DNA Ecology and Biological Surveillance. Frontiers in Ecology and Evolution, 9, 277.
Jo, T., Arimoto, M., Murakami, H., Masuda, R., & Minamoto, T. (2019). Particle size distribution of environmental DNA from the nuclei of marine fish. Environmental Science & Technology, 53(16), 9947-9956.
Jo, T., Fukuoka, A., Uchida, K., Ushimaru, A., & Minamoto, T. (2020a). Multiplex real-time PCR enables the simultaneous detection of environmental DNA from freshwater fishes: a case study of three exotic and three threatened native fishes in Japan. Biological Invasions, 22(2), 455-471.
Jo, T., & Minamoto, T. (2021). Complex interactions between environmental DNA (eDNA) state and water chemistries on eDNA persistence suggested by meta‐analyses. Molecular Ecology Resources, 21(5), 1490-1503.
Jo, T., Murakami, H., Masuda, R., & Minamoto, T. (2020b). Selective collection of long fragments of environmental DNA using larger pore size filter. Science of the Total Environment, 735, 139462.
Jo, T., Murakami, H., Masuda, R., Sakata, M. K., Yamamoto, S., & Minamoto, T. (2017). Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA. Molecular Ecology Resources, 17(6), e25-e33.
Jo, T., Sakata, M. K., Murakami, H., Masuda, R., & Minamoto, T. (2021b). Universal performance of benzalkonium chloride for the preservation of environmental DNA in seawater samples. Limnology and Oceanography: Methods, 19(11), 758-768.
Jo, T., Takao, K., & Minamoto, T. (2021a). Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes. Environmental DNA, in press. https://doi.org/10.1002/edn3.253
Kogure, T., Karasawa, S., Araki, T., Saito, K., Kinjo, M., & Miyawaki, A. (2006). A fluorescent variant of a protein from the stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy. Nature Biotechnology, 24(5), 577-581.
Kumar, G., Farrell, E., Reaume, A. M., Eble, J. A., & Gaither, M. R. (2021). One size does not fit all: Tuning eDNA protocols for high‐and low‐turbidity water sampling. Environmental DNA, in press. https://doi.org/10.1002/edn3.235
Kuznetsova, A., Brockhoff, P. B., & Christensen, R. H. B. (2017). lmerTest Package: Tests in Linear Mixed Effects Models. Journal of Statistical Software, 82(13), 1-26.
Levi, T., Allen, J. M., Bell, D., Joyce, J., Russell, J. R., Tallmon, D. A., … & Yu, D. W. (2019). Environmental DNA for the enumeration and management of Pacific salmon. Molecular Ecology Resources, 19(3), 597-608.
Levy-Booth, D. J., Campbell, R. G., Gulden, R. H., Hart, M. M., Powell, J. R., Klironomos, J. N., … & Dunfield, K. E. (2007). Cycling of extracellular DNA in the soil environment. Soil Biology and Biochemistry, 39(12), 2977-2991.
Lopes, C. M., Baêta, D., Valentini, A., Lyra, M. L., Sabbag, A. F., Gasparini, J. L., … & Zamudio, K. R. (2021). Lost and found: Frogs in a biodiversity hotspot rediscovered with environmental DNA. Molecular Ecology, 30(13), 3289-3298.
Minamoto, T., Hayami, K., Sakata, M. K., & Imamura, A. (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(1), 237-242.
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(7), 150088.
Pawlowski, J., Apothéloz‐Perret‐Gentil, L., & Altermatt, F. (2020). Environmental DNA: What’s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring. Molecular Ecology, 29(22), 4258-4264.
Pilliod, D. S., Goldberg, C. S., Arkle, R. S., & Waits, L. P. (2013). Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Canadian Journal of Fisheries and Aquatic Sciences, 70(8), 1123-1130.
Ponce, J. J., Arismendi, I., & Thomas, A. (2021). Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum ) in freshwaters. PeerJ, 9, e11835.
R Core Team. (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
Rodriguez‐Ezpeleta, N., Morissette, O., Bean, C. W., Manu, S., Banerjee, P., Lacoursière‐Roussel, A., … & Deiner, K. (2021). Trade‐offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What’s behind the term?” by Pawlowski et al., (2020). Molecular Ecology, 30(19), 4601-4605.
Roussel, J. M., Paillisson, J. M., Treguier, A., & Petit, E. (2015). The downside of eDNA as a survey tool in water bodies. Journal of Applied Ecology, 52(4), 823-826.
Shogren, A. J., Tank, J. L., Andruszkiewicz, E. A., Olds, B., Jerde, C., & Bolster, D. (2016). Modelling the transport of environmental DNA through a porous substrate using continuous flow-through column experiments. Journal of the Royal Society Interface, 13(119), 20160290.
Takahara, T., Minamoto, T., Yamanaka, H., Doi, H., & Kawabata, Z. (2012). Estimation of fish biomass using environmental DNA. PLoS ONE, 7(4), e35868.
Takasaki, K., Aihara, H., Imanaka, T., Matsudaira, T., Tsukahara, K., Usui, A., … & Doi, H. (2021). Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding. PLos ONE, 16(5), e0250162.
Thomsen, P. F., Kielgast, J., Iversen, L. L., Møller, P. R., Rasmussen, M., & Willerslev, E. (2012). Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE, 7(8), e41732.
Torti, A., Lever, M. A., & Jørgensen, B. B. (2015). Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Marine Genomics, 24, 185-196.
Tsuri, K., Ikeda, S., Hirohara, T., Shimada, Y., Minamoto, T., & Yamanaka, H. (2021). Messenger RNA typing of environmental RNA (eRNA): A case study on zebrafish tank water with perspectives for the future development of eRNA analysis on aquatic vertebrates. Environmental DNA, 3(1), 14-21.
Turner, C. R., Barnes, M. A., Xu, C. C., Jones, S. E., Jerde, C. L., & Lodge, D. M. (2014). Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods in Ecology and Evolution, 5(7), 676-684.
Ushio, M., Murata, K., Sado, T., Nishiumi, I., Takeshita, M., Iwasaki, W., & Miya, M. (2018). Demonstration of the potential of environmental DNA as a tool for the detection of avian species. Scientific reports, 8, 4493.
Uthicke, S., Lamare, M., & Doyle, J. R. (2018). eDNA detection of corallivorous seastar (Acanthaster cf. solaris ) outbreaks on the Great Barrier Reef using digital droplet PCR. Coral Reefs, 37(4), 1229-1239.
Valentin, R. E., Fonseca, D. M., Gable, S., Kyle, K. E., Hamilton, G. C., Nielsen, A. L., & Lockwood, J. L. (2020). Moving eDNA surveys onto land: Strategies for active eDNA aggregation to detect invasive forest insects. Molecular Ecology Resources, 20(3), 746-755.
Wu, Q., Kawano, K., Uehara, Y., Okuda, N., Hongo, M., Tsuji, S., … & Minamoto, T. (2018). Environmental DNA reveals nonmigratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters. Freshwater Science, 37(2), 307-314.
Yamanaka, H. & Minamoto, T. (2016). The use of environmental DNA of fishes as an efficient method of determining habitat connectivity. Ecological Indicators, 62, 147-153.
Yamanaka, H., Minamoto, T., Matsuura, J., Sakurai, S., Tsuji, S., Motozawa, H., … & Kondo, A. (2017). A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant. Limnology, 18(2), 233-241.
Yates, M. C., Cristescu, M. E., & Derry, A. M. (2021). Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro‐organism abundance. Molecular Ecology, 30(24), 6531-6550.
Yates, M. C., Fraser, D. J., & Derry, A. M. (2019). Meta‐analysis supports further refinement of eDNA for monitoring aquatic species‐specific abundance in nature. Environmental DNA, 1(1), 5-13.
Zhao, B., van Bodegom, P. M., & Trimbos, K. (2021). The particle size distribution of environmental DNA varies with species and degradation. Science of the Total Environment, 797, 149175.