Evaluation of fish biodiversity in estuaries using environmental DNA metabarcoding
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26. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010; 26: 2460–2461. https://doi.org/10.1093/bioinformatics/btq461 PMID: 20709691 27. Callahan BJ, McMurdie PJ. Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017; 11: 2639–2643. https://doi.org/10.1038/ismej.2017. 119 PMID: 28731476 28. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for big- ger datasets. Mol Biol Evol. 2016; 33: 1870–1874. https://doi.org/10.1093/molbev/msw054 PMID: 27004904 29. Hosoya K. Freshwater fishes of Japan. Tokyo, Japan: Yama-Kei Publishers; 2015. (in Japanese) 30. Nakabo T. Fishes of Japan with pictorial keys to the species. 3rd ed. Kanagawa, Japan: Tokai Univer- sity Press; 2013. (in Japanese) 31. Nakajima J. Loaches of Japan. Tokyo, Japan: Yama-Kei Publishers; 2017. (in Japanese) 32. Andruszkiewicz EA, Starks HA, Chavez FP, Sassoubre LM, Block BA, Boehm AB. Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding. PLOS ONE. 2017; 12: e0176343. https://doi.org/10.1371/journal.pone.0176343 PMID: 28441466 33. Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z. Estimation of fish biomass using environ- mental DNA. PLOS ONE. 2012; 7(4): 1–8. 34. Yamanaka H, Minamoto T, Takahara T, Uchii K, Doi H. Environmental DNA analysis in field research. Jpn J Ecol. 2016; 66: 601–611. (in Japanese) 35. Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM. Environmental conditions
influence eDNA persistence in aquatic system. Environ Sci Technol. 2014; 48: 1819–1827. https://doi. org/10.1021/es404734p PMID: 24422450 36. Nelson J.S. Fishes of the World. 4th ed. Wiley John & Sons: New Jersey xiv; 2006. 37. Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez J-C, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. 2011; 12: 77. 38. Fox J, Weisberg S. Companion to Applied Regression. 2019; 2: 24. Available from https://cran.r- project.org/web/packages/car/car.pdf. 39. Bartoń K. Multi-Model Inference. 2019; 1: 30. Available form https://cran.r-project.org/web/packages/ MuMIn/MuMIn.pdf. 40. Burnham KP, Anderson DR. Model selection and multimodel inference: a practical information-theoretic approach. New York: Springer; 2002. 41. R Core Team. R: A language and environment for statistical computing: R Foundation for Statistical Computing. Vienna, Austria; 2018. https://www.R-project.org/. 42. Barus V, Penaz M, Kohlmann K. Cyprinus carpio (Linnaeus, 1758). In: Banarescu PM, Paepke HJ, edi- tors. The Freshwater Fishes of Europe Vol. 5/ III: Aula-Verlag: Wiebelsheim; 2002. pp 85–179. 43. Shen KN, Jamandre BW, Hsu CC, Tzeng WN, Durand J-D. Plio-Pleistocene sea level and temperature fluctuation in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus. BMC Evol Biol. 2011; 11: 83. https://doi.org/10.1186/1471-2148-11-83 PMID: 21450111 44. Greenfield BK, Jahn A. Mercury in San Francisco Bay forage fish. Environ Pollut. 2010; 158(8): 2716–
2724. https://doi.org/10.1016/j.envpol.2010.04.010 PMID: 20537451 45. Lee KM, Kaneko T, Aida K. Low-salinity tolerance of juvenile fugu Takifugu rubripes. Fish Sci. 2005; 71: 1324–1331. 46. Kimizuka Y, Kobayashi H, Mizuno N. Geographic distributions and karyotypes of Cobitis takatsuensis and Niwaella delicta (Cobitididae). Jpn J Ichthyol. 1982; 29: 305–310. 47. Smith GC, Parrish JD. Estuaries as nurseries for the jacks Caranx ignobilis and Caranx melampygus (Carangidae) in Hawaii. ECSS. 2002; 55: 347–359. 48. Durieux EDH, Meekan MG, Ponton D, Vigliola L. Temperature, selective mortality and early growth in the short-lived clupeid Spatelloides gracilis. J Fish Biol. 2009; 74(4): 921–938. https://doi.org/10.1111/j. 1095-8649.2009.02179.x PMID: 20735608 49. Kasai A, Kurikawa Y, Ueno M, Robert D, Yamashita Y. Salt-wedge intrusion of seawater and its implica- tion for phytoplankton dynamics in the Yura Estuary, Japan. ECSS. 2010; 86(3): 408–414. 50. Kotwicki L, Szymelfenig M, Troch MD, Urban-Malinga B, Weslawski M. Latitudinal biodiversity pattern of meiofauna from sandy littoral beaches. Biodivers Conserv. 2005; 14: 461–474. 51. Deiner K, Altermatt F. Transport distance of invertebrate environmental DNA in a natural river. PLOS ONE. 2014; 9: e88786. https://doi.org/10.1371/journal.pone.0088786 PMID: 24523940 PLOS ONE Biodiversity of five estuaries PLOS ONE | https://doi.org/10.1371/journal.pone.0231127 October 6, 2020 14 / 15