MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental
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REVIEW ARTICLE
MiFish metabarcoding: a high‑throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples Masaki Miya1 · Ryo O. Gotoh1 · Tetsuya Sado1 Received: 16 July 2020 / Accepted: 20 August 2020 © The Author(s) 2020
Abstract We reviewed the current methodology and practices of the DNA metabarcoding approach using a universal PCR primer pair MiFish, which co-amplifies a short fragment of fish DNA (approx. 170 bp from the mitochondrial 12S rRNA gene) across a wide variety of taxa. This method has mostly been applied to biodiversity monitoring using environmental DNA (eDNA) shed from fish and, coupled with next-generation sequencing technologies, has enabled massively parallel sequencing of several hundred eDNA samples simultaneously. Since the publication of its technical outline in 2015, this method has been widely used in various aquatic environments in and around the six continents, and MiFish primers have demonstrably outperformed other competing primers. Here, we outline the technical progress in this method over the last 5 years and highlight some case studies on marine, freshwater, and estuarine fish communities. Additionally, we discuss various applications of MiFish metabarcoding to non-fish organisms, single-species detection systems, quantitative biodiversity monitoring, and bulk DNA samples other than eDNA. By recognizing the MiFish eDNA metabarcoding strengths and limitations, we argue that this method is useful for ecosystem conservation strategies and the sustainable use of fishery resources in “ecosystembased fishery management” through continuous biodiversity monitoring at multiple sites. Keywords eDNA · Fish community · Biodiversity monitoring · Ecosystem-based fishery management · Ecosystem conservation
Introduction In the past three decades biodiversity monitoring has been widely recognized as essential for ecosystem conservation and sustainable use of biological resources (Common and Norton 1994; Lepetz et al. 2009; Goodwin et al. 2018). Indeed, fisheries derive enormous benefits directly or indirectly from aquatic ecosystems, and those benefits are collectively referred to as ecosystem services (Costanza et al. 1997; Rapport et al. 1998; Barbier et al. 2011; Grizzetti et al. 2016). To maximize the benefits of these ecosystem services, fisheries management had previously focused on Published with support by the Japan Society for the Promotion of Science (JSPS) KAKENHI Grant no. JP19HP2002. * Masaki Miya miya@chiba‑muse.or.jp 1
Natural History Museum and Institute, Chiba, 955‑2 Aoba‑cho, Chuo‑ku, Chiba 260‑8682, Japan
maximizing the catch of a single target species, often ignoring habitat, predators, and prey of the target species and other ecosystem components and interactions (Pikitch et al. 2014; Darling et al. 2017; Hansen et al. 2018). However, worldwide fisheries management is currently undergoing a paradigm shift from such a single-species approach to an ecosystem approach (Koslow 2009; Fogarty 2014; Brinson and Wallmo 2015
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