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Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans

The Decapoda is one of the largest orders within the class Malacostraca, comprising approximately 14,000 extant species and including many commercially important species. For biodiversity monitoring in a non-invasive manner, a new set of PCR primers was developed for metabarcoding environmental DNA (eDNA) from decapod crustaceans. The new primers (herein named “MiDeca”) were...

Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model

Environmental DNA (eDNA) metabarcoding is a recently developed method to assess biodiversity based on a high-throughput parallel DNA sequencing applied to DNA present in the ecosystem. Although eDNA metabarcoding enables a rapid assessment of biodiversity, it is prone to species detection errors that may occur at sequential steps in field sampling, laboratory experiments, and...

Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic gene orders

illustrations. Author Contributions Conceptualization: Jan Y. Poulsen, Michael J. Miller, Masaki Miya. Data curation: Jan Y. Poulsen, Michael J. Miller. Formal analysis: Jan Y. Poulsen. Funding acquisition ... : Masaki Miya. Investigation: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado, Reinhold Hanel, Katsumi Tsukamoto, Masaki Miya. Methodology: Jan Y. Poulsen, Michael J. Miller, Tetsuya Sado. Project

Demonstration of the potential of environmental DNA as a tool for the detection of avian species

Research journals • PubMed • Google Scholar Search for Wataru Iwasaki in:Nature Research journals • PubMed • Google Scholar Search for Masaki Miya in:Nature Research journals • PubMed • Google Scholar ... or Masaki Miya. Electronic supplementary material Supplementary information Rights and permissions Open Access This article is licensed under a Creative Commons Attribution 4.0 International

Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing

Masaki Miya 4 Sho Sakurai 3 Hiroki Yamanaka 0 Toshifumi Minamoto 7 Michio Kondoh 0 Corresponding author: Masayuki Ushio (ong @gmail.com) 0 Department of Environmental Solution Technology, Faculty of

Structure and variation of the mitochondrial genome of fishes

Background The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study...

Molecular systematics of the anchovy genus Encrasicholina in the Northwest Pacific

Sado. Formal analysis: SeÂbastien LavoueÂ, Joris A. M. Bertrand, Tetsuya Sado. Funding acquisition: SeÂbastien LavoueÂ, Masaki Miya. Investigation: SeÂbastien LavoueÂ, Joris A. M. Bertrand ... . Methodology: Masaki Miya. Resources: SeÂbastien LavoueÂ. Supervision: SeÂbastien LavoueÂ. Writing ± original draft: SeÂbastien LavoueÂ, Joris A. M. Bertrand. Writing ± review & editing: SeÂbastien LavoueÂ

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

journals • PubMed • Google ScholarSearch for Masaki Miya in:Nature Research journals • PubMed • Google Scholar Contributions S.Y. conducted experiments and data analyses of community dataset, and wrote the

Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes)

The family Opisthoproctidae (barreleyes) constitutes one of the most peculiar looking and unknown deep-sea fish groups in terms of taxonomy and specialized adaptations. All the species in the family are united by the possession of tubular eyes, with one distinct lineage exhibiting also drastic shortening of the body. Two new species of the mesopelagic opisthoproctid mirrorbelly...

The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect

Some of the new, exciting molecular work is being done in the laboratories of Masaki Miya in Chiba, Japan; and Mutsumi Nishidain Tokyo, Japan. These workers and their colleagues as well as many others

Evolution of bidirectional sex change and gonochorism in fishes of the gobiid genera Trimma, Priolepis, and Trimmatom

Size-advantage and low-density models have been used to explain how mating systems favor hermaphroditism or gonochorism. However, these models do not indicate historical transitions in sexuality. Here, we investigate the evolution of bidirectional sex change and gonochorism by phylogenetic analysis using the mitochondrial gene of the gobiids Trimma (31 species), Priolepis (eight...

Composition of Glycosaminoglycans in Elasmobranchs including Several Deep-Sea Sharks: Identification of Chondroitin/Dermatan Sulfate from the Dried Fins of Isurus oxyrinchus and Prionace glauca

Shark fin, used as a food, is a rich source of glycosaminoglyans (GAGs), acidic polysaccharides having important biological activities, suggesting their nutraceutical and pharmaceutical application. A comprehensive survey of GAGs derived from the fin was performed on 11 elasmobranchs, including several deep sea sharks. Chondroitin sulfate (CS) and hyaluronic acid (HA) were found...

Mitogenomic Evidence for an Indo-West Pacific Origin of the Clupeoidei (Teleostei: Clupeiformes)

The clupeoid fishes are distributed worldwide, with marine, freshwater and euryhaline species living in either tropical or temperate environments. Regional endemism is important at the species and genus levels, and the highest species diversity is found in the tropical marine Indo-West Pacific region. The clupeoid distribution follows two general pattern of species richness, the...

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

Background Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary...

A ‘living fossil’ eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau

G. David Johnson Hitoshi Ida Jiro Sakaue Tetsuya Sado Takashi Asahida Masaki Miya () Articles on similar topics can be found in the following collections Receive free email alerts when new articles

Comparable Ages for the Independent Origins of Electrogenesis in African and South American Weakly Electric Fishes

One of the most remarkable examples of convergent evolution among vertebrates is illustrated by the independent origins of an active electric sense in South American and African weakly electric fishes, the Gymnotiformes and Mormyroidea, respectively. These groups independently evolved similar complex systems for object localization and communication via the generation and...

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei)

BMC Evolutionary Biology Jan Y Poulsen Ingvar Byrkjedal Endre Willassen David Rees Hirohiko Takeshima Takashi P Satoh Gento Shinohara Mutsumi Nishida Masaki Miya Poulsen et al. - Mitogenomic

MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish...

Correction: Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan

Takahashi Hideki Sawada Hiroaki Murakami Satsuki Tsuji Hiroki Hashizume Shou Kubonaga Tomoya Horiuchi Masamichi Hongo Jo Nishida Yuta Okugawa Ayaka Fujiwara Miho Fukuda Shunsuke Hidaka Keita W. Suzuki Masaki ... Miya Hitoshi Araki Hiroki Yamanaka Atsushi Maruyama Kazushi Miyashita Reiji Masuda Toshifumi Minamoto Michio Kondoh The images for Figs 2 and 3 are incorrectly switched. The image that appears as Fig 2

Multiple Invasions into Freshwater by Pufferfishes (Teleostei: Tetraodontidae): A Mitogenomic Perspective

Pufferfishes of the Family Tetraodontidae are the most speciose group in the Order Tetraodontiformes and mainly inhabit coastal waters along continents. Although no members of other tetraodontiform families have fully discarded their marine lives, approximately 30 tetraodontid species spend their entire lives in freshwaters in disjunct tropical regions of South America, Central...