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Marine Ecology Progress Series

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MEPS 701:83-98 (2022)  -  DOI:

Assessing the effectiveness of DNA barcoding for exploring hidden genetic diversity in deep-sea fishes

Akinori Teramura1,*, Keita Koeda2,3,6, Ayumi Matsuo4, Mitsuhiko P. Sato4, Hiroshi Senou5, Hsuan-Ching Ho3, Yoshihisa Suyama4, Kiyoshi Kikuchi1, Shotaro Hirase1

1Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bentenjima, Nishi, Maisaka, Hamamatsu, Shizuoka 431-0214, Japan
2The University Museum, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
3National Museum of Marine Biology and Aquarium, Checheng, Pingtung, 94450 Taiwan, ROC
4Kawatabi Field Science Center, Graduate School of Agricultural Science, Tohoku University, Yomogida, Naruko-onsen, Osaki, Miyagi 989-6711, Japan
5Kanagawa Prefectural Museum of Natural History, Iryuda, Odawara, Kanagawa 250-0031, Japan
6Present address: Faculty of Science, University of the Ryukyus, Senbaru, Nishihara, Okinawa 903-0213, Japan
*Corresponding author:

ABSTRACT: The numbers of deep-sea fish species and their genetic diversities are poorly understood because of taxonomic confusion and the lack of robust diagnostic features. However, DNA barcoding using mitochondrial DNA sequences may offer an effective approach to identifying cryptic species and characterizing their genetic diversities. To validate the genetic differentiation identified by DNA mitochondrial barcoding, it is necessary to show that these reflect variations present in nuclear genomic markers. Here, we performed DNA barcoding using cytochrome c oxidase subunit I (COI) sequences and also carried out multiplexed intersimple sequence repeat genotyping by sequencing (MIG-seq) for mesopelagic and demersal fish species from the continental shelf and upper slope of the northwestern Pacific Ocean. We obtained the COI sequences of 115 species from 48 families; the species were identified using the Barcode of Life Data System. Phylogenetic analyses using COI sequences showed high levels of intraspecific genetic differentiation (Kimura 2-parameter distances >2%) in 20 of 115 species, suggesting many cryptic species or intraspecific genetic differentiation previously unknown in these species. We performed phylogenetic and population genetic analyses using multiple single-nucleotide polymorphism loci obtained by MIG-seq of 3 species that showed high levels of intraspecific genetic differentiation in COI sequences. The nuclear markers confirmed the genetic differentiation in all 3 species identified by the COI sequences. The high concordance between these different genetic markers indicates the effectiveness of DNA barcoding for identifying cryptic deep-sea species and characterizing genetic differentiation in these species.

KEY WORDS: Cryptic species · Biogeography · Distribution barrier · Species diversity · COI · MIG-seq

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Cite this article as: Teramura A, Koeda K, Matsuo A, Sato MP and others (2022) Assessing the effectiveness of DNA barcoding for exploring hidden genetic diversity in deep-sea fishes. Mar Ecol Prog Ser 701:83-98.

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