DNA barcoding of deep-sea fishes from the northwestern Pacific Ocean: a resource for identifying hidden genetic diversity in deep-sea fishes

Abstract

COI-based DNA barcoding could be an efficient tool for species identification of deep-sea fishes and could lead to the discovery of cryptic species diversity. However, the availability of reference sequences of deep-sea fishes for DNA barcoding is limited, especially for fishes in the northwestern Pacific Ocean. In this study, we performed DNA barcoding of mesopelagic and demersal fish species on the continental shelf and upper slope, collected from deepwater fisheries around Japan and southern Taiwan, to accumulate the reference sequences of deep-sea fishes in the northwestern Pacific Ocean. Overall, we obtained the COI sequences of 123 species from 50 families. Genetic diversity within each species for which COI sequences were obtained from multiple specimens was examined, and we found that Chimaera phantasma (Chimaeridae), Harpadon microchir (Synodontidae), and Pyramodon ventralis (Carapidae) showed high intraspecific genetic differentiation of more than 2% Kimura two-parameter distance. Moreover, for 19 widespread deep-sea fishes, a comparison between our data and previously acquired COI sequence data suggested a high level (more than 2% Kimura two-parameter distance) of genetic differentiation between the northwestern Pacific Ocean and other oceans in each widespread species. These results suggest that many cryptic species or regional populations have not yet been discovered in deep-sea fishes. Alternatively, genetic differentiation was not found worldwide for six species. These results indicate that many taxonomic and biogeographical issues remain for deep-sea fishes, and our DNA barcoding data would provide better understanding of these issues.

Geographic Range Expansion and Taxonomic Notes of the Shortfin Neoscopelid Neoscopelus cf. microchir (Myctophiformes: Neoscopelidae) in the North-Eastern Atlantic

“…Gaither et al [23] noted that sequences of N. microchir in BOLD fall into three BINs, indicating divergent and overlapping lineages. Teramura et al [24] found that N. microchir was divided into four lineages, and two lineages are sympatrically distributed in the northwestern Pacific Ocean and South Africa.…”

Population Genetic Structure of Marine Fishes

“…High intraspecific genetic differentiation showed based on COI sequences of samples of Chimaera phantasma (Chimaeridae), Harpadon microchir (Synodontidae), and Pyramodon ventralis (Carapidae). Moreover, for 19 widespread deep-sea fish species, suggested a high level of genetic differentiation for the northwestern Pacific Ocean, that suggest many cryptic species or regional populations not described yet, in deep-sea fishes [40].…”

Mystery egg revealing secrets from the deep

“…Nowhere is this more true than in the deep-sea, where new records are continually being made (Bañ on et al, 2020;Mincarone et al, 2022Mincarone et al, , 2014. Not only is a huge amount of the deep sea underexplored, with visual evidence of organisms sparce, but when samples are retrieved from the deep sea they can be prone to taxonomic confusion and have poor diagnostic features (Teramura et al, 2021). Or in the case of soft bodied fish, the difference in pressure can cause them to become disfigured, as the famous blob fish can attest, making morphological identification difficult.…”