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

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.

Assessing mesopelagic fish diversity and diel vertical migration with environmental DNA

“…variation and expand the geographic representation for this marker on GenBank. COI barcodes provided validation for our species identification and will also add to knowledge on intraspecific variation and geographic differentiation, which can facilitate the discovery of cryptic species (Kenchington et al, 2017;Teramura et al, 2022). Importantly, because we barcoded both the COI and 12S markers from the same specimens, we were able to detect species identification discrepancies on GenBank.…”

“…DNA sequences were blasted against the GenBank database for comparison with publicly available sequences. Matches with 98% identity or greater for at least 90% of the read length were considered species-level identifications (e.g., Kenchington et al, 2017;Teramura et al, 2022). Barcode identifications were compared with morphological identifications.…”

Population Genetic Structure of Marine Fishes

“…DNA barcoding using mitochondrial DNA sequences may offer an effective approach to identifying cryptic species and characterizing genetic diversities of deep-sea fish species [39]. DNA barcoding of mesopelagic and demersal fish collected around Japan and southern Taiwan.…”

Unveiling taxonomic diversity in the deep‐sea fish genus Notacanthus (Notacanthiformes: Notacanthidae) with description of Notacanthus arrontei n. sp.

“…The additive effects of high habitat heterogeneity, on both small and large scales, are known to contribute to a highly diverse deep‐sea fauna (Paulus, 2021). Indeed, current systematics has shown that many meso‐ and bathypelagic fishes with a worldwide distribution have highly divided population structures or include several cryptic species (de Carlos et al, 2020; Teramura et al, 2022).…”