Barcoding Atlantic Canada’s mesopelagic and upper bathypelagic marine fishes

Abstract

DNA barcode sequences were developed from 557 mesopelagic and upper bathypelagic teleost specimens collected in waters off Atlantic Canada. Confident morphological identifications were available for 366 specimens, of 118 species and 93 genera, which yielded 328 haplotypes. Five of the species were novel to the Barcode of Life Database (BOLD). Most of the 118 species conformed to expectations of monophyly and the presence of a “barcode gap”, though some known weaknesses in existing taxonomy were confirmed and a deficiency in published keys was revealed. Of the specimens for which no firm morphological identification was available, 156 were successfully identified to species, and a further 11 to genus, using their barcode sequences and a combination of distance- and character-based methods. The remaining 24 specimens were from species for which no reference barcode is yet available or else ones confused by apparent misidentification of publicly available sequences in BOLD. Addition of the new sequences to those previously in BOLD contributed support to recent taxonomic revisions of Chiasmodon and Poromitra, while it also revealed 18 cases of potential cryptic speciation. Most of the latter appear to result from genetic divergence among populations in different ocean basins, while the general lack of strong horizontal environmental gradients within the deep sea has allowed morphology to be conserved. Other examples of divergence appear to distinguish individuals living under the sub-tropical gyre of the North Atlantic from those under that ocean’s sub-polar gyre. In contrast, the available sequences for two myctophid species, Benthosema glaciale and Notoscopelus elongatus, showed genetic structuring on finer geographic scales. The observed structure was not consistent with recent suggestions that “resident” populations of myctophids can maintain allopatry despite the mixing of ocean waters. Rather, it indicates that the very rapid speciation characteristic of the Myctophidae is both on-going and detectable using barcodes.

Deep‐sea anglerfishes (Lophiiformes: Ceratioidei) from the western North Atlantic: Testing the efficacy ofDNAbarcodes

“…The available barcode sequences form two distinct clusters in the NJ tree, each containing exclusively sequences from the Atlantic or Pacific Oceans, respectively, as previously found by Kenchington et al. () using a very similar set of sequences. Apparent cases of cryptic species can arise from specimens of known species being misidentified.…”

“…TA B L E 3 Summary of p-distance distributions among Ceratioidei taxa comparing the original and the proposed assignments of the barcodes The available barcode sequences form two distinct clusters in the NJ tree, each containing exclusively sequences from the Atlantic or Pacific Oceans, respectively, as previously found byKenchington et al (2017) using a very similar set of sequences.Apparent cases of cryptic species can arise from specimens of known species being misidentified. That possibility cannot be rejected for C. couesii but the nominal species belongs to a monotypic genus and that the genetic distances observed between the two clusters fit within the observed distribution of intrageneric genetic distances seen in the Ceratioidei.…”

“…Among them, more than 200 are assigned to lophiiform voucher specimens. Recent faunal studies in waters off Atlantic Canada (Kenchington, Baillie, Kenchington, & Bentzen, ) and the Pacific coast of Central America (Robertson et al., ) have notably increased the number of barcodes of ceratioid species. These barcode sequences have been employed in the identification of Oneirodes species from the Pacific Ocean (Steinke, Zemlak, Boutillier, & Hebert, ) and Melanocetus johnsonii Günther, 1864, from Antarctic waters (Orlov, Orlova, Volkov, & Pelenev, ).…”

“…Recent faunal studies in waters off Atlantic Canada (Kenchington, Baillie, Kenchington, & Bentzen, 2017) and the Pacific coast of Central America (Robertson et al, 2018) have notably increased the number of barcodes of ceratioid species. These barcode sequences have been employed in the identification of Oneirodes species from the Pacific Ocean (Steinke, Zemlak, Boutillier, & Hebert, 2009)…”

Morphology and evolution of bioluminescent organs in the glowbellies (Percomorpha: Acropomatidae) with comments on the taxonomy and phylogeny of Acropomatiformes

“…The molecular terminals analyzed in this study and GenBank accession numbers corresponding to the gene fragments sequenced are listed in Supporting Information Table 1. For these analyses, the 94 novel DNA sequences were combined with 436 previously published DNA sequences from the following sources: (Alfaro et al, ; Betancur‐R, Broughton et al, ; Betancur‐R, Li, Munroe, Ballesteros, & Ortí, ; Bossu, Beaulieu, Ceas, & Near, ; Cawthorn, Steinman, & Witthuhn, ; Chang et al, ; Chen, Ruiz‐Carus, & Ortí, ; Davis et al, ; Dunlap et al, ; Durand et al, ; Holcroft & Wiley, ; Kenchington, Baillie, Kenchington, & Bentzen, ; Kimmerling et al, ; Li et al, ; Li, Ortí, & Zhao, ; Near et al, , , , ; Near & Keck, ; Rabosky et al, ; Sanciangco et al, ; Satoh, ; Satoh, Miya, Mabuchi, & Nishida, ; Smith et al, ; Smith, Smith, & Wheeler, ; Smith & Craig, ;Smith & Wheeler, , ; Sparks & Smith, ; Thacker et al, ; Tsunashima et al, ; Wainwright et al, ; Yagishita et al, ; Yamanoue et al, ; and 21 unpublished studies). The matrix was 70.4% complete at the amplicon level.…”