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An annotated and photographically illustrated checklist with DNA barcodes of the species of bony fishes collected during a month-long research cruise of the Spanish Research vessel B/O Miguel Oliver is presented. The vessel made trawls on the continental shelf of the Pacific coast of Central America, in November-December 2010, at depths of 108–1625...
Citations
... This record expands considerably the previously known distribution of the species and helps to improve our knowledge about the biology of the species, genus, and family in the region. On the other hand, aligned with several relatively recent works (e.g., Angulo 2014, Angulo et al. 2015, Robertson et al. 2017, Cruz-Acevedo et al. 2018, Sánchez-Jiménez et al. 2018, this paper seeks to increase our knowledge about the ichthyological diversity associated with deep environments in the Eastern Pacific Ocean, particularly in the Tropical region. Contributions like this represent a first step to understand the current and historical distribution, ecology, and evolution of such taxa and their respective environments, as well as the impact that various human activities may have on species and ecosystems. ...
... 2014; Angulo et al. 2015;Robertson et al. 2017;Cruz-Acevedo et al. 2018;Sánchez-Jiménez et al. 2018). Hand in hand with exploration and increased knowledge are anthropogenic threats to this diversity, with shrimp trawling and deep-sea mining perhaps the biggest threats. ...
n 1973, a specimen of the deep‑sea anglerfish Ceratias uranoscopus Murray, 1877 was collected at a depth of 1000 m off the Pacific coast of Panama. This specimen represents (1) the first verified occurrence record of this species and genus in the Tropical Eastern Pacific Ocean and (2) an extension of about 7000 km east on this species’ previously known distribution. In this contribution, we provide and discuss unpublished and comparative morphometric, meristic, and occurrence data, corroborating the identity of the specimen and species and validating the new geographic range.
... Recent studies have highlighted the existence of cryptic diversity within N. chemnitzii with the possible existence of unknown species (Poulsen et al., 2018;Robertson et al., 2017) Matsubara, 1938, appeared to be no more than a geographic variation of N. cheminitzii and were consequently considered synonyms of the latter (McDowell, 1973). ...
Notacanthid fishes constitute a common part of benthopelagic deep‐sea fish communities on seamounts and continental slopes around the world. However, their highly conserved morphology and the usual lack of information on deep‐water organisms make it difficult to appropriately address their biodiversity. A multidisciplinary approach combining morphological data with a DNA‐based species delimitation analyses was used to explore the taxonomy of Notacanthus species. For this purpose, morphological and molecular data were obtained from 43 individuals, and the resulting information was combined with the available data. The results showed the occurrence of Notacanthus arrontei n. sp. from the Iberian Peninsula and highlighted several taxonomic conundrums regarding the Notacanthus genus. For instance, no significant differences were found between Notacanthus indicus and the recently described Notacanthus laccadiviensis, questioning its taxonomic status. Similarly, the result of the species delimitation molecular analysis coincided with previous DNA barcoding studies supporting the snubnosed spiny eel Notacanthus chemnitzii as a species complex that requires further research. Moreover, two unidentified records from the Indian Ocean were confirmed to belong to an unknown species pending formal description, and barcoding data show for the first time the occurrence of the shortfin spiny eel Notacanthus bonaparte in the Australia‐New Zealand area. This research confirms the existence of important gaps in the knowledge of notacanthid fishes and represents a step forward toward a better understanding of their biological diversity.
... For coastal and demersal species, studies are limited to the molecular identification of species of the genus Cynoscion at Panama Bay [56] as well in some important commercial species such as corvinas (Cynoscion albus) and snappers (Lutjanus peru and Lutjanus guttatus) from Pacific Costa Rica [57].; demersal shark species such as Mustelus lunulatus and Mustelus henlei [58] and deep-sea water species [59]. Therefore, values of genetic diversity for commercial species in the Eastern Tropical Pacific are reduced and for Panama Pacific are completely absent. ...
Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of 34 species from 14 families (Ariidae, Caranjidae, Centropomidae, Gerreidae, Haemulidae, Lobotidae, Lutjanidae, Malacanthidae, Mugilidae, Scianidae, Scombridae, Serranidae, Sphyraenidae, Stromateidae) were identified at the species level from 164 sequences. Additionally, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with five or more individual sequences, genetic diversity and genetic connectivity parameters such as total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). The high level of connectivity observed between the Gulf of Chiriqui and the Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. The demographic history of the most common species was examined using Tajima’s D values, suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual-labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas.
... The DNA barcoding technique involving the examination of about 650 nucleotides of the mitochondrial gene cytochrome c oxidase I (COI) is a molecular taxonomy tool that has been successfully integrated with traditional morphological analysis in the systematic studies of fishes since first proposed (Hebert et al. 2003). These techniques have been successfully employed in the molecular identification of anglerfishes, either specifically, or broader studies of the suborder (Orlov et al. 2015;Poulsen 2019;Bañón et al. 2019) or regional studies of deep-sea fishes (Steinke et al. 2009;Kenchington et al. 2017;Ross-Robertson et al. 2017). ...
... The COI sequence of O. carlsbergi grouped with the only public available sequence assigned to O. rosenblatti from the Costa Rica waters, in the eastern Pacific (Ross-Robertson et al. 2017). However, a BOLD search returns highly similar sequences from the Gulf of Mexico and the US waters, assigned only to the genus or family levels, suggesting an unreported occurrence of O. carlsbergi in these areas. ...
Fifteen specimens representing nine species of ceratioid fishes (Lophiiformes: Ceratioidei) were caught in Flemish Cap and Grand Banks of the western North Atlantic: Ceratias holboelli Krøyer, 1845 (Ceratiidae), Melanocetus murrayi Günther, 1887
(Melanocetidae), Leptacanthichthys gracilispinis (Regan, 1925), Dolopichthys karsteni Leipertz & Pietsch, 1987, Dolopichthys pullatus Regan & Trewavas, 1932, Oneirodes eschrichtii Lütken, 1871, Oneirodes macrosteus Pietsch 1974 and Oneirodes
carlsbergi (Regan & Trewavas, 1932) (Oneirodidae), and Linophryne cf. brevibarbata Beebe, 1932 (Linophrynidae). Identification was carried out by means of integrative taxonomy, combining the examination of morphological and molecular characters (DNA barcoding). The analysis showed two morphological types of D. pullatus distinguishable by the shape and morphology of the esca and the number and size of the teeth. The occurrence of Oneirodes carlsbergi represents the northernmost record in the western Atlantic. As results of the molecular analysis, 15 new ceratioid sequences were added to molecular repositories, two of them, O. carlsbergi and Linophryne cf. brevibarbata for the first time. The comparison of some nucleotide sequences shows new relationships between the genera Bertella and Dolopichthys, and also makes it possible to correct some of the erroneous assignments made in the databases. The combination of classical and molecular taxonomy has been useful for the delimitation and characterisation of these ceratioid species, contributing to a better understanding of their distribution and inter- and intraspecific variability.
... P r e p r i n t n o t p e e r r e v i e w e d Molecular taxonomy has been successfully implemented with the traditional morphological analysis in the systematic study of fishes. Thus, a variety of molecular markers such as the combination of 16S, COI, ND5+, H3 and 28S (Chakrabarty et al., 2011), complete mitochondrial DNA sequences (Miya et al. 2003), the mitochondrial cytochrome c oxidase subunit I COI (Ross-Robertson et al. 2017), RH1 and RH2 opsin genes (Lupše et al., 2021) has been employed for taxonomic or phylogenetic purposes in A. cornuta. ...
... Nine other species were upper continental shelf demersal fish. Among them, multiple cryptic species in Notacanthus chemnitzi are also suggested by previous studies (Robertson et al. 2017, Poulsen et al. 2018). The other 8 species also showed 2 or more lineages with a high intraspecific genetic differentiation. ...
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.
... We paired the Liparidae COI phylogeny with species depth ranges to evaluate depth relationships between clades ( Table 2). The species depth ranges were compiled from FishBase (Froese and Pauly (2021) and checked in the primary literature (Chernova et al. 2004;Chernova 2008;Steinke et al. 2009;Dettai et al. 2011;Orlov and Tokranov 2011;Stein 2012;Linley et al. 2016;Stein 2016;Robertson et al. 2017;Solomatov and Orlov 2018;Gerringer 2019;Orr et al. 2020). While the species used within the Liparidae COI dataset are a good representation of known snailfishes, the absence of deep abyssal species is most likely an artefact of reduced sampling effort at these depths (Gerringer 2019). ...
Snailfishes are among the most rapidly radiating families of marine fishes, resulting in a global distribution from the coastal intertidal to deep subduction trenches. The true diversity and distribution of deep-water snailfishes, particularly at hadal depths (>6000 m) and in the Southern Hemisphere, remain uncertain due to the rarity of samples. Here, we present the snailfish diversity at near-hadal and hadal depths in the Atacama Trench, which runs along the southwest coast of South America. Using free-fall baited cameras and traps, we documented at least three species of hadal snailfishes between 5920 and 7608 m based on distinct morphologies. One snailfish specimen was recovered from 6714 m, which we describe herein as Paraliparis selti sp. nov., based on a combined morphological and molecular taxonomic approach (16S, COI, and Cyt-b). Paraliparis selti sp. nov. is morphologically distinct from described snailfishes due to a combination of high number of; vertebrae (65) particularly the abdominal vertebrae (12), dorsal fin rays (60), anal fin rays (52), and caudal fin rays (8); comparatively low number of pectoral fin rays (18) which forms a deep notch with two widely spaced non-rudimentary rays. Micro-CT was used to minimise dissection of the specimen and to provide a digital holotype. Paraliparis selti sp. nov. highlights the importance of the Liparidae at hadal depths and provides evidence for at least two independent radiations of snailfishes into the hadal zone.
... Trichiurus nitens was described in 1899, and it is distributed in the eastern Pacific, from California south to Peru. Nakamura and Parin (1993) considered it synonymous with T. lepturus, but some researchers have suggested that it is the real T. nitens (Eschmeyer and Herald 1983;Burhanuddin and Parin 2008;Robertson et al. 2017). In addition, T. margarites is considered a valid species in FishBase (Froese and Pauly 2021) and ECoF (Fricke et al. 2021). ...
Four Trichiurus species, T. japonicus , T. lepturus , T. nanhaiensis , and T. brevis , from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T. gangeticus . The mitogenomes contained 16.568–16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNA Pro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T. lepturus nor T. nanhaiensis but they are T. gangeticus ; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.
... Between 2007 and 2011, a series of research cruises were made by the Spanish research vessel R/V Miguel Oliver along the continental shelves and slopes of the Pacific and Atlantic coasts of Central and South America (Robertson et al. 2017). The R/V Miguel Oliver is operated by the Spanish Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente (MAPAMA; http://www.mapama.gob.es). ...
... The specific epithet mapama refers to the acronym MAPAMA, the Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente, which is the Spanish governmental organization that operates the R/V Miguel Oliver. This name recognizes the support of MAPAMA for the research cruises to Central and South America that facilitated the capture of this angelshark, and other new species of deepwater fishes on both sides of the Central American isthmus (Vázquez et al. 2015, Concha et al. 2016, Robertson et al. 2017. Suggested common name of Small-crested Angelshark or angelote de cresta pequeña is in reference to the short and narrow median line of small dermal denticles. ...
Integrating both morphological and genetic data, we describe Squatina mapama, a new species of the angel shark genus Squatina, found on the upper continental slope off the Caribbean coast of Panama. Distinguishing characters of S. mapama include a wider pectoral and pelvic span; a shorter head length; a narrower mouth; short fringed nasal flaps and barbels; a few large denticles on top of the head; a single dorsal midline row of slightly enlarged denticles from the level of the posterior insertion of the pelvic fin to the first dorsal fin and continuing past the first dorsal fin to the second dorsal-fin origin; and the presence of smaller scattered spots in males, which, in combination, allow separation of this new species from the closely related and sympatric species Squatina david. The new species can be distinguished from all other currently recognized Squatina species by meristic and morphometric measures, as well as by sequence differences in the mtDNA COI marker. Phylogenetic analysis shows Squatina mapama n. sp. to be a basal member of a small clade of western Atlantic Squatina species that includes Squatina occulta, Squatina guggenheim, and S. david, which likely evolved in the late Oligocene or Miocene period. We also report a western range extension of S. david from Colombia to the western Caribbean coast of Panama.. (2021) Squatina mapama n. sp., a new cryptic species of angel shark (Elasmobranchii: Squatinidae) from the southwestern Caribbean Sea.
... Sharks were collected in 2010, during a deep-water demersal survey conducted by the Spanish research vessel Miguel Oliver off the Pacific coast of Central America (see Robertson et al. 2017 for details). The specimens were deposited, in part, in the fish collection of the Museo de Zoología of the University of Costa Rica (UCR), fixed in 10% formalin and preserved in 70% ethanol. ...
Anelasma squalicola is a parasitic barnacle of members of the deep-water shark families Etmopteridae, Pentanchidae and Scyliorhinidae. We report the first published confirmation of this species in the Eastern Pacific Ocean, based on material collected off Costa Rica, its first record as a parasite of the Ninja lantern shark, Etmopterus benchley (Etmopteridae), and a new size record for the host. The information presented herein expands the knowledge (distribution and host usage) of this enigmatic species.
