On the occurrence of a post-larval specimen of Brosme brosme (Gadiformes: Lotidae) on Porcupine Bank (west Ireland).

The occurrence of a small specimen of Brosme brosme (Gadiformes: Lotidae) from the Porcupine Bank is reported. A single specimen with a total length of 73.2 mm was caught with bottom trawl at a depth of 322 m depth in 2017. The specimen was identified morphologically and confirmed by molecular taxonomy using DNA barcoding. Based on the size and ontogenetic characters found, the specimen was identified as a post-larval individual, and a pelagic habitat of the specimen seems more likely.

Molecular mechanism and history of non-sense to sense evolution of antifreeze glycoprotein gene in northern gadids.

A fundamental question in evolutionary biology is how genetic novelty arises. De novo gene birth is a recently recognized mechanism, but the evolutionary process and function of putative de novo genes remain largely obscure. With a clear life-saving function, the diverse antifreeze proteins of polar fishes are exemplary adaptive innovations and models for investigating new gene evolution. Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence. We constructed genomic DNA libraries for AFGP-bearing and AFGP-lacking species across the gadid phylogeny and performed fine-scale comparative analyses of the AFGP genomic loci and homologs. We identified the noncoding founder region and a nine-nucleotide (9-nt) element therein that supplied the codons for one Thr-Ala-Ala unit from which the extant repetitive AFGP-coding sequence (cds) arose through tandem duplications. The latent signal peptide (SP)-coding exons were fortuitous noncoding DNA sequence immediately upstream of the 9-nt element, which, when spliced, supplied a typical secretory signal. Through a 1-nt frameshift mutation, these two parts formed a single read-through open reading frame (ORF). It became functionalized when a putative translocation event conferred the essential cis promoter for transcriptional initiation. We experimentally proved that all genic components of the extant gadid AFGP originated from entirely nongenic DNA. The gadid AFGP evolutionary process also represents a rare example of the proto-ORF model of de novo gene birth where a fully formed ORF existed before the regulatory element to activate transcription was acquired.

Diversity of the CO1 Gene of Mitochondrial DNA in Representatives of Genus Antimora (Moridae, Gadiformes) in the World Oceans.

The frequency of occurrence of the COI gene of mitochondrial DNA in the Pacific flatnose Antimora microlepis and blue antimora Antimora rostrata (Moridae, Gadiformes) was analyzed in samples collected in different areas of the World Ocean. The revealed maximum haplotype diversity of COI in the blue antimora in the North Atlantics may indicate that this species emerged in this region, from which it widely distributed in the World Ocean. The Pacific flatnose Antimora microlepis originated from Antimora rostrata. Antimora might penetrate into the North Pacific by several routes: through the Panama Strait, along the coast of Antarctica, or through the Indian Ocean along the coast of Australia.

Depth as a driver of evolution in the deep sea: Insights from grenadiers (Gadiformes: Macrouridae) of the genus Coryphaenoides.

Here we consider the role of depth as a driver of evolution in a genus of deep-sea fishes. We provide a phylogeny for the genus Coryphaenoides (Gadiformes: Macrouridae) that represents the breadth of habitat use and distributions for these species. In our consensus phylogeny species found at abyssal depths (>4000m) form a well-supported lineage, which interestingly also includes two non-abyssal species, C. striaturus and C. murrayi, diverging from the basal node of that lineage. Biogeographic analyses suggest the genus may have originated in the Southern and Pacific Oceans where contemporary species diversity is highest. The abyssal lineage seems to have arisen secondarily and likely originated in the Southern/Pacific Oceans but diversification of this lineage occurred in the Northern Atlantic Ocean. All abyssal species are found in the North Atlantic with the exception of C. yaquinae in the North Pacific and C. filicauda in the Southern Ocean. Abyssal species tend to have broad depth ranges and wide distributions, indicating that the stability of the deep oceans and the ability to live across wide depths may promote population connectivity and facilitate large ranges. We also confirm that morphologically defined subgenera do not agree with our phylogeny and that the Giant grenadier (formerly Albatrossia pectoralis) belongs to Coryphaenoides, indicating that a taxonomic revision of the genus is needed. We discuss the implications of our findings for understanding the radiation and diversification of this genus, and the likely role of adaptation to the abyss.

New records of larval stages of the eel cod genus Muraenolepis Günther 1880 (Gadiformes: Muraenolepididae) from the western Antarctic Peninsula.

Three newly discovered larval specimens of the genus Muraenolepis collected from the waters of the western Antarctic Peninsula are described. Knowledge of their natural history is sparse and information about their early life history is based on only a few larval stages. Here, the available literature on larval eel cods is reviewed, and the specimens placed in context.

Material properties of Pacific hake, Humboldt squid, and two species of myctophids in the California Current.

Material properties of the flesh from three fish species (Merluccius productus, Symbolophorus californiensis, and Diaphus theta), and several body parts of the Humboldt squid (Dosidicus gigas) collected from the California Current ecosystem were measured. The density contrast relative to seawater varied within and among taxa for fish flesh (0.9919-1.036), squid soft body parts (mantle, arms, tentacle, braincase, eyes; 1.009-1.057), and squid hard body parts (beak and pen; 1.085-1.459). Effects of animal length and environmental conditions on nekton density contrast were investigated. The sound speed contrast relative to seawater varied within and among taxa for fish flesh (0.986-1.027) and Humboldt squid mantle and braincase (0.937-1.028). Material properties in this study are similar to values from previous studies on species with similar life histories. In general, the sound speed and density of soft body parts of fish and squid were 1%-3% and 1%-6%, respectively, greater than the surrounding seawater. Hard parts of the squid were significantly more dense (6%-46%) than seawater. The material properties reported here can be used to improve target strength estimates from acoustic scattering models, which could increase the accuracy of biomass estimates from acoustic surveys for these nekton.

New tools (DNA barcoding), old hypothesis: the case of the taxonomic identity of the Argentine hakes (Actinopterygii: Merluccius).

The present study evaluated the possible occurrence of cryptic species among Merluccidae from Argentina by examining sequences of cytochrome c oxidase subunit I (coI) mtDNA. This approach can discriminate Merluccius hubbsi and Merluccius australis; specimens with morphological diagnostic characters of Merluccius patagonicus formed a cohesive cluster with M. hubbsi specimens. BIN analysis confirmed the effectiveness of barcoding within a global context.

Evaluating the resolution power of new microsatellites for species identification and stock delimitation in the Cape hakes Merluccius paradoxus and Merluccius capensis (Teleostei: Merlucciidae).

The utility of 15 new and 17 previously published microsatellite markers was evaluated for species identification and stock delimitation in the deep-water hake Merluccius paradoxus and the shallow-water hake Merluccius capensis. A total of 14 microsatellites were polymorphic in M. paradoxus and 10 in M. capensis. Two markers could individually discriminate the species using Bayesian clustering methods and a statistical power analysis showed that the set of markers for each species is likely to detect subtle genetic differentiation (FST < 0·006) that will be valuable to delimit and characterize genetic stocks.

Characterization of mitochondrial control region in Merlucciidae: sequence variation and molecular phylogeny.

In order to describe the structure and evolution of Merlucciidae and related Gadiformes mitochondrial control region we analysed 470 bp of 31 taxa belonging to 28 different species. The general structure and conserved sequence blocks observed in Gadiformes mitochondrial control region are similar to those present in other teleost fishes. The length of this segment is variable among related species due to the presence of numerous indels at domain I. Domain II is the most conserved region with a high G content. The GTGGG-box is absent in all Merluccius and seven other Gadidae species. Several methods of phylogenetic analyses has revealed the monophyly of Gadiformes, Gadinae and Merlucciidae. Merlucciidae is most closely related to Gadidae. Within Merlucciidae, American and Euroafrican clades show similar levels of differentiation to those within Gadinae where Trisopterus and Micromesistius are sister taxa. Genetic distance values for Merluccius subspecies pairs are less than half of those between species, comparable to intra specific differentiation levels in marine fish species.

Gaidropsarus (Gadidae, Teleostei) of the North Atlantic Ocean: a brief phylogenetic review.

The phylogenetic relationships among the North Atlantic Gaidropsarus and between the three Gaidropsarinae genera Gaidropsarus, Ciliata and Enchelyopus are reviewed with the hitherto most comprehensive taxonomic sampling of this group. Phylogenetic results (maximum parsimony, maximum likelihood and Bayesian inference) based on nuclear (rhodopsin) and concatenated mitochondrial (12s, 16s and cytb) markers clearly support this subfamily. For the north-eastern Atlantic species of Gaidropsarus, two previously unreported clades were strongly supported, clarifying the relationships within the genus, and revealing fewer distinct taxa in the north Atlantic Gaidropsarus than previously stipulated. The data challenge the specific status of Gaidropsarus mediterraneus and Gaidropsarus guttatus and raise doubts concerning the distinctiveness of other species. A taxonomic revision of the genus is suggested.

Population genetic structure and geographical differentiation of burbot (Lota lota) in China.

The burbot (Lota lota Linnaeus, 1758) is the only freshwater species of the family Gadidae. There is a long-standing controversy about taxonomic status of the burbot from the Amur River basin. It is necessary to investigate population genetic structure and geographical differentiation among burbot populations from the Irtysh River basin and Amur River basin by mitochondrial DNA nucleotide sequence analysis. A 572 bp segment of cytochrome b and 425 bp segment of control region gene were sequenced from 4 populations. The results showed that there was lower genetic diversity of burbot in China and highly significant genetic difference between populations in the Amur Riverbasin (P < 0.01). Demographic analysis indicated that the burbot from the Amur River basin experienced population expansion (Cytb: F(s) = -0.912 (P = 0.287), D = -0.399 (P = 0.375); CR: F(s) = -4.771 (P = 0.015), D = -1.523 (P = 0.03 )). The data of 4 populations in China combining with the published data representing the Eurasian and North American burbot, revealed three distinct phylogenetic lineages (labelled EB, NA, Amur).

Taxonomic study of Bathygadidae fishes (Gadiformes) from Atlantic Spanish waters combining morphological and molecular approaches.

From 2009 to 2011 eleven specimens belonging to four bathygadid species of the family Bathygadidae were captured in two different locations in the northern waters of Spain. The morphometric measurements and meristic characters of these specimens are given. The specimens were identified as belonging to the genera Gadomus Regan, 1903, and Bathygadus Günther, 1878, including the following species: Gadomus dispar (Vaillant, 1888), Gadomus longifilis (Goode & Bean, 1885), Gadomus arcuatus (Goode & Bean, 1886) and Bathygadus melanobranchus Vaillant, 1888. As a result, a new northern limit of distribution of G. arcuatus from the northeastern Atlantic is reported. The first molecular identification and genetic interrelationships of Bathygadidae species, based on the mitochondrial COI nucleotide sequences -DNA barcodes- is reported. Sequences corresponding to specimens from the same species were identical and the overall mean genetic diversity (uncorrected p-distance) was 0.096 ± 0.008. Based on a morphological and meristic examination of the specimens, as well as on the available literature, an updated key of the members of the family Bathygadidae from the north-eastern Atlantic Ocean is provided.

Evolutionary history of the genus Trisopterus.

The group of small poor cods and pouts from the genus Trisopterus, belonging to the Gadidae family, comprises four described benthopelagic species that occur across the North-eastern Atlantic, from the Baltic Sea to the coast of Morocco, and the Mediterranean. Here, we combined molecular data from mitochondrial (cytochrome b) and nuclear (rhodopsin) genes to confirm the taxonomic status of the described species and to disentangle the evolutionary history of the genus. Our analyses supported the monophyly of the genus Trisopterus and confirmed the recently described species Trisopterus capelanus. A relaxed molecular clock analysis estimated an Oligocene origin for the group (~30 million years ago; mya) indicating this genus as one of the most ancestral within the Gadidae family. The closure and re-opening of the Strait of Gibraltar after the Messinian Salinity Crisis (MSC) probably triggered the speciation process that resulted in the recently described T. capelanus.

Population structure in Chilean hake Merluccius gayi as revealed by mitochondrial DNA sequences.

Genetic variation and divergence among samples of Chilean hake Merluccius gayi, from three localities off the coast of Chile and one locality off the coast of northern Peru, were assessed using sequences from the control region of mitochondrial DNA. Homogeneity tests revealed occurrence of at least three distinct genetic stocks of M. gayi within the region sampled. Factors potentially contributing to genetic divergence among M. gayi probably include hydrodynamics and behaviour.

Mitochondrial DNA differentiation between the antitropical blue whiting species Micromesistius poutassou and Micromesistius australis.

This study investigated the biogeography and genetic variation in the antitropically distributed Micromesistius genus. A 579 bp fragment of the mitochondrial coI gene was analysed in 279 individuals of Micromesistius poutassou and 163 of Micromesistius australis. The time since divergence was estimated to be c. 2 million years before present (Mb.p.) with an externally derived clock rate by Bayesian methods. Congruent estimates were obtained with an additional data set of cytochrome b sequences derived from GenBank utilizing a different clock rate. The divergence time of 2 Mb.p. was in disagreement with fossil findings in New Zealand and previous hypotheses which suggested the divergence to be much older. It, therefore, appears likely that Micromesistius has penetrated into the southern hemisphere at least two times. Paleoceanographic records indicate that conditions that would increase the likelihood for transequatorial dispersals were evident c. 2-1·6 Mb.p.. Haplotype frequency differences, along with pairwise F(ST) values, indicated that Mediterranean M. poutassou is a genetically isolated population.

Endoparasite fauna of five Gadiformes fish species from the coast of Chile: host ecology versus phylogeny.

The aims of the present study were to compare, using multivariate analyses, the degree of similarity of the endoparasite fauna of five fish species belonging to the order Gadiformes: Merluccius gayi, Merluccius australis, Macruronus magellanicus (Gadoidei) and Micromesistius australis and Nezumia pulchella (Macrouroidei), from the southern and central Chilean coast, and to evaluate whether the composition of the endoparasite fauna was determined by phylogenetic or ecological relationships. We employed our database of Merluccius australis, M. magellanicus and Micromesistius australis, which was complemented with published information for M. magellanicus, Merluccius australis, Micromesistius australis, M. gayi and N. pulchella. A higher number of endoparasite species was recorded for Merluccius australis, Micromesistius australis and M. magellanicus, namely Anisakis sp. and Hepatoxylon trichiuri, which is the most prevalent parasite among these hosts. Aporocotyle wilhelmi and Hysterothylacium sp. were detected only in M. gayi, whereas Lepidapedon sp. was found exclusively in N. pulchella. These results suggest that fish ecology rather than host phylogeny was the most important factor for the determination of similarity in parasite composition. This result could be explained by the similar trophic patterns of hosts and by the predominance of generalist larval species among these fish parasite communities.

DNA barcoding highlights a cryptic species of grenadier Macrourus in the Southern Ocean.

Although three species of the genus Macrourus are recognized in the Southern Ocean, DNA sequencing of the mitochondrial COI gene revealed four well-supported clades. These barcode data suggest the presence of an undescribed species, a conclusion supported by meristic and morphometric examination of specimens.

Morphological, morphometric, meristic and osteological evidence for two species of hake (Actinopterygii: Gadiformes: Merluccius) in Argentinean waters.

Morphologically, both classic and landmark-based morphometry and meristic analyses of 241 specimens of Merluccius, along with the re-examination of six paratype specimens of Merluccius hubbsi, the holotype and three paratypes of Merluccius patagonicus and the syntype of Merluccius australis revealed the presence of only two species of Merluccius in Argentinean waters. Internal structures (hyomandibula, urohyal and sagitta otolith) of M. hubbsi were compared to those reported for M. patagonicus and were shown to have identical morphology. Type specimens of M. patagonicus showed a complete overlap in morphometric and meristic characters with M. hubbsi, whereas M. australis had a greater number of second dorsal and anal-fin rays, and more lateral-line scales. In addition, M. australis had a smaller eye and longer snout than M. hubbsi and M. patagonicus. The results indicate that there is no evidence for a third hake species in Argentinean waters. Merluccius patagonicus is a synonym of M. hubbsi.

Taxonomic review of the genus Trisopterus(Teleostei: Gadidae) with recognition of the capelan Trisopterus capelanus as a valid species.

Trisopterus is demonstrated to be monophyletic, including four distinct species: T. capelanus, T. esmarkii, T. luscus and T. minutus. The capelan T. capelanus is resurrected from the synonymy of poor cod T. minutus, and is shown to be morphologically more similar to T. luscus, to which species it is also more closely related, indicated by a phylogenetic analysis presented here. A lectotype is designated for T. luscus. Trisopterus fasciatus, the type species of Trisopterus, is a junior synonym of T. luscus, and the lectotype of T. luscus is designated as the neotype of T. fasciatus. The lectotype of T. luscus is also designated as the neotype of Gadus barbatus. Gadus barbatus has priority over T. luscus but the name is suppressed by prevailing usage of T. luscus. A neotype is designated also for T. minutus. A phylogenetic analysis using mitochondrial cytochrome b, and a fragment of the nuclear rhodopsin gene, shows that T. capelanus and T. luscus are sister species, and in turn sister to a clade formed by T. minutus and T. esmarkii.

Phylogenetic prospecting for cryptic species of the genus Merluccius (Actinopterygii: Merlucciidae).

Hakes of the genus Merluccius include 11 valid species as well a number of rare morphotypes suspected to be "cryptic species". Concatenated nucDNA ITS1-rDNA and mtDNA cyt b sequences plus nested ITS1Nes sequences allowed to ascribe 14 specimens of nine rare morphotypes from the South Pacific and the South Atlantic to the phylogenetic backbone of this genus. Bayesian analyses pointed to M. bilinearis and M. albidus as the oldest species of the genus and the New World cluster, respectively. The phylogenetic status of M. angustimanus from the upper Gulf of California suggests its hybrid origin between M. gayi and M. productus from about 0.25 MYA, although an ever since confinement of a subset of those species cannot be ruled out. The molecular phylodiagnostic test suggests a common origin of all rare morphotypes and the absence of cryptic hake species in the Southern Cone. The molecular background of the morphotypes distributed between the Western Pacific South of New Zealand and the western Atlantic South of Argentina is compatible with their hybrid origin between M. gayi and both, M. australis or M. hubbsi, respectively.