Discrimination of the redfish (Sebastes mentella) stock components in the Irminger Sea and adjacent waters based on meristics,morphometry and biological characteristics

Redfish Sebastes mentella samples were collected in 2004 and 2005 during commercial cruises to the Irminger Sea on board the Polish vessel M/T ‘Wiesbaden’. Ichthyological studies included length and weight measurements, sex, gonad maturity stages and age determinations. Meristic and morphometric measurements were performed on digital images of the redfish. Comparison of the pelagic redfish from the northeastern (depths deeper than 500 m) and southwestern (depths shallower than 500 m) fishing grounds of the Irminger Sea indicates a number of differences including spatial and vertical distribution, ambient temperature, length and age composition. Moreover, 12 morphometric and 4 meristic characters differed significantly between fish samples from these two areas. Results of Cluster Analysis showed the clear grouping of samples into that of the ‘oceanic’ component (depth 300–450 m) and the ‘deep sea’ component (depth 550–800 m). These results were confirmed by Principal Component Analysis, which revealed the separation of samples into two catch depth groups. The share of fish allocated by Discriminant Analysis into the pelagic ‘deep sea’ component in the northeastern area was nearly 92%, while the ‘oceanic’ component was dominant in the southwestern area and comprised more than 88% of the fish. Cluster and Principal Component analyses suggest that the ‘oceanic’ component is a more homogeneous group than the ‘deep sea’ component. These results support the management units recently established by ICES.     

Phylogenetic relationships among North Atlantic redfish (genus Sebastes) as revealed by mitochondrial DNA sequence analyses

Species structure and phylogenetic relationships among the four currently recognised North Atlantic redfish species, Sebastes mentella (‘deep‐sea’ and ‘oceanic’ phenotype), S. marinus (including ‘giant’ phenotype), S. fasciatus and S. viviparus, were investigated by sequencing the complete mitochondrial NADH dehydrogenase subunit 3 (ND3) gene for 313 individuals (333 including outliers). Low levels of sequence divergence of 0.3–2.3% between the North Atlantic Sebastes haplotypes, low resolution in phylogenetic trees and a star‐like statistical parsimony network indicate a population bottleneck and/or founder event with a subsequent population expansion and a rapid speciation in North Atlantic Sebastes. Diagnostic mutations within the ND3 gene were recognised for some of the species. The results lead to the hypothesis that the ancestral haplotype lineage is now very rare or has suffered extinction and that the most basal lineage is found in S. viviparus. The results further indicate direct descendants in the S. fasciatus and S. marinus lineages from the S. mentella lineage, whereas the S. viviparus lineage originates from an earlier division. The observation of two haplotype lineages in S. marinus with a relatively high level of intraspecific genetic divergence, points towards a possible cryptic speciation.     

Recruitment of stock of deepwater redfish <Emphasis Type="Italic">Sebastes mentella</Emphasis> (Scorpaeniformes,Scorpaenidae) in the pelagial of the Irminger Sea and adjacent waters

Results of comparative analysis of several ecologo-populational characteristics and fauna of parasites of deepwater redfish Sebastes mentella from the pelagial of the Irminger Sea and slopes of Greenland are provided. It was established that the nursery area of the species in this part of the northern Atlantic is located in the shelf and shallow-water sites of the Greenland slopes. Near the nursery area, at deepwater sites of the Greenland slope, aggregations of mainly immature specimens (68–86%) with an average length of 35–38 cm are located, and, in the oceanic pelagial, there are mainly mature specimens (91–95%) with a length of more than 30 cm. Considerable similarity and specific features of fauna of parasites of S. mentella from the southeastern slope of Greenland and the pelagial of the Irminger Sea indicate the belonging of fish aggregations in these areas to a single intraspecies group and the migration of maturing specimens from the slope to the pelagial. A conclusion is made that the aggregations of S. mentella in the pelagial of the Irminger and Labrador seas represent a pelagic ecological group formed by rapidly maturing specimens; a near-bottom ecological group at deepwater sites of the slope of Greenland is formed by slowly maturing specimens. No mass migration of the redfish from deepwater areas to shallow sites of the slope and to the oceanic pelagial of the northern Atlantic was recorded.     

Structure of aggregations and principal populational characteristics of redfish <Emphasis Type="Italic">Sebastes mentella</Emphasis> (Scorpaeniformes: Scorpaenidae) in the pelagic zone of the Irminger Sea and adjacent waters

The spatial distribution of redfish Sebastes mentella in the pelagic zone of the northern part of the Atlantic Ocean (the Irminger Sea and the Labrador Sea) is investigated. Analysis of the data on size-age composition, sex ratio, ratio of mature and immature specimens, rate of maturation, composition of the parasite fauna, infestation level, infestation with the copepod Sphyrion lumpi, and occurrence of pigment formations on the body of redfish from the investigated areas indicate the absence of stable isolated aggregations of this species in the oceanic pelagial of the North Atlantic. Pelagic aggregations are formed of rapidly maturating specimens migrated from the slopes of Greenland. The spatial variation of the size-age composition of redfish depends on the life cycle and regional hydrological conditions.     

Intraspecies structure of beaked redfish <Emphasis Type="Italic">Sebastes mentella</Emphasis> of the Atlantic and Arctic oceans

On the basis of the results of complex interdisciplinary investigations of the population composition and structure of the beaked redfish Sebastes mentella of the Atlantic and Arctic oceans, its three populations are discerned relatively isolated from each other by the system of permanent marine currents—North Atlantic, Flemish-Cape, and Norway-Barents Sea. The population structure of the species in the southern part of its area corresponds to the model of a local stock. Interaction of the North Atlantic and the Norway-Barents Sea populations well correspond to the model of fluctuating stocks. Redfish aggregations in different biotopes (mesobenthal and mesopelagial) are intrapopulational epigenetic groups. In the period of warm and anomalously warm years, a part of mature specimens from the pelagial of the North Irminger Sea make an irreversible migration to the southern part of the Norwegian Sea and form there mixed aggregations of fish from the North Atlantic and Norway-Barents Sea populations. With consideration of the effect of climatic–oceanological processes, a principally new scheme is elaborated describing the process of seasonal migrations of redfish in the mesobenthal and mesopelagial. The previous views on direction of return migrations of redfish of the Norway-Barents Sea population are reconsidered. Juveniles from the western part of the Barents Sea and Spitsbergen not only supplement the demersal aggregations but also migrate to the pelagial of the Norwegian Sea.     

Structure and specific features of formation of aggregations of deepwater redfish <Emphasis Type="Italic">Sebastes mentella</Emphasis> (Scorpaenidae) in the Norwegian Sea pelagial

Results of studies of the structure and specific features of formation of aggregations of deepwater redfish Sebastes mentella in the Norwegian Sea pelagial are provided. Data on the biological characteristics of S. mentella from different regions of the Norwegian Sea pelagial do not allow us to consider its aggregations as separate populations. On the basis of comparative analysis of the structure of aggregations in the Norwegian Sea and of population parameters and specific features of the life cycle of S. mentella in different parts of the Atlantic Ocean, its complex intraspecies organization at sites of overlapping of two largest populations—North Atlantic and Norwegian-Barents Sea-was established. The formation of pelagic aggregations in the water area of the Norwegian Sea occurs due to migration of maturing and mature individuals from the adjoining water areas. In the southern areas of the Norwegian Sea, dominant recruitment comes from the pelagial of the northeastern part of the Irminger Sea, which is promoted by the direction of streams of the North-Atlantic Current; it is not excluded either that fish can migrate to the southern part of the sea from the slopes of the Faeroes, Faeroes-Icelandic threshold, and the western coast of Norway. Migration to the northern areas of the sea is mainly performed by rapidly maturing fish from the rearing region from the western slopes of the Barents Sea and Spitsbergen Archipelago. The presence of seasonal migrations hinders the formation in the pelagial of perch isolated groups and promotes their migration.     

Features of the reproductive cycle in females of the beaked redfish <Emphasis Type="Italic">Sebastes mentella</Emphasis> (Sebastidae)

The reproductive status of some categories of females of the beaked redfish Sebastes mentella has been determined as a result of the histological analysis. The histological characteristic of gonads of large nonreproductive females of redfish is presented for the first time. Gonads of mature females that skip spawning are studied. The cytomorphological characteristic of ovaries after larvae extrusion is specified. A broadened maturity scale for gonads of females of S. mentella supplemented with stages that characterize fish that skip spawning and large nonreproductive females is proposed.     

Parasites as Biological Tags for Stock Discrimination of Beaked Redfish (Sebastes mentella): Parasite Infra-Communities vs. Limited Resolution of Cytochrome Markers

The use of parasites as biological tags for discrimination of fish stocks has become a commonly used approach in fisheries management. Metazoan parasite community analysis and anisakid nematode population genetics based on a mitochondrial cytochrome marker were applied in order to assess the usefulness of the two parasitological methods for stock discrimination of beaked redfish Sebastes mentella of three fishing grounds in the North East Atlantic. Multivariate, model-based approaches demonstrated that the metazoan parasite fauna of beaked redfish from East Greenland differed from Tampen, northern North Sea, and Bear Island, Barents Sea. A joint model (latent variable model) was used to estimate the effects of covariates on parasite species and identified four parasite species as main source of differences among fishing grounds; namely Chondracanthus nodosus, Anisakis simplex s.s., Hysterothylacium aduncum, and Bothriocephalus scorpii. Due to its high abundance and differences between fishing grounds, Anisakis simplex s.s. was considered as a major biological tag for host stock differentiation. Whilst the sole examination of Anisakis simplex s.s. on a population genetic level is only of limited use, anisakid nematodes (in particular, A. simplex s.s.) can serve as biological tags on a parasite community level. This study confirmed the use of multivariate analyses as a tool to evaluate parasite infra-communities and to identify parasite species that might serve as biological tags. The present study suggests that S. mentella in the northern North Sea and Barents Sea is not sub-structured.     

Hook selectivity as a mitigating measure in the catches of the stingray Pteroplatytrygon violacea (Bonaparte, 1832) (Elasmobranchii,Dasyatidae)

Hook selectivity, sex ratio of catches and relative abundance (Catch Per Unit Effort – CPUE) were assessed for the pelagic stingray Pteroplatytrygon violacea (Bonaparte, 1872), caught by longline gear in the southwestern Atlantic Ocean over the continental slope and adjacent oceanic area. The catches were carried out at depths of 200–4000 m by research cruises in 2002 and 2003, from Cabo Frio (22°52′S) to Laguna (28°28′S); and by hook selectivity experiments from 2004 to 2008, from Itajaí (26°54′S) to Tramandaí (29°59′S). Hook selectivity experiments indicated higher catches of stingrays with ‘J’ hooks (9/0, 10° offset) commonly used by the pelagic longline fleet than with ‘circle’ hooks (18/0, 10° offset). ‘circle’ hooks reduce the longline by‐catches of this species. Most of the stingrays caught were males (6 : 1). One female aborted mid‐term embryos at the time of capture. CPUE was highest between spring and autumn and lowest during winter.     

Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator,the common dolphin (genus Delphinus)

Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Population samples representing the three major morphotypes of Delphinus were obtained from 10 oceanic regions. Our results suggest that short‐beaked common dolphins are likely to have originated in the eastern Indo‐Pacific Ocean during the Pleistocene and expanded into the Atlantic Ocean through the Indian Ocean. On the other hand, long‐beaked common dolphins appear to have evolved more recently and independently in several oceans. Our results also suggest that short‐beaked common dolphins had recurrent demographic expansions concomitant with changes in sea surface temperature during the Pleistocene and its associated increases in resource availability, which differed between the North Atlantic and Pacific Ocean basins. By proposing how past environmental changes had an effect on the demography and speciation of a widely distributed marine mammal, we highlight the impacts that climate change may have on the distribution and abundance of marine predators and its ecological consequences for marine ecosystems.     

A genomewide catalogue of single nucleotide polymorphisms in white‐beaked and Atlantic white‐sided dolphins

The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high‐throughput sequencing platforms increases. In this study, we used restriction‐site‐associated DNA sequencing (RADSeq) to recover genomewide genotypes from 70 white‐beaked (Lagenorhynchus albirostris) and 43 Atlantic white‐sided dolphins (L. acutus) gathered throughout their north‐east Atlantic distribution range. Both species are at a high risk of being negatively affected by climate change. Here, we provide a resource of 38 240 RAD‐tags and 52 981 nuclear SNPs shared between both species. We have estimated overall higher levels of nucleotide diversity in white‐sided (π = 0.0492 ± 0.0006%) than in white‐beaked dolphins (π = 0.0300 ± 0.0004%). White‐sided dolphins sampled in the Faroe Islands, belonging to two pods (N = 7 and N = 11), showed similar levels of diversity (π = 0.0317 ± 0.0007% and 0.0267 ± 0.0006%, respectively) compared to unrelated individuals of the same species sampled elsewhere (e.g. π = 0.0285 ± 0.0007% for 11 Scottish individuals). No evidence of higher levels of kinship within pods can be derived from our analyses. When identifying the most likely number of genetic clusters among our sample set, we obtained an estimate of two to four clusters, corresponding to both species and possibly, two further clusters within each species. A higher diversity and lower population structuring was encountered in white‐sided dolphins from the north‐east Atlantic, in line with their preference for pelagic waters, as opposed to white‐beaked dolphins that have a more patchy distribution, mainly across continental shelves.     

Population structure of beaked redfish (<Emphasis Type="Italic">Sebastes mentella</Emphasis> Travin, 1951) in the Irminger Sea and adjacent waters inferred from microsatellite data

Samples of beaked redfish from the Irminger Sea and adjacent waters were examined for polymorphism at ten microsatellite loci. The strategy of the material collection enabled investigation of geographic, bathymetric, and temporal variation of this species. The results did not support the evidence on spatial differentiation and temporal stability of the species distribution, favoring the idea that the water area examined was inhabited by a single pelagic population of beaked redfish.     

Habitat‐driven population structure of bottlenose dolphins,Tursiops truncatus,in the North‐East Atlantic

Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North‐West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. ‘coastal’ and ‘pelagic’) have been identified. Here, we investigated the genetic population structure of North‐East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy‐sampled or stranded animals using 25 microsatellites and a 682‐bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer‐scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.     

Diet assessment of the Atlantic Sea Nettle Chrysaora quinquecirrha in Barnegat Bay,New Jersey,using next‐generation sequencing

Next‐generation sequencing (NGS) methodologies have proven useful in deciphering the food items of generalist predators, but have yet to be applied to gelatinous animal gut and tentacle content. NGS can potentially supplement traditional methods of visual identification. Chrysaora quinquecirrha (Atlantic sea nettle) has progressively become more abundant in Mid‐Atlantic United States’ estuaries including Barnegat Bay (New Jersey), potentially having detrimental effects on both marine organisms and human enterprises. Full characterization of this predator's diet is essential for a comprehensive understanding of its impact on the food web and its management. Here, we tested the efficacy of NGS for prey item determination in the Atlantic sea nettle. We implemented a NGS ‘shotgun’ approach to randomly sequence DNA fragments isolated from gut lavages and gastric pouch/tentacle picks of eight and 84 sea nettles, respectively. These results were verified by visual identification and co‐occurring plankton tows. Over 550 000 contigs were assembled from ~110 million paired‐end reads. Of these, 100 contigs were confidently assigned to 23 different taxa, including soft‐bodied organisms previously undocumented as prey species, including copepods, fish, ctenophores, anemones, amphipods, barnacles, shrimp, polychaete worms, flukes, flatworms, echinoderms, gastropods, bivalves and hemichordates. Our results not only indicate that a ‘shotgun’ NGS approach can supplement visual identification methods, but targeted enrichment of a specific amplicon/gene is not a prerequisite for identifying Atlantic sea nettle prey items.     

The developmental biogeography of hawksbill sea turtles in the North Pacific

High seas oceanic ecosystems are considered important habitat for juvenile sea turtles, yet much remains cryptic about this important life‐history period. Recent progress on climate and fishery impacts in these so‐called lost years is promising, but the developmental biogeography of hawksbill sea turtles (Eretmochelys imbricata) has not been widely described in the Pacific Ocean. This knowledge gap limits the effectiveness of conservation management for this globally endangered species. We address this with 30 years of stranding observations, 20 years of bycatch records, and recent simulations of natal dispersal trajectories in the Hawaiian Archipelago. We synthesize the analyses of these data in the context of direct empirical observations, anecdotal sightings, and historical commercial harvests from the insular Pacific. We find hawksbills 0–4 years of age, measuring 8–34 cm straight carapace length, are found predominantly in the coastal pelagic waters of Hawaii. Unlike other species, we find no direct evidence of a prolonged presence in oceanic habitats, yet satellite tracks of passive drifters (simulating natal dispersal) and our small sample sizes suggest that an oceanic phase for hawksbills cannot be dismissed. Importantly, despite over 600 million hooks deployed and nearly 6000 turtle interactions, longline fisheries have never recorded a single hawksbill take. We address whether the patterns we observe are due to population size and gear selectivity. Although most sea turtle species demonstrate clear patterns of oceanic development, hawksbills in the North Pacific may by contrast occupy a variety of ecosystems including coastal pelagic waters and shallow reefs in remote atolls. This focuses attention on hazards in these ecosystems – entanglement and ingestion of marine debris – and perhaps away from longline bycatch and decadal climate regimes that affect sea turtle development in oceanic regions.     

Productional characteristics of redfish <Emphasis Type="Italic">Sebastes mentella</Emphasis> (Scorpaeniformes,Sebastidae) in the Barents Sea and adjacent waters

The annual production of redfish Sebastes mentella of the Norway-Barents Sea population is estimated. The main contribution to the formation of production is made by specimens of the 10–15 year age and in the period of high abundance of recruitment the main contribution is by immature specimens of the 1–8 year age. The generative production of redfish is, on average, by four times lower than the somatic production. The ratio between generative and somatic production is estimated in relation to the population structure. The value of P/B coefficient is in reverse relationship with the individual age and weight. As the part of the junior age groups in the population decreases P/B coefficient increases, and with the increase of the individual average weight in the population it decreases. The relationship between the specific rate of weight growth of redfish and the value of P/B coefficient is shown. The average value of P/B coefficient for the Norway-Barents Sea population of redfish is 0.3.     

Population structure of beaked redfish (Sebastes mentella Travin, 1951) in the Irminger Sea and adjacent waters inferred from microsatellite data

Samples of beaked redfish from the Irminger Sea and adjacent waters were examined for polymorphism at ten microsatellite loci. The strategy of the material collection enabled investigation of geographic, bathymetric, and temporal variation of this species. The results did not support the evidence on spatial differentiation and temporal stability of the species distribution, favoring the idea that the water area examined was inhabited by a single pelagic population of beaked redfish.     

Ecologal and parasitological chracteristics of redfish <Emphasis Type="Italic">Sebastes mentella</Emphasis> (Scorpaeniformes: Sebastidae) from the Norwegian Sea and adjacent waters

Special traits of ecology, zoogeography, formation of fauna of parasites, and occurrence of external lesions are investigated in redfish Sebastes mentella from the Norwegian Sea and the adjacent area of the Barents Sea. A considerable weakening of connection with bottom biocenoses in redfish in the pelagial of the Norwegian Sea indicates that it lives here for most of its annual life cycle. In redfish from south of the open part of the Norwegian Sea, there are noticeable differences in the fauna of parasites and in occurrence of external lesions from those in the fish from the north and east of this sea while traits characteristic of redfish from the Irminger Sea are present.     

Identification of a Novel 1033‐Nucleotide Deletion Polymorphism in the Prophage Region of ‘Candidatus Liberibacter asiaticus’: Potential Applications for Bacterial Epidemiology

The prophage/phage region in the genome of ‘Candidatus Liberibacter asiaticus’, an alpha‐proteobacterium associated with citrus Huanglongbing, included many valuable loci for genetic diversity studies. Previously, a mosaic genomic region (CLIBASIA_05640 to CLIBASIA_05650) was characterized, and this revealed inter‐ and intracontinental variations of ‘Ca. L. asiaticus’. In this study, 267 ‘Ca. L. asiaticus’ isolates collected from eight provinces in China were analysed with a primer set flanking the same mosaic region plus downstream sequence. While most amplicon sizes ranged from 1400 to 2000 bp, an amplicon of 550 bp (S550) was found in 14 samples collected from south‐western China. Sequence analyses showed that S550 was the result of a 1033 bp deletion which included the previously known mosaic region. The genetic nature of the deletion event remains unknown. The regional restriction of S550 suggests that the ‘Ca. L. asiaticus’ population from south‐western China is different from those in eastern China. The small and easy‐to‐detect S550 amplicon could serve as a molecular marker for ‘Ca. L. asiaticus’ epidemiology.     

Origins of the Greenland shark (Somniosus microcephalus): Impacts of ice‐olation and introgression

Herein, we use genetic data from 277 sleeper sharks to perform coalescent‐based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic‐Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub‐Arctic, and temperate Eastern Atlantic regions, suggesting introgressive hybridization upon secondary contact following the initial species divergence. Conservative substitution rates fitted to an Isolation with Migration (IM) model indicate a likely species divergence time of 2.34 Ma, using the mitochondrial sequence DNA, which in conjunction with the geographic distribution of admixtures and Pacific signatures likely indicates speciation associated with processes other than the closing of the Isthmus of Panama. This time span coincides with further planetary cooling in the early Quaternary period followed by the onset of oscillating glacial‐interglacial cycles. We propose that the initial S. microcephalus–S. pacificus split, and subsequent hybridization events, were likely associated with the onset of Pleistocene glacial oscillations, whereby fluctuating sea levels constrained connectivity among Arctic oceanic basins, Arctic marginal seas, and the North Atlantic Ocean. Our data demonstrates support for the evolutionary consequences of oscillatory vicariance via transient oceanic isolation with subsequent secondary contact associated with fluctuating sea levels throughout the Quaternary period—which may serve as a model for the origins of Arctic marine fauna on a broad taxonomic scale.