Characteristics of the spiny dogfish (Squalus acanthias) nuclear genome.

Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated.

A holistic and comprehensive data approach validates the distribution of the critically endangered flapper skate (Dipturus intermedius).

Morphological similarities between skates of the genus Dipturus in the north-eastern Atlantic and Mediterranean have resulted in longstanding confusion, misidentification and misreporting. Current evidence indicates that the common skate is best explained as two species, the flapper skate (Dipturus intermedius) and the common blue skate (D. batis). However, some management and conservation initiatives developed prior to the separation continue to refer to common skate (as 'D. batis'). This taxonomic uncertainty can lead to errors in estimating population viability, distribution range, and impact on fisheries management and conservation status. Here, we demonstrate how a concerted taxonomic approach, using molecular data and a combination of survey, angler and fisheries data, in addition to expert witness statements, can be used to build a higher resolution picture of the current distribution of D. intermedius. Collated data indicate that flapper skate has a more constrained distribution compared to the perceived distribution of the 'common skate', with most observations recorded from Norway and the western and northern seaboards of Ireland and Scotland, with occasional specimens from Portugal and the Azores. Overall, the revised spatial distribution of D. intermedius has significantly reduced the extant range of the species, indicating a possibly fragmented distribution range.

Benthic animal-borne sensors and citizen science combine to validate ocean modelling.

Developments in animal electronic tagging and tracking have transformed the field of movement ecology, but interest is also growing in the contributions of tagged animals to oceanography. Animal-borne sensors can address data gaps, improve ocean model skill and support model validation, but previous studies in this area have focused almost exclusively on satellite-telemetered seabirds and seals. Here, for the first time, we develop the use of benthic species as animal oceanographers by combining archival (depth and temperature) data from animal-borne tags, passive acoustic telemetry and citizen-science mark-recapture records from 2016-17 for the Critically Endangered flapper skate (Dipturus intermedius) in Scotland. By comparing temperature observations to predictions from the West Scotland Coastal Ocean Modelling System, we quantify model skill and empirically validate an independent model update. The results from bottom-temperature and temperature-depth profile validation (5,324 observations) fill a key data gap in Scotland. For predictions in 2016, we identified a consistent warm bias (mean = 0.53 °C) but a subsequent model update reduced bias by an estimated 109% and improved model skill. This study uniquely demonstrates the use of benthic animal-borne sensors and citizen-science data for ocean model validation, broadening the range of animal oceanographers in aquatic environments.

Extensive oceanic mesopelagic habitat use of a migratory continental shark species.

The identification of movement and behaviour patterns, as well as inter- and intra-population connectivity is crucial in order to implement effective and functional management and conservation measures for threatened migratory species such as tope (Galeorhinus galeus). Yet, previous studies struggled to elucidate clear and consistent movement and depth usage patterns of adult tope in the Northeast Atlantic, suggesting a high plasticity in the migration and behaviour. We deployed pop-up satellite archival tags on adult tope during their seasonal summer aggregations in the inner German Bight of the south-eastern North Sea and near a presumed mating site in southwest Scotland. Depth distribution and migration pathways were derived from time series data with location processing. Four individuals followed migration trajectories leaving coastal areas and crossed the European shelf slope into oceanic areas of the Northeast Atlantic, remaining fully pelagic for the rest of the deployment duration. These sharks showed far-ranging migration trajectories and undertook regular and frequent diel vertical migrations, reaching daytime depths of over 700 m. Vertical migration patterns closely overlapped with biological mesopelagic habitat structures and closely tracked the diel migration of organisms from deep scattering layers derived from hydroacoustic recordings. It is hypothesized that adult tope regularly utilize oceanic habitats, foraging on mesopelagic layers in an environment generally considered of low prey density.

First confirmed complete incubation of a flapper skate (Dipturus intermedius) egg in captivity.

An egg of the critically endangered flapper skate Dipturus intermedius was successfully incubated to hatching in captivity in what is believed to be a first for the species. Water conditions (temperature, salinity, flow rate) were recorded, with mean water temperatures ranging from a monthly mean of 8.3 ± 1.2 to 13.2 ± 0.3°C and salinity from a monthly mean of 30.5 ± 1.2 to 36.6 ± 2.3 ppt. Hatching occurred after 534 days, suggesting that flapper skate eggs take c. 5700 growing degree-days to incubate to hatching. The egg's prolonged embryonic development raises concerns about flapper skate eggs' vulnerability to anthropogenic disturbance.

Evidence of egg-laying grounds for critically endangered flapper skate (Dipturus intermedius) off Orkney, UK.

Essential fish habitats (EFHs) are critical for fish life-history events, including spawning, breeding, feeding or growth. This study provides evidence of EFHs for the critically endangered flapper skate (Dipturus intermedius) in the waters around the Orkney Isles, Scotland, based on citizen-science observation data. The habitats of potential egg-laying sites were parametrised as >20 m depth, with boulders or exposed bedrock, in moderate current flow (0.3-2.8 knots) with low sedimentation. This information provides a significant contribution to the understanding of EFHs for flapper skate.

Melanin-concentrating hormone receptor 1 polymorphisms are associated with components of energy balance in the Complex Diseases in the Newfoundland Population: Environment and Genetics (CODING) study.

BACKGROUND: The melanin-concentrating hormone receptor 1 (MCHR1) is a G protein-coupled receptor that regulates energy balance and body composition in animal models. Inconsistent effects of MCHR1 polymorphisms on energy homeostasis in humans may partly be attributable to environmental factors. OBJECTIVES: We examined the effect of 4 single nucleotide polymorphisms (rs133073, rs133074, rs9611386, and rs882111) in the MCHR1 gene on body composition as well as energy-related lifestyle factors (diet and physical activity). We also examined the effect of gene-lifestyle interactions on body composition. DESIGN: A total of 1153 participants (248 men and 905 women) from the cross-sectional Complex Diseases in the Newfoundland Population: Environment and Genetics (CODING) study were genotyped by using probe-based chemistry validated assays. Diet and physical activity were estimated by using validated frequency questionnaires, and body composition was assessed by using dual-energy X-ray absorptiometry. RESULTS: Three polymorphisms (rs9611386, rs882111, and rs133073) were associated with differences in body-composition measurements (all P < 0.05). There was an interaction between rs9611386 and carbohydrate intake on total mass and waist circumference (both P ≤ 0.01). There was also an interaction between rs9611386 and body mass index categories (normal weight, overweight, and obese) on energy intakes (P = 0.02). A similar interaction was shown with rs882111 (P = 0.02). Interactions were also observed between each of these polymorphisms (rs9611386, rs882111, and rs133073) and physical activity score on body-composition measurements (all P < 0.05). CONCLUSION: These findings suggest that polymorphisms in the MCHR1 gene are associated with differences in body composition and interact with physiologic and energy-related lifestyle factors.

Marital status and the risk of suicide: experience from England and Wales, 1982-1996.

This analysis examined suicide rates by age, sex, and marital status in England and Wales for the period 1982-1996. Never married, widowed, and divorced people had higher rates of suicide than those who were married, for both sexes. Among the widowed ages 20-39 years, both sexes had the highest rate, and the rate decreased with age. The suicide rate for divorced people was similar to those who had never married, except for the younger group ages 20-29 years. The male:female ratios for the relative suicide risk for never married, widowed, and divorced to married for both sexes were statistically significantly different for older adults. The decrease in suicide rates observed for the period 1982-1996 in England and Wales was mainly attributable to the reduction of suicide rates among the widowed and divorced.