Unidirectional trans-Atlantic gene flow and a mixed spawning area shape the genetic connectivity of Atlantic bluefin tuna.

The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.

Acid treatment of Atlantic salmon (Salmo salar) scales prior to analysis has negligible effects on δ13C and δ15N isotope ratios.

There is debate in the literature as to whether scales of fishes require acidification to remove inorganic carbonates prior to stable isotope analysis. Acid-treated and untreated scales from 208 Atlantic salmon from nine locations on both sides of the Atlantic were analysed for δ13C and δ15N. Linear mixed-effect models determined the effect of acid treatment to be statistically significant. However, the mean difference was small (δ13C 0.1 ± 0.2‰, δ15N -0.1 ± 0.2‰) and not of biological relevance. This study concludes that Atlantic salmon scales do not need to be acidified prior to stable isotope analysis.

Experimental investigation of the effects of temperature and feeding regime on scale growth in Atlantic salmon Salmo salar post-smolts.

Salmo salar post-smolts were reared in seawater under controlled laboratory conditions for 12 weeks. The fish were exposed to three constant temperature treatments (15, 10.5 and 6°C) and four feeding treatments (constant feeding, food withheld for 7 days, food withheld for 14 days and food withheld intermittently for four periods of 7 days). Scale growth was proportional to fish growth across all treatments, justifying the use of scale measurements as a proxy for growth during the early marine phase. The rate of circuli deposition was dependant on temperature and feeding regime and was generally proportional to fish growth but with some decoupling of the relationship at 15°C. Deposition rates varied from 4.8 days per circulus at 15°C (constant feeding) to 15.1 days per circulus at 6°C (interrupted feeding). Cumulative degree day (° D) was a better predictor of circuli number than age, although the rate of circuli deposition ° D-1 was significantly lower at 6°C compared with 15 and 10.5°C. Inter-circuli distances were highly variable and did not reflect growth rate; tightly packed circuli occurred during periods without food when growth was depressed, but also during periods of rapid growth at 15°C. The results further current understanding of scale growth properties and can inform investigations of declining marine growth in S. salar based on interpretations of scale growth patterns.

Evidence of a range expansion in sunfish from 47 years of coastal sightings.

Almost nothing is known about the historical abundance of the ocean sunfish. Yet as an ecologically and functionally important taxa, understanding changes in abundance may be a useful indicator of how our seas are responding to anthropogenic changes including overfishing and climate change. Within this context, sightings from a coastal bird observatory (51.26 ∘ N, 9.30 ∘ W) over a 47 year period (from April to October 1971-2017) provided the first long-term index of sunfish abundance. Using a general linear mixed effect model with a hurdle to deal with imperfect detectability and to model trends, a higher probability of detecting sunfish was found in the 1990s and 2000s. Continuous Plankton Recorder (CPR) phytoplankton color indices and the annual mean position of the 13  ∘ C sea surface isotherm were significantly correlated with the probability of detecting sunfish. An increase in siphonophore abundance (as measured by the CPR) was also documented. However, this increase occurred 10-15 years after the sunfish increase and was not significantly correlated with sunfish abundance. Our results suggest that the observed increase in sunfish sightings is evidence of a range expansion because it was significantly correlated with the mean position of the 13 ∘ C isotherm which moved northwards by over 200 km. Furthermore, the observed increase in sunfish occured  10 years before sunfish sightings are documented in Icelandic and Norwegian waters, and was concurrent with well-known range expansions for other fish species during the 1990s. This study demonstrates how sustained citizen science projects can provide unique insights on the historical abundance of this enigmatic species. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00227-021-04005-8.

Combining genetic markers with stable isotopes in otoliths reveals complexity in the stock structure of Atlantic bluefin tuna (Thunnus thynnus).

Atlantic bluefin tuna (Thunnus thynnus) from the two main spawning populations in the Mediterranean and Gulf of Mexico occur together in the western, central and eastern Atlantic. Stock composition of catches from mixing areas is uncertain, presenting a major challenge to the sustainable management of the fisheries. This study combines genetic and chemical markers to develop an integrated method of population assignment. Stable isotope signatures (δ13C and δ18O) in the otolith core of adults from the two main spawning populations (adult baselines) showed less overlap than those of yearlings (12-18 months old) from western and eastern nursery areas suggesting that some exchange occurs towards the end of the yearling phase. The integrated model combined δ18O with four genetic markers (SNPs) to distinguish the adult baselines with greater accuracy than chemical or genetic markers alone. When used to assign individuals from the mixing areas to their population of origin, the integrated model resolved some (but not all) discrepancies between the chemistry and genetic methods. Some individuals in the mixing area had otolith δ18O values and genetic profiles which when taken together, were not representative of either population. These fish may originate from another Atlantic spawning area or may represent population contingents that move away from the main spawning areas during the first year of life. This complexity in stock structure is not captured by the current two-stock model.

Trace element fingerprinting of blue mussel (Mytilus edulis) shells and soft tissues successfully reveals harvesting locations.

Globally, aquaculture products are expected to account for >60% of total seafood produce by 2030. In the European Union, the seafood sector is of considerable economic importance to member states with household spending on seafood produce totalling €54.8 billion in 2016. Within the EU, shellfish aquaculture supports livelihoods and employment in many rural communities throughout the region. Harmful algal blooms pose considerable risk to consumer safety and in turn, stability of the shellfish market. If contaminated produce was to make it to the market the health risk to the public could be considerable, but the damage to the sector through loss of trust in producers would also be significant. Mytilus edulis account for a considerable portion of the aquaculture sector in the Northeast Atlantic. At present, no scientific tool is available to industry regulators, to allow them to trace mussel produce to its source, uphold food safety standards and ensure consumer confidence. The present study uses chemical analysis of shells and soft tissues to classify individual M. edulis to their site of harvest. The use of random forest classification of trace element composition has revealed location specific elemental signatures for all examined sites. This led to the correct classification of 100% of individuals sampled to their respective harvesting locations, including two sites located just 6 km apart within the same bay. The protocol demonstrated here provides the basis for a scientifically driven traceability framework for shellfish produce.

Correction: Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning.

[This corrects the article DOI: 10.1371/journal.pone.0188955.].

Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning.

BOOSTED REGRESSION TREES. EXCELLENT FOR DATA-POOR SPATIAL MANAGEMENT BUT HARD TO USE: Marine resource managers and scientists often advocate spatial approaches to manage data-poor species. Existing spatial prediction and management techniques are either insufficiently robust, struggle with sparse input data, or make suboptimal use of multiple explanatory variables. Boosted Regression Trees feature excellent performance and are well suited to modelling the distribution of data-limited species, but are extremely complicated and time-consuming to learn and use, hindering access for a wide potential user base and therefore limiting uptake and usage. BRTS AUTOMATED AND SIMPLIFIED FOR ACCESSIBLE GENERAL USE WITH RICH FEATURE SET: We have built a software suite in R which integrates pre-existing functions with new tailor-made functions to automate the processing and predictive mapping of species abundance data: by automating and greatly simplifying Boosted Regression Tree spatial modelling, the gbm.auto R package suite makes this powerful statistical modelling technique more accessible to potential users in the ecological and modelling communities. The package and its documentation allow the user to generate maps of predicted abundance, visualise the representativeness of those abundance maps and to plot the relative influence of explanatory variables and their relationship to the response variables. Databases of the processed model objects and a report explaining all the steps taken within the model are also generated. The package includes a previously unavailable Decision Support Tool which combines estimated escapement biomass (the percentage of an exploited population which must be retained each year to conserve it) with the predicted abundance maps to generate maps showing the location and size of habitat that should be protected to conserve the target stocks (candidate MPAs), based on stakeholder priorities, such as the minimisation of fishing effort displacement. GBM.AUTO FOR MANAGEMENT IN VARIOUS SETTINGS: By bridging the gap between advanced statistical methods for species distribution modelling and conservation science, management and policy, these tools can allow improved spatial abundance predictions, and therefore better management, decision-making, and conservation. Although this package was built to support spatial management of a data-limited marine elasmobranch fishery, it should be equally applicable to spatial abundance modelling, area protection, and stakeholder engagement in various scenarios.