Predicting the future of our oceans-Evaluating genomic forecasting approaches in marine species

Climate change is restructuring biodiversity on multiple scales and there is a pressing need to understand the downstream ecological and genomic consequences of this change. Recent advancements in the field of eco-evolutionary genomics have sought to include evolutionary processes in forecasting species' responses to climate change (e.g., genomic offset), but to date, much of this work has focused on terrestrial species. Coastal and offshore species, and the fisheries they support, may be even more vulnerable to climate change than their terrestrial counterparts, warranting a critical appraisal of these approaches in marine systems. First, we synthesize knowledge about the genomic basis of adaptation in marine species, and then we discuss the few examples where genomic forecasting has been applied in marine systems. Next, we identify the key challenges in validating genomic offset estimates in marine species, and we advocate for the inclusion of historical sampling data and hindcasting in the validation phase. Lastly, we describe a workflow to guide marine managers in incorporating these predictions into the decision-making process.

The use of the IAEA MARIS database in determining the variability of sediment distribution coefficients in the marine environment and potential implications for marine dispersion modelling

A prototype tool has been developed for deriving sediment distribution coefficients,K_d, in the marine environment by harvesting simultaneous measurements of activity concentrations of radionuclides in seawater and sediments based on the International Atomic Energy Agency's Marine Radioactivity Information System (MARIS). As a case study, theK_dvariability in the Baltic Sea was investigated as this region has been extensively monitored by HELCOM since 1984 resulting in a comprehensive dataset with good spatial and temporal coverage and required ancillary parameters. The prototype tool was used to derive a dataset ofin-situapparentK_d(a)values derived from measurements of seawater and sediment in quasi-equilibrium conditions from the Baltic Sea over a period of approximately 35 years. For Cs, a comprehensive analysis of the Baltic SeaK_d(a)dataset was undertaken, focusing on the temporal trend ofK_d(a)and comparing the results toK_dvalues derived elsewhere. For Sr and Pu, for which there were fewer data records available a more rudimentary analysis was carried out. The CsK_d(a)median values derived from¹³⁷Cs data in this study were estimated to be 2154 l kg^-1for seabed sediment and 10 000 l kg^-1for suspended sediment. The value derived for seabed sediment is in good agreement with the previously recommended ocean margin CsK_dvalue of 4000 l kg^-1. The analysis demonstrated the important distinction in the Baltic Sea betweenK_dvalues for seabed sediment and suspended sediments, which differed by an order of magnitude. The analysis also highlighted the dependence ofK_dvalues on the variation in both the salinity of seawater and the type of seabed sediment. Such variability can significantly influence outcomes when modelling the behaviour of radionuclides in marine dispersion modelling.

Scavenging of select radionuclides and trace elements by pelagic Sargassum in the Caribbean Sea

In recent years, the North Atlantic and the Caribbean Sea have experienced unusual and unprecedented pelagic Sargassum blooms, which may adversely affect coastal ecosystems and productive ocean. Sargassum has the potential to scavenge trace elements and radionuclides from seawater, and when bioaccumulated and thus concentrated, can pose a potential threat to higher trophic organisms, including humans that consume impacted seafood. In this study, trace elements and naturally-occurring U/Th-series radionuclides were measured in Sargassum that were collected in the coastal waters of the Caribbean Sea (Antigua/Barbuda, Belize, and Barbados) to better define baseline concentrations and activities, and to assess the scavenging potential for these trace elements and radionuclides. The mean concentration of trace elements observed in Sargassum collected across these three Caribbean Sea are ranked accordingly to the following descending order: Sr > As>Fe > Mn > Zn > Ni > V > C > Cd > Se > Co > Cr > Pb > Ag > Hg. 210-Po and 210Pb activities in Sargassum were observed to be more elevated than previously reported values.

Isotopic signatures of plutonium and uranium at Bikar atoll, northern Marshall Islands

We present plutonium (Pu) and uranium (U) isotopic fingerprints (or signatures) in environmental samples collected at Bikar Atoll. Bikar is the second -most northern atoll of the Republic of the Marshall Islands, and therefore an important reference point to evaluate the extension of the regional fallout from the Pacific Proving Grounds (PPG) in Bikini and Enewetak Atolls. Previous studies have shown that regional fallout from atmospheric nuclear weapon testing (NWT) in Bikini and Enewetak has resulted in elevated levels of fallout radionuclides in this atoll. In order to optimally interpret the isotopic fingerprints, we compare our results with data obtained in eleven certified reference materials, representing different contamination sources. As well as ²³⁸Pu, ²³⁹Pu, ²⁴⁰Pu, ²⁴¹Pu, ²³⁸U and ²³⁵U, this study also encompasses less commonly reported radionuclides such as ²⁴²Pu, ²⁴⁴Pu and ²³⁶U. We show the importance of combining numerous fingerprints for improved assessment of the source of a nuclear contamination. In samples from Bikar, Pu and U isotope ratios were found to vary within narrow ranges. Pu and U fingerprints suggest that regional fallout from the Castle Bravo test in March 1954 was the main source of the contamination. This was further confirmed by two different age dating approaches that estimated 1954 as the year of the contamination. We demonstrate that use of an exponential function to approximate the yield of heavy radionuclides in thermonuclear explosions with increasing mass is a valid approach for estimating the age of a contamination. We show that, if sufficient radionuclide activity concentration measurement results with low uncertainties are available, this method is robust.

Fate of anthropogenic radionuclides (90Sr, 137Cs, 238Pu, 239Pu, 240Pu, 241Am) in seawater in the northern Benguela upwelling system off Namibia

A baseline study on anthropogenic radioactivity in the Namibian marine ecosystem, which is part of the northern Benguela upwelling system, known as one of the most productive ocean areas in the world, has been performed. A scientific cruise carried out in 2014 covering inshore and offshore areas, exhibiting different oceanographic features, has provided a basis for better understanding the distributions, ratios and inventories of six anthropogenic radionuclides (⁹⁰Sr, ¹³⁷Cs, ²³⁸Pu, ²³⁹Pu, ²⁴⁰Pu and ²⁴¹Am) in seawater. Although ³H was also measured, due to extremely low levels, its behaviour was not studied. The main source of ⁹⁰Sr, ¹³⁷Cs, ²³⁹Pu, ²⁴⁰Pu and ²⁴¹Am in the samples analysed was proven to be global fallout, a finding further confirmed by ²⁴⁰Pu/²³⁹Pu and ⁹⁰Sr/¹³⁷Cs ratios. Furthermore, the ²³⁸Pu SNAP-9A satellite accident signal was confirmed once again through the determination of the ²³⁸Pu/^239+240Pu activity ratio. Inshore and offshore samples showed different patterns due to the unique oceanographic features of this upwelling system. The levels of anthropogenic radionuclides, comprehensively assessed for the first time in this region, are comparable with the few existing data and filled a critical gap for the Southern Atlantic Ocean.

Assessment of residual radionuclide levels at the Bokak and Bikar Atolls in the northern Marshall Islands

The Bikar and Bokak Atolls, located in the northern Marshall Islands, are extremely isolated and consist of pristine marine and terrestrial ecosystems. Both atolls may have experienced significant radioactive deposition following the nuclear weapon testing conducted at Bikini and Enewetak proving grounds. Here we report activity concentrations of artificial radionuclides (²³⁹Pu, ²⁴⁰Pu, ²⁴¹Pu, ²⁴¹Am, ¹³⁷Cs and ⁹⁰Sr) in marine and terrestrial samples collected from Bikar and Bokak Atolls. Artificial radionuclides in soil from the Majuro Atoll are also reported and form a radiological baseline against which the levels at the other atolls can be compared. We observed low levels of artificial radionuclides in soil from Majuro and Bokak, but significantly higher levels in soil from Bikar. The residual radioactivity in the Bikar environment is comparable to the levels previously reported for other nearby atolls, including Taka and Utrik, but lower than for Rongerik, Rongelap, Bikini and Enewetak. An analysis of ²⁴⁰Pu/²³⁹Pu isotope ratios and estimations of the dates of contamination from ²⁴¹Am/²⁴¹Pu activity ratios both indicated that the Bikar Atoll was contaminated mainly by radioactive fallout from the Castle Bravo test in 1954. We compare the results of our measurements at Bikar and Bokak to data from other atolls in the Marshall Islands and to regions of the world affected by both global and regional fallout from atmospheric nuclear weapons testing and nuclear accidents.

From radiometry to chronology of a marine sediment core: A 210Pb dating interlaboratory comparison exercise organised by the IAEA

Laboratories from 14 countries (with different levels of expertise in radionuclide measurements and ²¹⁰Pb dating) participated in an interlaboratory comparison exercise (ILC) related to the application of ²¹⁰Pb sediment dating technique within the framework of the IAEA Coordinated Research Project. The laboratories were provided with samples from a composite sediment core and were required to provide massic activities of several radionuclides and an age versus depth model from the obtained results, using the most suitable ²¹⁰Pb dating model. Massic concentrations of Zn and Cu were also determined to be used for chronology validation. The ILC results indicated good analytical performances while the dating results didn't demonstrate the same degree of competence in part due to the different experience in dating of the participant laboratories. The ILC exercise enabled evaluation of the difficulties faced by laboratories implementing ²¹⁰Pb dating methods and identified some limitations in providing reliable chronologies.

Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar

In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered.IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.

Clinical management practices of life-threatening asthma: an audit of practices in intensive care

OBJECTIVE

Lack of management guidelines for lifethreatening asthma (LTA) risks practice variation. This study aims to elucidate management practices of LTA in the intensive care unit (ICU).

DESIGN

A retrospective cohort study.

SETTING

Thirteen participating ICUs in Australia between July 2010 and June 2013.

PARTICIPANTS

Patients with the principal diagnosis of LTA.

MAIN OUTCOME MEASURES

Clinical history, ICU management, patient outcomes, ward education and discharge plans.

RESULTS

Of the 270 (267 patients) ICU admissions, 69% were female, with a median age of 39 years (interquartile range [IQR], 26-53 years); 119 (44%) were current smokers; 89 patients (33%) previously required ICU admission, of whom 23 (25%) were intubated. The median ICU stay was 2 days (IQR, 2-4 days). Three patients (1%) died. Seventy-nine patients (29%) received non-invasive ventilation, with 11 (14%) needing subsequent invasive ventilation. Sixty-eight patients (25%) were intubated, with the majority of patients receiving volume cycled synchronised intermittent mechanical ventilation (n = 63; 93%). Drugs used included ß2-agonist by intravenous infusion (n = 69; 26%), inhaled adrenaline (n = 15; 6%) or an adrenaline intravenous infusion (n = 23; 9%), inhaled anticholinergics (n = 238; 90%), systemic corticosteroids (n = 232; 88%), antibiotics (n = 126; 48%) and antivirals (n = 22; 8%). When suitable, 105 patients (n = 200; 53%) had an asthma management plan and 122 (n = 202; 60%) had asthma education upon hospital discharge. Myopathy was associated with hyperglycaemia requiring treatment (odds ratio [OR], 31.6; 95% CI, 2.1-474). Asthma education was more common under specialist thoracic medicine care (OR, 3.0; 95% CI, 1.61-5.54).

CONCLUSION

In LTA, practice variation is common, with opportunities to improve discharge management plans and asthma education.

The novel use of pop-off satellite tags (PSATs) to investigate the migratory behaviour of European sea bass Dicentrarchus labrax

A total of 12 adult European sea bass Dicentrarchus labrax were tagged with pop-off satellite archival tags (PSAT) in Irish coastal waters and in offshore waters in the north-east Celtic Sea between 2015 and 2016. Archived data were successfully recovered from five of the 12 tags deployed, three from fish released in inshore Irish waters and two from fish released offshore in the eastern Celtic Sea. All three fish tagged in inshore waters were found to undertake migrations into the open ocean coinciding with the spawning period. These fish also exhibited fidelity to inshore sites post-migration, returning to the same general location (within c. 73 km, which is roughly the predicted mean accuracy of the method) of their original release site. Although the number of tracks obtained here was limited, some degree of aggregation between inshore and offshore tagged fish in the eastern Celtic Sea was noted during the expected spawning period suggesting PSATs can provide new information on specific spawning locations of European sea bass.

Recent evolution of 129I levels in the Nordic Seas and the North Atlantic Ocean

Most of the anthropogenic radionuclide ¹²⁹I released to the marine environment from the nuclear fuel reprocessing plants (NFRP) at Sellafield (England) and La Hague (France) is transported to the Arctic Ocean via the North Atlantic Current and the Norwegian Coastal Current. ¹²⁹I concentrations in seawater provides a powerful and well-established radiotracer technique to provide information about the mechanisms which govern water mass transport in the Nordic Seas and the Arctic Ocean and is gaining importance when coupled with other tracers (e.g. CFC, ²³⁶U). In this work, ¹²⁹I concentrations in surface and depth profiles from the Nordic Seas and the North Atlantic (NA) Ocean collected from four different cruises between 2011 and 2012 are presented. This work allowed us to i) update information on ¹²⁹I concentrations in these areas, required for the accurate use of ¹²⁹I as a tracer of water masses; and ii) investigate the formation of deep water currents in the eastern part of the Nordic Seas, by the analysis of ¹²⁹I concentrations and temperature-salinity (T-S) diagrams from locations within the Greenland Sea Gyre. In the Nordic Seas, ¹²⁹I concentrations in seawater are of the order of 10⁹ at·kg^-1, one or two orders of magnitude higher than those measured at the NA Ocean, not so importantly affected by the releases from the NFRP. ¹²⁹I concentrations of the order of 10⁸atoms·kg^-1 at the Ellet Line and the PAP suggest a direct contribution from the NFRP in the NA Ocean. An increase in the concentrations in the Nordic Seas between 2002 and 2012 has been detected, which agrees with the temporal evolution of the ¹²⁹I liquid discharges from the NFRPs in years prior to this. Finally, ¹²⁹I profile concentrations, ¹²⁹I inventories and T-S diagrams suggest that deep water formation occurred in the easternmost area of the Nordic Seas during 2012.

Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach

Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland, Scotland and Northern Norway. Only weak global structure was observed based on the full SNP dataset. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.

Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment

Farmed fish are typically genetically different from wild conspecifics. Escapees from fish farms may contribute one-way gene flow from farm to wild gene pools, which can depress population productivity, dilute local adaptations and disrupt coadapted gene complexes. Here, we reanalyse data from two experiments (McGinnity et al., 1997, 2003) where performance of Atlantic salmon (Salmo salar) progeny originating from experimental crosses between farm and wild parents (in three different cohorts) were measured in a natural stream under common garden conditions. Previous published analyses focussed on group-level differences but did not account for pedigree structure, as we do here using modern mixed-effect models. Offspring with one or two farm parents exhibited poorer survival in their first and second year of life compared with those with two wild parents and these group-level inferences were robust to excluding outlier families. Variation in performance among farm, hybrid and wild families was generally similar in magnitude. Farm offspring were generally larger at all life stages examined than wild offspring, but the differences were moderate (5-20%) and similar in magnitude in the wild versus hatchery environments. Quantitative genetic analyses conducted using a Bayesian framework revealed moderate heritability in juvenile fork length and mass and positive genetic correlations (>0.85) between these morphological traits. Our study confirms (using more rigorous statistical techniques) previous studies showing that offspring of wild fish invariably have higher fitness and contributes fresh insights into family-level variation in performance of farm, wild and hybrid Atlantic salmon families in the wild. It also adds to a small, but growing, number of studies that estimate key evolutionary parameters in wild salmonid populations. Such information is vital in modelling the impacts of introgression by escaped farm salmon.

Beaufort trout MicroPlex: a high-throughput multiplex platform comprising 38 informative microsatellite loci for use in resident and anadromous (sea trout) brown trout Salmo trutta genetic studies

A flexible panel consisting of 38 informative microsatellite markers for Salmo trutta is described. These markers were selected from a pool of over 150 candidate loci that can be readily amplified in four multiplex PCR groups but other permutations are also possible. The basic properties of each markers were assessed in six population samples from both the Burrishoole catchment, in the west of Ireland, and Lough Neagh, in Northern Ireland. A method to assess the relative utility of individual markers for the detection of population genetic structuring is also described. Given its flexibility, technical reliability and high degree of informativeness, the use of this panel of markers is advocated as a standard for S. trutta genetic studies.

An analysis of genetic stock identification on a small geographical scale using microsatellite markers, and its application in the management of a mixed-stock fishery for Atlantic salmon Salmo salar in Ireland

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed-stock fishery to an almost exclusively single-stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.

Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua

By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and >6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

Balancing selection on MHC class I in wild brown trout Salmo trutta

Evidence is reported for balancing selection acting on variation at major histocompatibility complex (MHC) in wild populations of brown trout Salmo trutta. First, variation at an MHC class I (satr-uba)-linked microsatellite locus (mhc1) is retained in small S. trutta populations isolated above waterfalls although variation is lost at neutral microsatellite markers. Second, populations across several catchments are less differentiated at mhc1 than at neutral markers, as predicted by theory. The population structure of these fish was also elucidated.

MHC-mediated spatial distribution in brown trout (Salmo trutta) fry

Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited dispersal from the nest (redd effect) would predict that all such pairs would have a similar distribution. However, this study demonstrates a strong, significant trend for reduced distance between pairs of full-sibling fry sharing more MHC class I alleles reflecting their closer aggregation (no alleles shared, 311.5 ± (s.e.)21.03 m; one allele shared, 222.2 ± 14.49 m; two alleles shared, 124.9 ± 23.88 m; P<0.0001). A significant trend for closer aggregation among fry sharing more MHC class I alleles was also observed in fry pairs, which were known to have different mothers and were otherwise unrelated (ML-r = 0) (no alleles: 457.6 ± 3.58 m; one allele (422.4 ± 3.86 m); two alleles (381.7 ± 10.72 m); P<0.0001). These pairs are expected to have emerged from different redds and a passive association would then be unlikely. These data suggest that sharing MHC class I alleles has a role in maintaining kin association among full-siblings after emergence. This study demonstrates a pattern consistent with MHC-mediated kin association in the wild for the first time.

Variation in Lyman-alpha fine structure components for Cl XVII during a tokamak plasma shot

In this Brief Report we study the measured and modeled Lyman-alpha intensity ratios for hydrogenlike Cl XVII in a deuterium base plasma in the Joint European Torus tokamak and examine the agreement between experiment and theory for a particular plasma shot. A collisional-radiative model is used to calculate the values of the intensity ratios using measured plasma parameters for comparison with line-of-sight values. When variations in the electron parameters during the discharge are taken into account, the variations in the modeled values are seen to follow the experimental data. The difference between the values of observed and modeled intensity ratios is discussed.