Forensic genomics as a novel tool for identifying the causes of mass mortality events

Effects of the toxic dinoflagellate Protoceratium reticulatum and its yessotoxins on the survival and feed ingestion of Argopecten purpuratus veliger larvae

The effects of yessotoxins (YTXs) produced by the dinoflagellate Protoceratium reticulatum in the early stages of bivalves have not been studied in detail. The present study evaluates the effects of P. reticulatum and YTXs on the survival and feed ingestion of veliger larvae of Argopecten purpuratus. Larvae were 96 h-exposed to 500, 1000 and 2000 P. reticulatum cells mL-1, and their equivalent YTX extract was prepared in methanol. Results show a survival mean of 82 % at the highest density of dinoflagellate, and 38 % for larvae with the highest amount of YTX extract. Feed ingestion is reduced in the dinoflagellate exposure treatments as a function of cell density. Therefore, the effect of YTXs on A. purpuratus represents a new and important area of study for investigations into the deleterious effects of these toxins in the early stages of the life cycle of this and, potentially, other bivalves.

ROS-mediated physiological activities and apoptotic effect on the survival of abalone (Haliotis discus hannai) under homoyessotoxin and ammonia stresses

Serious dinoflagellate blooms produce homoyessotoxin (homo-YTX) and ammonia (NH3-N) in eutrophic seawaters, posing threats to the healthy development of the mariculture industry. This study aimed to explore the toxicity mechanism of homo-YTX and NH3-N on the survival of abalone, which is important for the ecotoxicological research and cultivation of shellfish. The economy abalone Haliotis discus hannai was placed in homo-YTX (0, 2, 5, and 10 μg L-1) and NH3-N (0, 1.08, and 3.16 mg L-1) and a mixture of the two compounds to determine the survival rate (S), antioxidative responses, physiological activities, and apoptosis of abalone. Results show that the combination of homo-YTX and NH3-N increased the reactive oxygen species level, the malondialdehyde content, and the expression level of BCL2-associated X but decreased S; the activities of superoxide dismutase, catalase, adenosine triphosphatase, glutamic-pyruvic transaminase, xanthine oxidase, lactate dehydrogenase, and lysozyme; and the expression level of B-cell lymphoma-2. The activities of alkaline phosphatase and acid phosphatase in 10 μg L-1 of homo-YTX and 3.16 mg L-1 of NH3-N solutions and in the mixture of the two toxicants decreased. The caspase3 expression level was downregulated in 10 μg L-1 of homo-YTX. These results suggest that homo-YTX and NH3-N enhanced the oxidative stress and lipid peroxidation reactions, inhibited the energy supply, disrupted the metabolic and immune physiological functions, and activated apoptosis in the gills of abalone. ROS-mediated physiological activities and apoptosis were among the potential toxicity mechanisms of the interactive effects of homo-YTX and NH3-N on abalone.

Yessotoxins in Mollusks of the Galician Coast from 2014 to 2022: Variability, Biotransformation, and Resistance to Alkaline Hydrolysis

The presence of yessotoxins (YTXs) was analyzed in 10,757 samples of Galician bivalves from 2014 to 2022. Only YTX and 45-OH YTX were found. YTX was detected in 31% of the samples, while 45-OH YTX was found in 11.6% of them. Among the samples containing YTX, 45-OH YTX was detected in 37.3% of cases. The maximum recorded levels were 1.4 and 0.16 mg of YTX-equivalentsg-1, for YTX and 45-OH YTX, respectively, which are well below the regulatory limit of the European Union. The YTX and 45-OH YTX toxicities in the raw extracts and extracts subjected to alkaline hydrolysis were strongly and linearly related. Due to the lack of homo-YTX in Galician samples, the effect of alkaline hydrolysis on homo-YTX and 45OH-Homo-YTX was only checked in 23 additional samples, observing no negative effect but a high correlation between raw and hydrolyzed extracts. Hydrolyzed samples can be used instead of raw ones to carry out YTXs determinations in monitoring systems, which may increase the efficiency of those systems where okadaic acid episodes are very frequent and therefore a higher number of hydrolyzed samples are routinely analyzed. The presence of YTX in the studied bivalves varied with the species, with mussels and cockles having the highest percentages of YTX-detected samples. The presence of 45-OH YTX was clearly related to YTX and was detected only in mussels and cockles. Wild populations of mussels contained proportionally more 45-OH YTX than those that were raft-cultured. Spatially, toxin toxicities varied across the sampling area, with higher levels in raft-cultured mussels except those of Ría de Arousa. Ría de Ares (ARE) was the most affected geographical area, although in other northern locations, lower toxin levels were detected. Seasonally, YTX and 45-OH YTX toxicities showed similar patterns, with higher levels in late summer and autumn but lower toxicities of the 45-OH toxin in August. The relationship between the two toxins also varied seasonally, in general with a minimum proportion of 45-OH YTX in July-August but with different maximum levels for raft-cultured and wild mussel populations. Interannually, the average toxicities of YTX decreased from 2014 to 2017 and newly increased from 2018 to 2021, but decreased slightly in 2022. The relationship between 45-OH YTX and YTX also varied over the years, but neither a clear trend nor a similar trend for wild and raft mussels was observed.

Dissolved Algal Toxins along the Southern Coast of British Columbia Canada

Harmful algal blooms (HABs) in coastal British Columbia (BC), Canada, negatively impact the salmon aquaculture industry. One disease of interest to salmon aquaculture is Net Pen Liver Disease (NPLD), which induces severe liver damage and is believed to be caused by the exposure to microcystins (MCs). To address the lack of information about algal toxins in BC marine environments and the risk they pose, this study investigated the presence of MCs and other toxins at aquaculture sites. Sampling was carried out using discrete water samples and Solid Phase Adsorption Toxin Tracking (SPATT) samplers from 2017-2019. All 283 SPATT samples and all 81 water samples tested positive for MCs. Testing for okadaic acid (OA) and domoic acid (DA) occurred in 66 and 43 samples, respectively, and all samples were positive for the toxin tested. Testing for dinophysistoxin-1 (DTX-1) (20 samples), pectenotoxin-2 (PTX-2) (20 samples), and yessotoxin (YTX) (17 samples) revealed that all samples were positive for the tested toxins. This study revealed the presence of multiple co-occurring toxins in BC's coastal waters and the levels detected in this study were below the regulatory limits for health and recreational use. This study expands our limited knowledge of algal toxins in coastal BC and shows that further studies are needed to understand the risks they pose to marine fisheries and ecosystems.

Integrative monitoring strategy for marine and freshwater harmful algal blooms and toxins across the freshwater-to-marine continuum

Many coastal states throughout the USA have observed negative effects in marine and estuarine environments caused by cyanotoxins produced in inland waterbodies that were transported downstream or produced in the estuaries. Estuaries and other downstream receiving waters now face the dual risk of impacts from harmful algal blooms (HABs) that occur in the coastal ocean as well as those originating in inland watersheds. Despite this risk, most HAB monitoring efforts do not account for hydrological connections in their monitoring strategies and designs. Monitoring efforts in California have revealed the persistent detection of cyanotoxins across the freshwater-to-marine continuum. These studies underscore the importance of inland waters as conduits for the transfer of cyanotoxins to the marine environment and highlight the importance of approaches that can monitor across hydrologically connected waterbodies. A HAB monitoring strategy is presented for the freshwater-to-marine continuum to inform HAB management and mitigation efforts and address the physical and hydrologic challenges encountered when monitoring in these systems. Three main recommendations are presented based on published studies, new datasets, and existing monitoring programs. First, HAB monitoring would benefit from coordinated and cohesive efforts across hydrologically interconnected waterbodies and across organizational and political boundaries and jurisdictions. Second, a combination of sampling modalities would provide the most effective monitoring for HAB toxin dynamics and transport across hydrologically connected waterbodies, from headwater sources to downstream receiving waterbodies. Third, routine monitoring is needed for toxin mixtures at the land-sea interface including algal toxins of marine origins as well as cyanotoxins that are sourced from inland freshwater or produced in estuaries. Case studies from California are presented to illustrate the implementation of these recommendations, but these recommendations can also be applied to inland states or regions where the downstream receiving waterbody is a freshwater lake, reservoir, or river. Integr Environ Assess Manag 2023;19:586-604. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Advancing the protection of marine life through genomics

The rapid growth in genomic techniques provides the potential to transform how we protect, manage, and conserve marine life. Further, solutions to boost the resilience of marine species to climate change and other disturbances that characterize the Anthropocene require transformative approaches, made more effective if guided by genomic data. Although genetic techniques have been employed in marine conservation for decades and the availability of genomic data is rapidly expanding, widespread application still lags behind other data types. This Essay reviews how genetics and genomics have been utilized in management initiatives for ocean conservation and restoration, highlights success stories, and presents a pathway forward to enhance the uptake of genomic data for protecting our oceans.

Experimental evolution reveals the synergistic genomic mechanisms of adaptation to ocean warming and acidification in a marine copepod

Metazoan adaptation to global change relies on selection of standing genetic variation. Determining the extent to which this variation exists in natural populations, particularly for responses to simultaneous stressors, is essential to make accurate predictions for persistence in future conditions. Here, we identified the genetic variation enabling the copepod Acartia tonsa to adapt to experimental ocean warming, acidification, and combined ocean warming and acidification (OWA) over 25 generations of continual selection. Replicate populations showed a consistent polygenic response to each condition, targeting an array of adaptive mechanisms including cellular homeostasis, development, and stress response. We used a genome-wide covariance approach to partition the allelic changes into three categories: selection, drift and replicate-specific selection, and laboratory adaptation responses. The majority of allele frequency change in warming (57%) and OWA (63%) was driven by shared selection pressures across replicates, but this effect was weaker under acidification alone (20%). OWA and warming shared 37% of their response to selection but OWA and acidification shared just 1%, indicating that warming is the dominant driver of selection in OWA. Despite the dominance of warming, the interaction with acidification was still critical as the OWA selection response was highly synergistic with 47% of the allelic selection response unique from either individual treatment. These results disentangle how genomic targets of selection differ between single and multiple stressors and demonstrate the complexity that nonadditive multiple stressors will contribute to predictions of adaptation to complex environmental shifts caused by global change.

Changes in physiological activities are responsible for homoyessotoxin-induced toxicity in abalone Haliotis discus hannai

Homoyessotoxin (homo-YTX) is a lipid-soluble toxin produced by toxic dinoflagellates. It is widely distributed in marine ecosystems worldwide, and it poses a threat to the survival of aquatic animals. The tissues of the abalone Haliotis discus hannai are easily damaged by homo-YTX during harmful algal blooms. In this study, H. discus hannai was exposed to homo-YTX (0, 2, 5, and 10 µg L^-1) to evaluate the rates of survival (S) and death (D) and the antioxidative, metabolic, and digestive physiological responses in the gills and digestive gland of abalone. Homo-YTX decreased S and the activities of Na⁺/K⁺-adenosine triphosphatase, Ca²⁺/Mg²⁺-adenosine triphosphatase, superoxide dismutase, catalase, alkaline phosphatase, xanthine oxidase, lactate dehydrogenase, amylase, protease, and lipase. Meanwhile, D, the reactive oxygen species level, and the malondialdehyde content increased with increasing concentrations of homo-YTX. In addition, homo-YTX induced oxidative stress, enhanced the lipid peroxidation reaction, reduced the energy supply, and inhibited the metabolic and digestive physiological activities in the gills and digestive gland of abalone. Oxidative stress-mediated insufficient energy supply and physiological activity reduction caused the death of abalone.

Lipophilic Toxins in Chile: History, Producers and Impacts

A variety of microalgal species produce lipophilic toxins (LT) that are accumulated by filter-feeding bivalves. Their negative impacts on human health and shellfish exploitation are determined by toxic potential of the local strains and toxin biotransformations by exploited bivalve species. Chile has become, in a decade, the world's major exporter of mussels (Mytilus chilensis) and scallops (Argopecten purpuratus) and has implemented toxin testing according to importing countries' demands. Species of the Dinophysis acuminata complex and Protoceratium reticulatum are the most widespread and abundant LT producers in Chile. Dominant D. acuminata strains, notwithstanding, unlike most strains in Europe rich in okadaic acid (OA), produce only pectenotoxins, with no impact on human health. Dinophysis acuta, suspected to be the main cause of diarrhetic shellfish poisoning outbreaks, is found in the two southernmost regions of Chile, and has apparently shifted poleward. Mouse bioassay (MBA) is the official method to control shellfish safety for the national market. Positive results from mouse tests to mixtures of toxins and other compounds only toxic by intraperitoneal injection, including already deregulated toxins (PTXs), force unnecessary harvesting bans, and hinder progress in the identification of emerging toxins. Here, 50 years of LST events in Chile, and current knowledge of their sources, accumulation and effects, are reviewed. Improvements of monitoring practices are suggested, and strategies to face new challenges and answer the main questions are proposed.

An initial comparative genomic autopsy of wasting disease in sea stars

Beginning in 2013, sea stars throughout the Eastern North Pacific were decimated by wasting disease, also known as "asteroid idiopathic wasting syndrome" (AIWS) due to its elusive aetiology. The geographic extent and taxonomic scale of AIWS meant events leading up to the outbreak were heterogeneous, multifaceted, and oftentimes unobserved; progression from morbidity to death was rapid, leaving few tell-tale symptoms. Here, we take a forensic genomic approach to discover candidate genes that may help explain sea star wasting syndrome. We report the first genome and annotation for Pisaster ochraceus, along with differential gene expression (DGE) analyses in four size classes, three tissue types, and in symptomatic and asymptomatic individuals. We integrate nucleotide polymorphisms associated with survivors of the wasting disease outbreak, DGE associated with temperature treatments in P. ochraceus, and DGE associated with wasting in another asteroid Pycnopodia helianthoides. In P. ochraceus, we found DGE across all tissues, among size classes, and between asymptomatic and symptomatic individuals; the strongest wasting-associated DGE signal was in pyloric caecum. We also found previously identified outlier loci co-occur with differentially expressed genes. In cross-species comparisons of symptomatic and asymptomatic individuals, consistent responses distinguish genes associated with invertebrate innate immunity and chemical defence, consistent with context-dependent stress responses, defensive apoptosis, and tissue degradation. Our analyses thus highlight genomic constituents that may link suspected environmental drivers (elevated temperature) with intrinsic differences among individuals (age/size, alleles associated with susceptibility) that elicit organismal responses (e.g., coelomocyte proliferation) and manifest as sea star wasting mass mortality.

Standing genetic variation fuels rapid adaptation to ocean acidification

Global climate change has intensified the need to assess the capacity for natural populations to adapt to abrupt shifts in the environment. Reductions in seawater pH constitute a conspicuous global change stressor that is affecting marine ecosystems globally. Here, we quantify the phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the Mediterranean mussel, Mytilus galloprovincialis. We reared a genetically diverse larval population in two pH treatments (pH_T 8.1 and 7.4) and tracked changes in the shell-size distribution and genetic variation through settlement. Additionally, we identified differences in the signatures of selection on shell growth in each pH environment. Both phenotypic and genetic data show that standing variation can facilitate adaptation to declines in seawater pH. This work provides insight into the processes underpinning rapid evolution, and demonstrates the importance of maintaining variation within natural populations to bolster species’ adaptive capacity as global change progresses.

Reductions in seawater pH are affecting marine ecosystems globally. Here, the authors describe phenotypic and genetic modifications associated with rapid adaptation to reduced seawater pH in the mussel Mytilus galloprovincialis, and suggest that standing variation within natural populations plays an important role in bolstering species’ adaptive capacity to global change.

Trends in Dinophysis abundance and diarrhetic shellfish toxin levels in California mussels (Mytilus californianus) from Monterey Bay, California

Diarrhetic shellfish toxins (DSTs) are produced by the marine dinoflagellate, Dinophysis, as well as select species of benthic Prorocentrum. The DSTs can bioaccumulate in shellfish and cause gastrointestinal illness when humans consume high levels of this toxin. Although not routinely monitored throughout the U.S., recent studies in Washington, Texas, and New York suggest DSTs may be widespread throughout U.S. coastal waters. This study describes a four-year time series (2013-2016) of Dinophysis concentration and DST level in California mussels (Mytilus californianus) from Santa Cruz Municipal Wharf (SCMW) in Monterey Bay, California. Results show a maximum Dinophysis concentration of 9404 cells/L during this study and suggest Dinophysis persists as a member of the background phytoplankton community throughout the year. In California mussels, DSTs were found at persistent low levels throughout the course of this study, and exceeded the FDA guidance level of 160 ng/g 19 out of 192 weeks sampled. Concentrations of Dinophysis alone are a positive but weak predictor of DST level in California mussels, and basic environmental variables (temperature, salinity, and nutrients) do not sufficiently explain variation in Dinophysis concentration at SCMW. This study demonstrates that Dinophysis in Monterey Bay are producing DSTs that accumulate in local shellfish throughout the year, occasionally reaching levels of concern.

Cryptic speciation in Protoceratium reticulatum (Dinophyceae): Evidence from morphological, molecular and ecophysiological data

The cosmopolitan, potentially toxic dinoflagellate Protoceratium reticulatum possesses a fossilizable cyst stage which is an important paleoenvironmental indicator. Slight differences in the internal transcribed spacer ribosomal DNA (ITS rDNA) sequences of P. reticulatum have been reported, and both the motile stage and cyst morphology of P. reticulatum display phenotypic plasticity, but how these morpho-molecular variations are related with ecophysiological preferences is unknown. Here, 55 single cysts or cells were isolated from localities in the Northern (Arctic to subtropics) and Southern Hemispheres (Chile and New Zealand), and in total 34 strains were established. Cysts and/or cells were examined with light microscopy and/or scanning electron microscopy. Large subunit ribosomal DNA (LSU rDNA) and/or ITS rDNA sequences were obtained for all strains/isolates. All strains/isolates of P. reticulatum shared identical LSU sequences except for one strain from the Mediterranean Sea that differs in one position, however ITS rDNA sequences displayed differences at eight positions. Molecular phylogeny was inferred using maximum likelihood and Bayesian inference based on ITS rDNA sequences. The results showed that P. reticulatum comprises at least three ribotypes (designated as A, B, and C). Ribotype A included strains from the Arctic and temperate areas, ribotype B included strains from temperate regions only, and ribotype C included strains from the subtropical and temperate areas. The average ratios of process length to cyst diameter of P. reticulatum ranged from 15% in ribotype A, 22% in ribotype B and 17% in ribotype C but cyst size could overlap. Theca morphology was indistinguishable among ribotypes. The ITS-2 secondary structures of ribotype A displayed one CBC (compensatory change on two sides of a helix pairing) compared to ribotypes B and C. Growth response of one strain from each ribotype to various temperatures was examined. The strains of ribotypes A, B and C exhibited optimum growth at 15 °C, 20 °C and 20-25 °C, respectively, thus corresponding to cold, moderate and warm ecotypes. The profiles of yessotoxins (YTXs) were examined for 25 strains using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The parent compound yessotoxin (YTX) was produced by strains of ribotypes A and B, but not by ribotype C strains, which only produced the structural variant homoyessotoxin (homoYTX). Our results support the notion that there is significant intra-specific variability in Protoceratium reticulatum and the biogeography of the different ribotypes is consistent with specific ecological preferences.

Measuring viability selection from prospective cohort mortality studies: A case study in maritime pine

By changing the genetic background available for selection at subsequent life stages, stage-specific selection can define adaptive potential across the life cycle. We propose and evaluate here a neutrality test and a Bayesian method to infer stage-specific viability selection coefficients using sequential random genotypic samples drawn from a longitudinal cohort mortality study, within a generation. The approach is suitable for investigating selective mortality in large natural or experimental cohorts of any organism in which individual tagging and tracking are unfeasible. Numerical simulation results indicate that the method can discriminate loci under strong viability selection, and provided samples are large, yield accurate estimates of the corresponding selection coefficients. Genotypic frequency changes are largely driven by sampling noise under weak selection, however, compromising inference in that case. We apply the proposed methods to analyze viability selection operating at early recruitment stages in a natural maritime pine (Pinus pinaster Ait.) population. We measured temporal genotypic frequency changes at 384 candidate-gene SNP loci among seedlings sampled from the time of emergence in autumn until the summer of the following year, a period with high elimination rates. We detected five loci undergoing allele frequency changes larger than expected from stochastic mortality and sampling, with putative functions that could influence survival at early seedling stages. Our results illustrate how new statistical and sampling schemes can be used to conduct genomic scans of contemporary selection on specific life stages.

Devastating farmed abalone mortalities attributed to yessotoxin-producing dinoflagellates

A large dinoflagellate bloom in Walker Bay (South Africa) in January 2017 impacted 3 land-based abalone farms resulting in the death of several million animals. Satellite-derived images of Chl-a from the Ocean and Land Colour Imager (OLCI) on board the European Space Agency Sentinel-3 A showed bloom initiation in late December 2016 and dispersal in mid-February 2017. The bloom was dominated by two dinoflagellate species identified by light microscopy as Gonyaulax spinifera (Claparède & Lachmann) Diesing, 1866 and Lingulodinium polyedrum (Stein) Dodge, 1989. These morphologically based identifications were confirmed by phylogenetic analysis using partial sequences of the large subunit rDNA of both dinoflagellates. The appearance of yessotoxins (YTX) in abalone clearly coincided with increases in dinoflagellate concentrations. Yessotoxins in both the plankton and abalone were dominated by the two analogues homo-YTX and 45-hydroxy-YTX. The absence of toxins in a clonal culture of L. polyedrum implicated G. spinifera as the likely source of YTX. Toxin concentrations were found to be highest in the gills which showed the most significant pathology, including severe, generalized disruption of the gill epithelium characterized by degeneration and necrosis of epithelial cells accompanied by a modest inflammatory response. Some farms undertook pre-emptive or emergency harvesting to reduce financial losses.

Using photocatalyst powder to enhance the coagulation and sedimentation of cyanobacterial cells and enable the sludge to be self-purified under visible light

Removing harmful cyanobacteria intact by coagulation can prevent cell lysis and toxin release, which provides many benefits for drinking water production, including reduction of the burden on subsequent processes and guaranteeing the water quality. But the electronegativity and buoyancy of cyanobacterial cells make them settle slowly and their accumulation and concentration in flocs would still have severe adverse effects. In this study, we introduced a photocatalyst powder to act as a ballasting agent in the coagulation process and to degrade the cells and cyanotoxins during sludge storage. Results showed that adding N-TiO₂ would decrease the coagulant dose to half of the conventional value, and also allow Microcystis aeruginosa cells to completely settle within 10 min. During sludge storage, the algal cells, cyanotoxins and other organics in sludge would be degraded to safe levels after 32 h' visible-light irradiation. Meanwhile, the N-TiO₂, water and some of the coagulant in purified sludge will be directly and safely reused. Thus, this is an environmentally friendly and cost-effective technology which incorporates photocatalyst in algal flocs to enhance coagulation and sedimentation and to enable the sludge produced to be self-purified under visible-light.

Solid Phase Adsorption Toxin Tracking (SPATT) Technology for the Monitoring of Aquatic Toxins: A Review

The Solid Phase Adsorption Toxin Tracking (SPATT) technology, first introduced in 2004, uses porous synthetic resins capable of passively adsorbing toxins produced by harmful microalgae or cyanobacteria and dissolved in the water. This method allows for the detection of toxic compounds directly in the water column and offers numerous advantages over current monitoring techniques (e.g., shellfish or fish testing and microalgae/cyanobacteria cell detection), despite some limitations. Numerous laboratory and field studies, testing different adsorbent substrates of which Diaion^® HP20 resin appears to be the most versatile substrate, have been carried out worldwide to assess the applicability of these passive monitoring devices to the detection of toxins produced by a variety of marine and freshwater microorganisms. SPATT technology has been shown to provide reliable, sensitive and time-integrated sampling of various aquatic toxins, and also has the potential to provide an early warning system for both the occurrence of toxic microalgae or cyanobacteria and bioaccumulation of toxins in foodstuffs. This review describes the wide range of lipophilic and hydrophilic toxins associated with toxin-producing harmful algal blooms (HABs) that are successfully detected by SPATT devices. Implications in terms of monitoring of emerging toxic risks and reinforcement of current risk assessment programs are also discussed.

Local oceanographic variability influences the performance of juvenile abalone under climate change

Climate change is causing warming, deoxygenation, and acidification of the global ocean. However, manifestation of climate change may vary at local scales due to oceanographic conditions. Variation in stressors, such as high temperature and low oxygen, at local scales may lead to variable biological responses and spatial refuges from climate impacts. We conducted outplant experiments at two locations separated by ~2.5 km and two sites at each location separated by ~200 m in the nearshore of Isla Natividad, Mexico to assess how local ocean conditions (warming and hypoxia) may affect juvenile abalone performance. Here, we show that abalone growth and mortality mapped to variability in stress exposure across sites and locations. These insights indicate that management decisions aimed at maintaining and recovering valuable marine species in the face of climate change need to be informed by local variability in environmental conditions.

Evolution caused by extreme events

Extreme events can be a major driver of evolutionary change over geological and contemporary timescales. Outstanding examples are evolutionary diversification following mass extinctions caused by extreme volcanism or asteroid impact. The evolution of organisms in contemporary time is typically viewed as a gradual and incremental process that results from genetic change, environmental perturbation or both. However, contemporary environments occasionally experience strong perturbations such as heat waves, floods, hurricanes, droughts and pest outbreaks. These extreme events set up strong selection pressures on organisms, and are small-scale analogues of the dramatic changes documented in the fossil record. Because extreme events are rare, almost by definition, they are difficult to study. So far most attention has been given to their ecological rather than to their evolutionary consequences. We review several case studies of contemporary evolution in response to two types of extreme environmental perturbations, episodic (pulse) or prolonged (press). Evolution is most likely to occur when extreme events alter community composition. We encourage investigators to be prepared for evolutionary change in response to rare events during long-term field studies.This article is part of the themed issue 'Behavioural, ecological and evolutionary responses to extreme climatic events'.

Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection

Diseases of marine mammals can be difficult to diagnose because of their life history and protected status. Stranded marine mammals have been a particularly useful resource to discover and comprehend the diseases that plague these top predators. Additionally, advancements in high-throughput sequencing (HTS) has contributed to the discovery of novel pathogens in marine mammals. In this study, we use a combination of HTS and stranded harbor seals (Phoca vitulina) to better understand a known and unknown brain disease. To do this, we used transcriptomics to evaluate brain tissues from seven neonatal harbor seals that expired from an unknown cause of death (UCD) and compared them to four neonatal harbor seals that had confirmed phocine herpesvirus (PhV-1) infections in the brain. Comparing the two disease states we found that UCD animals showed a significant abundance of fatty acid metabolic transcripts in their brain tissue, thus we speculate that a fatty acid metabolic dysregulation contributed to the death of these animals. Furthermore, we were able to describe the response of four young harbor seals with PhV-1 infections in the brain. PhV-1 infected animals showed a significant ability to mount an innate and adaptive immune response, especially to combat viral infections. Our data also suggests that PhV-1 can hijack host pathways for DNA packaging and exocytosis. This is the first study to use transcriptomics in marine mammals to understand host and viral interactions and assess the death of stranded marine mammals with an unknown disease. Furthermore, we show the value of applying transcriptomics on stranded marine mammals for disease characterization.

Selection on oxidative phosphorylation and ribosomal structure as a multigenerational response to ocean acidification in the common copepod Pseudocalanus acuspes

Ocean acidification is expected to have dramatic impacts on oceanic ecosystems, yet surprisingly few studies currently examine long-term adaptive and plastic responses of marine invertebrates to pCO 2 stress. Here, we exposed populations of the common copepod Pseudocalanus acuspes to three pCO 2 regimes (400, 900, and 1550 μatm) for two generations, after which we conducted a reciprocal transplant experiment. A de novo transcriptome was assembled, annotated, and gene expression data revealed that genes involved in RNA transcription were strongly down-regulated in populations with long-term exposure to a high pCO 2 environment, even after transplantation back to control levels. In addition, 747 000 SNPs were identified, out of which 1513 showed consistent changes in nucleotide frequency between replicates of control and high pCO 2 populations. Functions involving RNA transcription and ribosomal function, as well as ion transport and oxidative phosphorylation, were highly overrepresented. We thus conclude that pCO 2 stress appears to impose selection in copepods on RNA synthesis and translation, possibly modulated by helicase expression. Using a physiological hypothesis-testing strategy to mine gene expression data, we herein increase the power to detect cellular targets of ocean acidification. This novel approach seems promising for future studies of effects of environmental changes in ecologically important nonmodel organisms.

Patterns of Mass Mortality among Rocky Shore Invertebrates across 100 km of Northeastern Pacific Coastline

Mass mortalities in natural populations, particularly those that leave few survivors over large spatial areas, may cause long-term ecological perturbations. Yet mass mortalities may remain undocumented or poorly described due to challenges in responding rapidly to unforeseen events, scarcity of baseline data, and difficulties in quantifying rare or patchily distributed species, especially in remote or marine systems. Better chronicling the geographic pattern and intensity of mass mortalities is especially critical in the face of global changes predicted to alter regional disturbance regimes. Here, we couple replicated post-mortality surveys with preceding long-term surveys and historical data to describe a rapid and severe mass mortality of rocky shore invertebrates along the north-central California coast of the northeastern Pacific Ocean. In late August 2011, formerly abundant intertidal populations of the purple sea urchin (Strongylocentrotus purpuratus, a well-known ecosystem engineer), and the predatory six-armed sea star (Leptasterias sp.) were functionally extirpated from ~100 km of coastline. Other invertebrates, including the gumboot chiton (Cryptochiton stelleri) the ochre sea star (Pisaster ochraceus), and subtidal populations of purple sea urchins also exhibited elevated mortality. The pattern and extent of mortality suggest the potential for long-term population, community, and ecosystem consequences, recovery from which may depend on the different dispersal abilities of the affected species.

Genome scans for the contemporary response to selection in quantitative traits

Genome scans have been an important approach for discovering historical signatures of selection in both model and nonmodel species. An exciting new experimental design for genome scans is to measure the change in allele frequency before and after contemporary selection within a generation, from a single population. The most widely-used methods, however, have two major limitations: they are based on testing one locus at a time, and they only have power to uncover loci that have evolved under relatively strong selection. On the other hand, complex quantitative traits are common in nature and are caused by several loci of small effect. Selection on a quantitative trait at the phenotypic level is predicted to be accompanied by subtle allele frequency changes in many loci that covary (a polygenic soft sweep), rather than a large, single-effect allele (a selective sweep). In this issue of Molecular Ecology, Bourret et al. (2014) measure the contemporary response to natural selection across the genome in multiple cohorts of Atlantic salmon during their first year at sea. They introduce a multilocus framework based on groups of markers that covary in their genotypic distribution. While the traditional, single-locus approach did not find evidence for repeated patterns of selection, the multivariate approach found that a group of covarying SNPs was selected for in different cohorts at one site. Their multilocus framework has potential to be a more fruitful approach for uncovering the genomic basis of adaptation in quantitative traits, although caution should be applied as the framework has yet to be validated with simulated data.