NOAA National Marine Fisheries Service Northeast Fisheries Science Center

Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Identifying causal networks is important for effective policy and management recommendations on climate, epidemiology, financial regulation, and much else. We introduce a method, based on nonlinear state space reconstruction, that can distinguish causality from correlation. It extends to nonseparable weakly connected dynamic systems (cases not covered by the current Granger causality paradigm). The approach is illustrated both by simple models (where, in contrast to the real world, we know the underlying equations/relations and so can check the validity of our method) and by application to real ecological systems, including the controversial sardine-anchovy-temperature problem.

After a long history of overexploitation, increasing efforts to restore marine ecosystems and rebuild fisheries are under way. Here, we analyze current trends from a fisheries and conservation perspective. In 5 of 10 well-studied ecosystems, the average exploitation rate has recently declined and is now at or below the rate predicted to achieve maximum sustainable yield for seven systems. Yet 63% of assessed fish stocks worldwide still require rebuilding, and even lower exploitation rates are needed to reverse the collapse of vulnerable species. Combined fisheries and conservation objectives can be achieved by merging diverse management actions, including catch restrictions, gear modification, and closed areas, depending on local context. Impacts of international fleets and the lack of alternatives to fishing complicate prospects for rebuilding fisheries in many poorer regions, highlighting the need for a global perspective on rebuilding marine resources.

The distribution and interactions of aquatic organisms across space and time structure our marine, freshwater, and estuarine ecosystems. Over the past decade, technological advances in telemetry have transformed our ability to observe aquatic animal behavior and movement. These advances are now providing unprecedented ecological insights by connecting animal movements with measures of their physiology and environment. These developments are revolutionizing the scope and scale of questions that can be asked about the causes and consequences of movement and are redefining how we view and manage individuals, populations, and entire ecosystems. The next advance in aquatic telemetry will be the development of a global collaborative effort to facilitate infrastructure and data sharing and management over scales not previously possible.

Organisms are expected to adapt or move in response to climate change, but observed distribution shifts span a wide range of directions and rates. Explanations often emphasize biological distinctions among species, but general mechanisms have been elusive. We tested an alternative hypothesis: that differences in climate velocity-the rate and direction that climate shifts across the landscape-can explain observed species shifts. We compiled a database of coastal surveys around North America from 1968 to 2011, sampling 128 million individuals across 360 marine taxa. Climate velocity explained the magnitude and direction of shifts in latitude and depth much more effectively than did species characteristics. Our results demonstrate that marine species shift at different rates and directions because they closely track the complex mosaic of local climate velocities.

Climate change is a pervasive and growing global threat to biodiversity and ecosystems. Here, we present the most up-to-date assessment of climate change impacts on biodiversity, ecosystems, and ecosystem services in the U.S. and implications for natural resource management. We draw from the 4th National Climate Assessment to summarize observed and projected changes to ecosystems and biodiversity, explore linkages to important ecosystem services, and discuss associated challenges and opportunities for natural resource management. We find that species are responding to climate change through changes in morphology and behavior, phenology, and geographic range shifts, and these changes are mediated by plastic and evolutionary responses. Responses by species and populations, combined with direct effects of climate change on ecosystems (including more extreme events), are resulting in widespread changes in productivity, species interactions, vulnerability to biological invasions, and other emergent properties. Collectively, these impacts alter the benefits and services that natural ecosystems can provide to society. Although not all impacts are negative, even positive changes can require costly societal adjustments. Natural resource managers need proactive, flexible adaptation strategies that consider historical and future outlooks to minimize costs over the long term. Many organizations are beginning to explore these approaches, but implementation is not yet prevalent or systematic across the nation.

BACKGROUND: The rising temperature of the world's oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin. METHODOLOGY/PRINCIPAL FINDINGS: Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles. CONCLUSIONS/SIGNIFICANCE: Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch's Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.

We utilized a long-term data base collected over a broad geographic range to examine predator size -prey size relationships for 18 species of marine fish predators from continental shelf waters off the northeast US coast. Regression analysis was used to illustrate interspecific variation in ontogenetic patterns of prey size use, gape allometries, and ratio-based trophic niche breadths. Sizebased feeding strategies were assessed through comparison of frequency distributions of relative prey sizes eaten and were related to general predator feeding tactics and gape morphology. The results demonstrated that the range of prey sizes eaten expanded with increasing predator body size for each of the marine predators examined, leading to asymmetric predator size -prey size distributions. Absolute maximum prey size and slopes of maximum prey size versus predator size varied widely among predator taxa. Distinct size-based feeding strategies were evident, as diets of some predators were dominated by prey that were 10 to 20% of predator size, whereas other predators frequently consumed prey > 50% of predator size. Gape sizes and allometric relationships with body size were also diverse among predators and often were closely associated with maximum prey sizes. Ratio-based trophic-niche breadths generally did not expand with predator ontogeny and tended to narrow for the largest predators, which may be common for animal taxa.

We tested the hypothesis that recent oceanographic changes associated with climate change in the Northeast United States continental shelf ecosystem have caused a change in spatial distribution of marine fish. To do this, we analyzed temporal trends from 1968 to 2007 in the mean center of biomass, mean depth, mean temperature of occurrence, and area occupied in each of 36 fish stocks. Temporal trends in distribution were compared to time series of both local-and large-scale environmental variables, as well as estimates of survey abundance. Many stocks spanning several taxonomic groups, life-history strategies, and rates of fishing exhibited a poleward shift in their center of biomass, most with a simultaneous increase in depth, and a few with a concomitant expansion of their northern range. However, distributional changes were highly dependent on the biogeography of each species. Stocks located in the southern extent of the survey area exhibited much greater poleward shifts in center of biomass and some occupied habitats at increasingly greater depths. In contrast, minimal changes in the center of biomass were observed in stocks with distributions limited to the Gulf of Maine, but mean depth of these stocks increased while stock size decreased. Largescale temperature increase and changes in circulation, represented by the Atlantic Multidecadal Oscillation, was the most important factor associated with shifts in the mean center of biomass. Stock size was more often correlated with the total area occupied by each species. These changes in spatial distribution of fish stocks are likely to persist such that stock structure should be re-evaluated for some species.

Integrated ecosystem assessments challenge the broader scientific community to move beyond the important task of tallying insults to marine ecosystems to developing quantitative tools that can support the decisions national and regional resource managers must make.

Abstract Models are key tools for integrating a wide range of system information in a common framework. Attempts to model exploited marine ecosystems can increase understanding of system dynamics; identify major processes, drivers and responses; highlight major gaps in knowledge; and provide a mechanism to ‘road test’ management strategies before implementing them in reality. The Atlantis modelling framework has been used in these roles for a decade and is regularly being modified and applied to new questions (e.g. it is being coupled to climate, biophysical and economic models to help consider climate change impacts, monitoring schemes and multiple use management). This study describes some common lessons learned from its implementation, particularly in regard to when these tools are most effective and the likely form of best practices for ecosystem‐based management (EBM). Most importantly, it highlighted that no single management lever is sufficient to address the many trade‐offs associated with EBM and that the mix of measures needed to successfully implement EBM will differ between systems and will change through time. Although it is doubtful that any single management action will be based solely on Atlantis, this modelling approach continues to provide important insights for managers when making natural resource management decisions.

Acoustic masking from anthropogenic noise is increasingly being considered as a threat to marine mammals, particularly low-frequency specialists such as baleen whales. Low-frequency ocean noise has increased in recent decades, often in habitats with seasonally resident populations of marine mammals, raising concerns that noise chronically influences life histories of individuals and populations. In contrast to physical harm from intense anthropogenic sources, which can have acute impacts on individuals, masking from chronic noise sources has been difficult to quantify at individual or population levels, and resulting effects have been even more difficult to assess. This paper presents an analytical paradigm to quantify changes in an animal's acoustic communication space as a result of spatial, spectral, and temporal changes in background noise, providing a functional definition of communication masking for free-ranging animals and a metric to quantify the potential for communication masking. We use the sonar equation, a combination of modeling and analytical techniques, and measurements from empirical data to calculate time-varying spatial maps of potential communication space for singing fin (Balaenoptera physalus), singing humpback (Megoptera novaeangliae), and calling right (Eubalaena glacialis) whales. These illustrate how the measured loss of communication space as a result of differing levels of noise is converted into a time-varying measure of communication masking. The proposed paradigm and mechanisms for measuring levels of communication masking can be applied to different species, contexts, acoustic habitats and ocean noise scenes to estimate the potential impacts of masking at the individual and population levels.

Abstract Oogenesis in fishes follows a universal plan; yet, due to differences in the synchrony and rate of egg development, spawning frequency varies from daily to once in a lifetime. Some species spawn and feed in separate areas, during different seasons, by storing energy and drawing on it later for reproduction (i.e. capital breeding). Other species spawn using energy acquired locally, throughout a prolonged spawning season, allocating energy directly to reproduction (i.e. income breeding). Capital breeders tend to ovulate all at once and are more likely to be distributed at boreal latitudes. Income breeding allows small fish to overcome allometric constraints on egg production. Income breeders can recover more quickly when good‐feeding conditions are re‐established, which is a benefit to adults regarding bet‐hedging spawning strategies. Many species exhibit mixed capital‐ and income‐breeding patterns. An individual's position along this capital–income continuum may shift with ontogeny or in relation to environmental conditions, so breeding patterns are a conditional reproductive strategy. Poor‐feeding environments can lead to delayed maturation, skipped spawning, fewer spawning events per season or fewer eggs produced per event. In a few cases, variations in feeding environments appear to affect recruitment variability. These flexible processes of energy acquisition and allocation allow females to prioritize their own condition over their propagules' condition at any given spawning opportunity, thereby investing energy cautiously to maximize lifetime reproductive value. These findings have implications for temporal and spatial sampling designs, for measurement and interpretation of fecundity, and for interpreting fishery and ecosystem assessments.

Climate change and decadal variability are impacting marine fish and invertebrate species worldwide and these impacts will continue for the foreseeable future. Quantitative approaches have been developed to examine climate impacts on productivity, abundance, and distribution of various marine fish and invertebrate species. However, it is difficult to apply these approaches to large numbers of species owing to the lack of mechanistic understanding sufficient for quantitative analyses, as well as the lack of scientific infrastructure to support these more detailed studies. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species with existing information. These methods combine the exposure of a species to a stressor (climate change and decadal variability) and the sensitivity of species to the stressor. These two components are then combined to estimate an overall vulnerability. Quantitative data are used when available, but qualitative information and expert opinion are used when quantitative data is lacking. Here we conduct a climate vulnerability assessment on 82 fish and invertebrate species in the Northeast U.S. Shelf including exploited, forage, and protected species. We define climate vulnerability as the extent to which abundance or productivity of a species in the region could be impacted by climate change and decadal variability. We find that the overall climate vulnerability is high to very high for approximately half the species assessed; diadromous and benthic invertebrate species exhibit the greatest vulnerability. In addition, the majority of species included in the assessment have a high potential for a change in distribution in response to projected changes in climate. Negative effects of climate change are expected for approximately half of the species assessed, but some species are expected to be positively affected (e.g., increase in productivity or move into the region). These results will inform research and management activities related to understanding and adapting marine fisheries management and conservation to climate change and decadal variability.

Abstract Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site‐associated DNA sequencing ( RAD seq), a popular reduced representation method, has ushered in a new era of genome‐scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RAD seq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RAD seq‐based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RAD seq studies, we developed a simple model using different numbers of RAD ‐tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best‐case modelling scenario, we found that RAD seq using six‐ or eight‐base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RAD seq for genome scans and found that the median density of markers across these studies was 4.08 RAD ‐tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RAD seq study. Thus, we conclude that genome scans based on RAD seq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.

Abstract The Intergovernmental Panel on Climate Change (IPCC) fifth assessment of projected global and regional ocean temperature change is based on global climate models that have coarse (∼100 km) ocean and atmosphere resolutions. In the Northwest Atlantic, the ensemble of global climate models has a warm bias in sea surface temperature due to a misrepresentation of the Gulf Stream position; thus, existing climate change projections are based on unrealistic regional ocean circulation. Here we compare simulations and an atmospheric CO 2 doubling response from four global climate models of varying ocean and atmosphere resolution. We find that the highest resolution climate model (∼10 km ocean, ∼50 km atmosphere) resolves Northwest Atlantic circulation and water mass distribution most accurately. The CO 2 doubling response from this model shows that upper‐ocean (0–300 m) temperature in the Northwest Atlantic Shelf warms at a rate nearly twice as fast as the coarser models and nearly three times faster than the global average. This enhanced warming is accompanied by an increase in salinity due to a change in water mass distribution that is related to a retreat of the Labrador Current and a northerly shift of the Gulf Stream. Both observations and the climate model demonstrate a robust relationship between a weakening Atlantic Meridional Overturning Circulation (AMOC) and an increase in the proportion of Warm‐Temperate Slope Water entering the Northwest Atlantic Shelf. Therefore, prior climate change projections for the Northwest Atlantic may be far too conservative. These results point to the need to improve simulations of basin and regional‐scale ocean circulation.

This review considers the effect of anthropogenic sound on beaked whales2. Two major conclusions are presented: (1) gas-bubble disease, induced in supersaturated tissue by a behavioural response to acoustic exposure, is a plausible pathologic mechanism for the morbidity and mortality seen in cetaceans associated with sonar exposure and merits further investigation; and (2) current monitoring and mitigation methods for beaked whales are ineffective for detecting these animals and protecting them from adverse sound exposure. In addition, four major research priorities, needed to address information gaps on the impacts of sound on beaked whales, are identified: (1) controlled exposure experiments to assess beaked whale responses to known sound stimuli; (2) investigation of physiology, anatomy, pathobiology and behaviour of beaked whales; (3) assessment of baseline diving behaviour and physiology of beaked whales; and (4) a retrospective review of beaked whale strandings.

Abstract This study presents a Monte Carlo method ( CMSY ) for estimating fisheries reference points from catch, resilience and qualitative stock status information on data‐limited stocks. It also presents a Bayesian state‐space implementation of the Schaefer production model ( BSM ), fitted to catch and biomass or catch‐per‐unit‐of‐effort ( CPUE ) data. Special emphasis was given to derive informative priors for productivity, unexploited stock size, catchability and biomass from population dynamics theory. Both models gave good predictions of the maximum intrinsic rate of population increase r , unexploited stock size k and maximum sustainable yield MSY when validated against simulated data with known parameter values. CMSY provided, in addition, reasonable predictions of relative biomass and exploitation rate. Both models were evaluated against 128 real stocks, where estimates of biomass were available from full stock assessments. BSM estimates of r , k and MSY were used as benchmarks for the respective CMSY estimates and were not significantly different in 76% of the stocks. A similar test against 28 data‐limited stocks, where CPUE instead of biomass was available, showed that BSM and CMSY estimates of r , k and MSY were not significantly different in 89% of the stocks. Both CMSY and BSM combine the production model with a simple stock–recruitment model, accounting for reduced recruitment at severely depleted stock sizes.

Abstract Most species of baleen whales were subject to intensive overexploitation by commercial whaling in this and previous centuries, and many populations were reduced to small fractions of their original sizes. Here, we review the status of baleen whale stocks, with an emphasis on those that are known or thought to be critically endangered. Current data suggest that, of the various threats potentially affecting baleen whales, only entanglement in fishing gear and ship strikes may be significant at the population level, and then only in those populations which are already at critically low abundance. The impact of some problems (vessel harassment, and commercial or aboriginal whaling) is at present probably minor. For others (contaminants, habitat degradation, disease), existing data either indicate no immediate cause for concern, or are insufficient to permit an assessment. While the prospect for many baleen whales appears good, there are notable exceptions; populations that are of greatest concern are those suffering from low abundance and associated problems, including (in some cases) anthropogenic mortality. These include: all Northern Right Whales Eubalaena glacialis , Bowhead Whales Balaena mysticetus of the Okhotsk Sea and various eastern Arctic populations, western Gray Whales Eschrichtius robustus , and probably many Blue Whale Balaenoptera musculus populations. We review the status of these populations and, where known, the issues potentially affecting their recovery. Although Humpback Whales Megaptera novaeangliae and Southern Right Whales Eubalaena australis were also heavily exploited by whaling, existing data indicate strong recovery in most studied populations of these species.

Georges Bank, a shallow submarine plateau located off the New England coast, has supported valuable commercial fisheries for several centuries. The region is characterized by high levels of primary productivity and, historically, high levels of fish production. Within the last four decades Georges Bank has been subjected to major perturbations that have profoundly altered levels of catch, abundance, and species composition. The arrival of distant water fleets during the early 1960s resulted in dramatic increases in effective fishing effort and the subsequent commercial collapse of several fish populations. Total fish biomass is estimated to have declined by >50% on Georges Bank during the period of operation of the distant water fleets. The implementation of extended jurisdiction (the 200-mile [370.4-km] limit) in 1977 was followed by modernization and increased capacity of the domestic fleet, resulting in a second perturbation to the system that resulted in further declines in groundfish populations to historically low levels. A subsequent increase in the abundance of species of low commercial value was documented, with an apparent replacement of gadid and flounder species by small elasmobranchs (including dogfish sharks and skates). Examination of feeding guild structure suggests that this switch in species dominance may have been linked to a competitive release. The small elasmobranchs, notably dogfish sharks, also prey on species of commercial importance (primarily small pelagics, including herring and mackerel). The cumulative impacts on the groundfish populations as a result of intense exploitation and predation pressure may have been further exacerbated by effects of fishing gear on the physical structure of the habitat. Implications for the development of an ecosystem-based management approach are described.