Attempts to decipher the life cycle of Haplosporidium nelsoni began almost immediately after it was identified as the pathogen causing MSX disease in eastern oysters, Crassostrea virginica. But transmission experiments failed and the spore stage, characteristic of haplosporidans, was extremely rare. Researchers concluded that another host was involved: an intermediate host in which part of the life cycle was produced, or—if the oyster was an accidental host—an alternate host that produces infective elements. A later finding that spores were found more often in spat (<1 y old) than in adults revived the idea of direct transmission between oysters. The new findings and the availability of molecular diagnostics led us to revive life cycle investigations. Over several years, oyster spat were examined for spores and searched for H. nelsoni in potential non-oyster hosts using both histological and polymerase chain reaction (PCR) methodologies. Although spores occurred in a high proportion of spat with advanced infections, it was concluded that they were unlikely to be a principal source of infective elements because naïve oysters used as sentinels to assess infection pressure became highly infected even after native oysters developed resistance, and infected spat could no longer be found. A histological survey of zooplankton and small bivalves in Delaware Bay found few recognizable parasites and nothing resembling a haplosporidan. A subsequent PCR study of water, sediment, and macroinvertebrates from Chesapeake, Delaware, and Oyster bays resulted in many positive samples, but in situ hybridization failed to identify any recognizable structures. PCR analysis of potential intermediate hosts for other molluscan pathogens has also resulted in many species yielding positive results but required in situ hybridization to verify infections. It is suggested that any future search for a nonoyster host of H. nelsoni be conducted in a relatively confined system and/or target specific phyla, strategies that have been successful in other life cycle studies. It is noted that candidate phyla could include those known to host haplosporidans and species whose abundance or distribution may have changed in concert with outbreaks of MSX disease in the northeastern United States in recent years.

The Nutrient Database for Standard Reference published by the U.S.D.A. describes molluscan shellfish as an excellent source of vitamin B12, omega-3 fatty acids, choline, iron, selenium, and zinc. Edible molluscs consist primarily of mussels, clams, scallops, and oysters and are naturally low in carbohydrate, as well as total and saturated fat. With regard to omega-3 fatty acids, iron, selenium, and zinc, the nutrient value of some shellfish is superior to land-based protein sources, such as beef, chicken, and pork. Unfortunately, adverse human health considerations need to be noted because of naturally occurring pathogens, particularly Vibrio species, and algal toxins (brevetoxin, saxitoxin, and domoic acid) that may be present in these shellfish, as well as fecal-associated viruses (hepatitis A and norovirus) and bacteria (Salmonella) as a consequence of contamination of shellfish harvest sites. Other environmental contaminants (mercury, methylmercury, and polychlorinated biphenyls) may bioaccumulate in molluscan shellfish tissues as part of their filter feeding behavior and have potential health implications. Cooking molluscan shellfish greatly reduces the risk of foodborne infections and increases the nutrient value because of water loss; however, some vitamins are destroyed by cooking and natural toxins and environmental contaminants are not always eliminated by normal cooking temperatures. Coastal monitoring of water quality and postharvest processing of some products should help mitigate risks associated with shellfish consumption and promote a safer, nutrient-rich product.

Carrying capacity models for aquaculture have increased in complexity over the last decades, partly because aquaculture growth, sustainability, and licensing are themselves extremely complex. Moreover, there is an asymmetric pattern to all these components, when considered from an international perspective, because of very different regulation and governance of the aquaculture sector in Asia, Europe, and America. Two case studies were used, from Long Island Sound in the United States, and Belfast Lough, in Europe, to examine the interactions between cultivated shellfish and other autochthonous benthic filter-feeders. The objective is to illustrate how such interactions can be incorporated in system-scale ecological models and analyzed from the perspective of ecological carrying capacity. Two different models are described, one based on equations that relate the filtration rate of the hard clam Mercenaria mercenaria to physiological and population factors and one based on a habitat-specific analysis of multiple species of benthic filter-feeders. Both types of models have relative advantages and challenges, and both were integrated in ecosystem modeling frameworks with substantial numbers of state variables representing physical and biogeochemical processes. These models were applied to (1) examine the relative role of the two components (cultivated and wild) in the filtration of particulate organic matter (both phytoplankton and organic detritus), (2) quantify the effect of wild species on harvest of cultivated organisms (eastern oyster and blue mussel), and (3) assess the role of organically extractive aquaculture and other filter-feeders on top–down control of eutrophication.

Suspension-feeding bivalve molluscs are foundation species in coastal intertidal systems. The selective feeding capabilities of these animals can have a large influence on phytoplankton communities and nutrient flow to the benthos. Particle selection, including the types of particles chosen for ingestion and the possible mechanisms mediating selection, has been studied extensively and reported in the literature. To date, however, the possible mechanisms mediating these selective processes have remained elusive. Generally, the focus on a few key commercial species, and their demonstrated range of selective capabilities, has made it difficult to design studies that elucidate the mechanisms behind particle selection. This review focuses on key research that has been carried out in the last 20 y toward better understanding the mechanism that underlays selective capture and ingestion of particles in this important group of animals. Recently, work has been completed which has advanced the field in pointing to a passive mechanism as a mediator of selection, with the interactions between the physicochemical properties of particles and the mucus covering the pallial organs most likely mediating food choice. Although no strong evidence for an immediate, active mechanism which underlies particle selection was found, avenues for future research are suggested in this review. The possible mechanisms that control capture, including qualitative precapture selection, are also summarized and discussed in depth. Methodological considerations for rigorous experiments to advance the field are also discussed, including suggestions of general guidelines for experimental designs, which will allow better comparison of findings across studies.

As computational and sequencing technologies continue to flourish, the barrier for those interested in complementing traditional ecological and physiological studies with functional genomics is easier to overcome. Here, an overview of transcriptome sequencing and DNA methylation analyses in shellfish is provided, primarily for those with fundamental interests and training in a different domain. The approaches covered here can provide valuable information on how organisms respond to their environment and also be used to evaluate evolutionary relationships. First, biological and technological background is provided, highlighting studies in shellfish that have applied these approaches. This is followed by practical methods and tools for conducting this work at the laboratory bench and in front of a computer. In an effort to provide educational resources and the ability to update computational and analytical resources as they become available, a supplementary repository for this work has been created and is available at  https://github.com/sr320/fun-gen.

Oysters are difficult to classify because of plasticity in shell morphology. Difficulties in classification have hindered the understanding of oyster diversity and evolution. Recent molecular studies of living oysters have revealed high genetic diversity at species, population, and genome levels. New and cryptic species have been discovered, revealing surprisingly high species diversity under similar shell morphology. Genetic analyses have identified several species complexes where low genetic divergence indicates recent or ongoing speciation during the past 3–4 million years. Ongoing speciation is also supported by exceptionally high population divergence within some species. The oyster genome is highly polymorphic and gene-rich, with extensive expansion of genes related to stress and immune responses. High levels of genetic diversity and gene expansion in oysters are likely adaptations to variable environments. Local adaptation in oysters may be pervasive but countered by strong gene flow and balancing or multidirectional selections that favor diversity. Oysters have experienced several expansion and contraction events because of climate change since their origin in Permian. Studies on molecular adaptations to recent and historic climate change may provide insights into the evolution and speciation of oysters.

Gastropoda is a large and diverse group of the Mollusca found almost ubiquitously throughout freshwater, terrestrial, and marine habitats. Marine gastropods often support large commercially important fisheries, many of which are facing concerns over sustainability as landings have increased and populations have dwindled over recent decades. For effective fishery management, the inclusion of an age estimation technique is vital to understand growth rates and population structures to feed into analytical stock assessments. Unlike many bivalve species, gastropods are often difficult to age, especially those which exhibit planispiral coiling of their shells, as no single growth axis can be easily uncovered via sectioning. This review covers a range of techniques that can be used to estimate age and growth rates for many marine gastropod species. Although there is no universal aging technique to cover all species, individual techniques have varying success levels for different species groups.

Global abundances and commercial fisheries of cephalopods have increased over recent decades, creating a need for effective fishery management. This management is often focused on the ability to ascertain the age structure of key populations. There are several main techniques for age and growth rate determination in cephalopods. Because of biological differences between species groups, not all techniques are applicable for every species. This review outlines the use of five main ageregistering structures (statoliths, gladii, beaks, stylets, and eye lenses) along with one chemical aging technique (lipofuscin) and their application to cephalopod species groups.

Rapid improvements in the technology used to assess microbial communities have led to an expansion of the breadth and scope of microbial ecology research over the past 20 y. The rapid increase in microbiome research, spurred by nextgeneration amplicon sequencing, has allowed researchers to characterize the microbial communities of organisms and environments which were previously poorly understood. Research on marine invertebrates is still developing, with the mechanisms that determine interactions between the host and their associated microbes largely unknown. Bivalves are of particular interest because of their crucial ecological and economic roles. With the anticipation of shifting environmental conditions, defining the natural variation and role of bivalve-associated microbes is vital to more complex research questions. The current knowledge of the spatial and temporal distributions of bivalve-associated microbes, microbial functional and genetic diversity, host-specific and tissue-specific interactions, and core microbial community composition is summarized here, as well as the beginning stages of understanding the role of microbiome in bivalve physiology and disease susceptibility.

QPX (Quahog Parasite Unknown), a thraustochytrid, is the source of morbidity and mortality in hard clams, Mercenaria mercenaria along the northeast coast of North America. The QPX organism is a facultative pathogen that results in disease in clams held at high densities and salinities. The disease most commonly causes losses in two-year-old aquacultured clams. In some locations, nodules and swellings containing QPX can be identified in the mantle often in areas adjacent to the siphon. Histologically, the organism is surrounded by thick mucus that inhibits phagocytosis by the clam's inflammatory cells especially during the spring and fall when the clam's immune system is less active. Variability in severity of infection and morbidity has been associated with origin of the brood stock with juvenile clams from southern U.S. brood stock being the most affected.

The Atlantic surfclam (Spisula solidissima) is a dominant member of the biological community of the Middle Atlantic Bight continental shelf and a commercially harvested species. Climate warming is affecting the biology and distribution of this species, which provides an opportunity to investigate the processes and conditions that are restructuring this fishery and the implications for ecological and socioeconomic systems. A Management Strategy Evaluation (MSE) developed for the surfclam fishery provides a mechanistic description of the surfclam's response to climate change and understanding of the cascade of effects initiated by changes in oceanographic conditions that ultimately appear as social and economic effects. This understanding in turn informs development of management policies for the resource. This overview considers the components of the surfclam MSE, relevant results, and implications for management and policy. The lessons learned from the surfclam MSE provide a basis for applying similar approaches to other ecologically important species that are also commercially exploitable resources.

This review focuses on the eastern oyster Crassostrea virginica and its pathogen Perkinsus marinus, but the reference points considered are applicable to a wide range of sessile hosts suffering significant mortality from disease. The biological characteristics and imperatives that constrain the deduction of reference points are first reviewed. This is followed by a review of the various models and their reference points that have been implemented or considered in an effort to sustainably manage C. virginica stocks. The last section evaluates the application of reference points addressing maximum sustainable yield (msy) as management tools. Characteristics and imperatives include the preference of abundance over biomass or biovolume as the primary metric for the stock and the bipartite partition of the mortality rate into natural mortality and the additive portion contributed by disease that depends upon the distribution of the stock over the salinity gradient. Other contributing factors include female biases in natural mortality and fishery landings, application of a Ricker model for the broodstock-recruitment relationship, the influence of disease on the surplus production trajectory of the stock, and the importance of managing shell as well as live oysters. Reference points may be developed to manage the disease or the diseased stock. All reference points used in management at this writing are of the latter type. One is volume based; the remainder are abundance based. Constant-abundance reference points have received most attention. Reference points focused on msy have received little use. Constant-abundance reference points stabilize the stock at a known (usually the present) state. Constancy reference points can be applied to the management of the stock and also to the management of the shell resource critical to maintenance of reef habitat. The alternative msy approach is used to stabilize the stock at a state maximizing sustainable production. Though little used, consideration of the behavior of surplus production formulations suggests that msy-based reference points may be feasible and that this approach could then be used to identify management goals other than the present state.

The goal of this article was to use a systematic review of studies on the larval stages of gastropods reared to metamorphosis to determine whether there are general patterns for the effects of temperature, rearing density, and food availability on larval development and performance among species, major taxa, and modes of development. Most studies did not include sufficient metadata to be included in many of the analyses. For all analyses, there were differences among major groups of taxa in terms of response to the considered variables. Increased temperature was frequently correlated with decreased development time and increased growth but often not for the same taxa. Increased larval density was generally correlated with increased development time, but again, the patterns were not consistent across taxa. The most consistent pattern was the positive correlation between per capita food availability and larval growth. In all but two cases, patterns for the most studied species, Crepidula fornicata, were opposite those of other caenogastropods. This indicates that caution should be used when drawing general patterns among species based on studies of C. fornicata. Among lecithotrophs, the vetigastropod Haliotis rufescens was the most studied. In this case, patterns found for this species were similar to those for all other vetigastropods; however, few species outside the genus Haliotis have been studied. Increased temperature was associated with reduced survivorship and, in the most studied clade, the Vetigastropoda, reduced time to metamorphosis, which suggests that there may be an energetic cost to more rapid development or physiological mechanisms for coping with heat stress. Curiously, increased larval density was associated with increased survivorship for lecithotrophs. In several cases, however, there were too few studies, or the studies that were found did not provide enough metadata to be included in analyses. Although some patterns emerged from existing research on gastropod larvae, studies on a more diverse set of species that report all metadata are required for cross-study comparisons, which are crucial for drawing robust general conclusions.

Pinto abalone (Haliotis kamtschatkana), the widest ranging abalone species in North America, occurs from Alaska, United States to Central Baja California, Mexico. The species has been observed in intertidal and subtidal habitats from 0 to 40mdepth. The best available data indicate that pinto abalone abundance has declined in many areas throughout the species' range due to fisheries harvest. Subsistence and personal use fisheries in Alaska and a commercial fishery in Mexico persist. Preliminary data from 2008 to 2016 indicate signs of recovery for some pinto abalone populations along the British Columbia coast due to multiple contributing factors including a reduction in illegal harvest, natural recovery following fishery closure, and low predation pressure. By contrast, pinto abalone populations at the San Juan Islands in Washington are experiencing recruitment failure and continuing to decline, despite closure of the fisheries and no evidence of poaching. Throughout the remainder of the species' range, trends are less clear, due to the lack of regular, long-term monitoring surveys for pinto abalone. The limited data from surveys and/or opportunistic sightings indicate that pinto abalone populations are small, patchily distributed, and/or fluctuate episodically in Alaska, California, and Mexico, with evidence of recent recruitment in a number of locations within these three areas. Baseline abundance and trend data for the species before the advent of commercial fisheries and, in some areas, the local extirpation of sea otters is lacking. Without a clear baseline with which to compare the current abundance levels and trend information, it is difficult to interpret what these levels mean for the status and viability of the species. Threats to pinto abalone were evaluated and characterized using a qualitative rating (i.e., low, moderate, high, very high) based on the threats' scope, severity, and persistence and the sufficiency of the data to support the rating. Several threats that posed a moderate level of risk to pinto abalone were identified including the following: low densities as a result of historical overfishing; the potential threat posed by ocean acidification; and illegal take because of poaching and inadequate law enforcement. The overall risk that pinto abalone face throughout their range was evaluated, and it was determined that they have a low to moderate level of extinction risk now and in the foreseeable future (over both the 30-y and 100-y time horizons). There is a high level of uncertainty regarding demographic factors, in particular regarding whether abundance and productivity levels are sufficient to support the persistence and recovery of the species in the face of continuing and potential future threats. Although recruitment failure may be occurring in some areas (e.g., San Juan Islands Archipelago), in other areas throughout the range recurring and/or recent recruitment events have been observed, despite low densities, and have even resulted in increased densities (across all size classes) at several index sites in British Columbia. Limitations in using demographic data to guide conservation actions and help ensure species persistence could be overcome by conducting consistent monitoring of pinto abalone populations throughout their range.