Transmissible cancers are infectious parasitic clones that metastasize to new hosts, living past the death of the founder animal in which the cancer initiated. We investigated the evolutionary history of a cancer lineage that has spread though the soft-shell clam (Mya arenaria) population by assembling a chromosome-scale soft-shell clam reference genome and characterizing somatic mutations in transmissible cancer. We observe high mutation density, widespread copy-number gain, structural rearrangement, loss of heterozygosity, variable telomere lengths, mitochondrial genome expansion and transposable element activity, all indicative of an unstable cancer genome. We also discover a previously unreported mutational signature associated with overexpression of an error-prone polymerase and use this to estimate the lineage to be >200 years old. Our study reveals the ability for an invertebrate cancer lineage to survive for centuries while its genome continues to structurally mutate, likely contributing to the evolution of this lineage as a parasitic cancer.

Natural variability in habitat characteristics, including their interactions, can affect marine invertebrate development. Controlled laboratory experiments seek to assess responses to such variability. For marine invertebrates, responses to temperature are typically assessed but a continuous gradient of all temperatures that a species may encounter is not frequently used. For planktonic larvae of marine invertebrates, biotic factors such as food availability receive less attention due to difficulty in simulating planktonic biotic interactions in a controlled laboratory setting. Here, a laboratory experiment was used to quantify larval development (growth, pelagic larval duration and survival) of the Atlantic surfclam, Spisula solidissima, in response to a continuous range of temperatures and food (phytoplankton) concentrations, allowing quantification of thermal and food availability niches. A second experiment was conducted to quantify the thermal and food availability niches for recruit (post-settlement) surfclams. These experiments were uniquely designed to inform future climate change-based forecasting and habitat suitability modeling. Larval growth and survival increased with increased food availability, while pelagic larval duration decreased with increased food availability. Larval survival decreased with increased temperature, growth peaked near 22 °C and pelagic larval duration was lowest near 22 °C. For recruits, survival and growth increased with both temperature and food availability, but growth decreased at temperatures >22 °C. Broadly, results suggest potential food limitation for continental shelf bivalve larvae and demonstrate that natural variation in food availability may affect thermal tolerances. Results also suggest that throughout the range of the surfclam, high food and moderate temperature areas such as New York Bight and Georges Bank are ideal for larvae and early recruits, whereas low food and high temperature areas, including continental shelf waters in the southern Middle Atlantic Bight, are suboptimal for early life stages of surfclams. This framework may be used for habitat suitability modeling, from an energetic perspective, for other marine invertebrate taxa.

Atlantic sea scallops, Placopecten magellanicus, are the most economically important marine bivalves along the northeastern coast of North America. Wild harvest landings generate hundreds of millions of dollars, and wild-caught adults and juvenile spat are increasingly being cultured in aquaculture facilities and coastal farms. However, the last two weeks of the larval maturation phase in hatcheries are often plagued by large mortality events. Research into other scallop- and aquacultured-species point to bacterial infections or altered functionality of microbial communities which associate with the host. Despite intense filtering and sterilization of seawater, and changing tank water every 48 h, harmful microbes can still persist in biofilms and mortality is still high. There are no previous studies of the bacterial communities associated with the biofilms growing in scallop hatchery tanks, nor studies with wild or hatchery sea scallops. We characterized the bacterial communities in veliger-stage wild or hatchery larvae, and tank biofilms using the 16 S rRNA gene V3-V4 region sequenced on the Illumina MiSeq platform. Hatchery larvae had lower bacterial richness (number of bacteria taxa present) than the wild larvae and tank biofilms, and hatchery larvae had a similar bacterial community (which taxa were present) to both wild larvae and tank biofilms. Bacterial richness and community similarity between tank samples fluctuated over the trial in repeated patterns of rise and fall, which showed some correlation to lunar cycle that may be a proxy for the effects of spring tides and trends in seawater bacteria and phages which are propagated into hatchery tanks. These results along with future work, will inform hatcheries on methods that will increase larval survival in these facilities, for example, implementing additional filtering or avoiding seawater collection during spring tides, to reduce bacterial taxa of concern or promote a more diverse microbial community which would compete against pathogens.

The negative impacts of ocean warming and acidification on bivalve fisheries are well documented but few studies investigate parameters relevant to energy budgets and larval dispersal. This study used laboratory experiments to assess developmental, physiological and behavioral responses to projected climate change scenarios using larval Atlantic surfclams Spisula solidissima solidissima, found in northwest Atlantic Ocean continental shelf waters. Ocean warming increased feeding, scope for growth, and biomineralization, but decreased swimming speed and pelagic larval duration. Ocean acidification increased respiration but reduced immune performance and biomineralization. Growth increased under ocean warming only, but decreased under combined ocean warming and acidification. These results suggest that ocean warming increases metabolic activity and affects larval behavior, while ocean acidification negatively impacts development and physiology. Additionally, principal component analysis demonstrated that growth and biomineralization showed similar response profiles, but inverse response profiles to respiration and swimming speed, suggesting alterations in energy allocation under climate change.

ABSTRACTTransmissible cancers are infectious parasitic clones of malignant cells that metastasize to new hosts, living past the death of the founder animal in which the cancer initiated. Several lineages of transmissible cancer have recently been identified in bivalves, including one that has spread through the soft-shell clam (Mya arenaria) population along the east coast of North America. To investigate the evolutionary history of this transmissible cancer lineage, we assembled a highly contiguous 1.2 Gb soft-shell clam reference genome and characterized somatic mutations from cancer sequences. We show that all cancer cases observed descend from a single founder and cluster into two geographically distinct sub-lineages. We discover a previously unreported clock-like mutational signature that predicts the cancer lineage to be 344 to 877 years old, indicating that it spread undetected long before it was first observed in the 1970s. We observe high mutation density, widespread copy number gain, structural rearrangement, loss of heterozygosity, variable telomere lengths, mitochondrial genome expansion, and transposable element activity, all indicative of an unstable cancer genome. Our study reveals the ability for an invertebrate cancer lineage to survive for centuries while its genome continues to structurally mutate, likely contributing to the ability of this lineage to adapt as a parasitic cancer.SUMMARYThe genome of a contagious cancer in clams reveals structural instability of multiple types throughout the ∼500 years since its origin.

AbstractTo investigate the coastal current in the Gulf of Maine (GoME) and its relation to forcing from outside of the gulf, a high‐resolution circulation model was developed and validated. Our model shows that the Eastern Maine Coastal Current (EMCC) possesses two cores, an offshore and a nearshore core that peak in summer and spring, respectively. The two cores can be traced back to outflows from the Bay of Fundy from opposite sides of Grand Manan Island, and both cores are deeper and slightly more onshore in summer and fall in response to tidal mixing, surface thermal stratification and wind. The two cores merge south of Pleasant Bay, then split into two branches again east of Mount Desert Rock, where the nearshore branch flows along the coast, while the offshore branch turns southward to recirculate in the eastern GoME. Subject to variations of Scotian Shelf Water and Slope Water (SW) inflows, the offshore veering occurs further upstream (northeastward) in late winter and summer, but gradually shifts downstream (southwestward) from summer to winter. Diagnosis of momentum balance demonstrates that the EMCC is primarily driven by the pressure gradient force (PG), of which the barotropic PG is dominant and offshore, while the baroclinic PG is onshore and increases with depth. The large baroclinic PG at depths, modulated by SW, that is, blended by tidal mixing, offsets the barotropic PG. Near the surface, the barotropic PG is nearly balanced by the Coriolis force, forming the geostrophic EMCC.

Shellfish hatcheries have become an increasingly important component of aquaculture production in the United States. Although the industry has been advancing technologically over time to stabilize production and supply, many hatcheries suffer regularly from bouts of stalled or failed production, termed crashes. Crashes are widely acknowledged to occur and are considered a persistent problem in the industry but also an understudied phenomenon in the field of shellfish aquaculture that warrants greater investigation. Furthermore, there are few thorough reports on production variability from established hatcheries. To help fill the data gap and initiate a broader discussion on the causes of hatchery crashes, we provide testimonials from research hatchery managers across the Atlantic Coast about their experiences with crashes. As a case study, we report on long-term production trends (2011−2020) at Horn Point Laboratory's oyster hatchery, which included persistent production failure during the 2019 season. During the 2019 season, larval assays were conducted to determine drivers of production failure; however, no clear culprits were identified. Machine learning was used to help characterize production variability and hindcast the specific conditions when the hatchery's production was most efficient. Microbial community structure of larval associated microorganisms was shown to differ between a crash and non-crash time-point. We highlight the ubiquity of hatchery crashes along the Atlantic Coast of the US, the range of severity at which crashes can occur, and the difficulty of identifying the underlying causes of crashes, even at world-class research facilities. Collectively, we conclude that more research, data sharing, and cross-institution collaboration are needed to prevent crashes, and to develop mitigation strategies to maintain high levels of consistent shellfish aquaculture production.

The intertidal soft-shell clam Mya arenaria fishery in Maine is comanaged under a cooperative agreement, or shellfish ordinance, between coastal communities and the state. The ordinance, among other things, defines conservation tools that encourage communities to engage in activities with a goal to enhance local densities of 0-y class individuals of this infaunal bivalve. One method used by communities for over 75 y is referred to as “brushing,” which involves forcing dozens of the recently cut white spruce Picea glauca boughs (approximately 70 cm in length) vertically into the soft sediments of a mudflat so that 40–45 cm protrudes into the water column. Typically, multiple rows of boughs are deployed on flats in the spring before clam spawning where they remain through the fall after annual settlement and recruitment have ended. Brushing purportedly results in slowing down tidal currents and creating eddies that allow recently settled clams that otherwise are susceptible to bedload transport away from the flat to establish themselves in the vicinity of the boughs. During spring–fall 2019, a comparative field experiment was conducted at three intertidal flats within a 160-km stretch of the Maine Coast to test, for the first time, the efficacy of this traditional management tool versus another approach used to enhance local densities of 0-y class clams—predator-exclusion netting. At each flat, neither treatment enhanced densities when compared with controls of recruits of Mya as well as recruits of another commercially important infaunal bivalve that occurred at a single site, the northern quahog Mercenaria mercenaria. That is, neither bivalve responded positively to experimental additions of spruce boughs to soft sediments at any study site. Passive bivalve collectors demonstrated that both species settled into plots, ruling out recruitment limitation. Comparison of recruit densities between collectors and core samples from both brushed and netted plots demonstrated losses greater than 97% for Mya and greater than 93% for Mercenaria. Collectors also provided data on densities of recruits of the invasive green crab Carcinus maenas, which ranged from 1.2 to 13.9 ind. m–2 across sites, and were 3–6× more abundant in collectors within plots with brush or netting versus adjacent control plots, suggesting that this predator selects heterogeneous versus homogeneous environments during its early life history. As green crab populations in Maine vary directly with seawater temperatures, and the Gulf of Maine is warming relatively rapidly, adding potential habitat for green crabs, such as brush, to intertidal flats should be discontinued in favor of more effective methods to enhance local densities of 0-y class individuals.