Incorporating Environmental Variability Into Assessment and Management of American Lobster (Homarus americanus)

The American lobster (Homarus americanus) support one of the most valuable fisheries in the United States. A growing body of literature recognizes the importance of environmental variables in regulating this species’ biogeography and population dynamics. However, the current lobster stock assessment and management do not explicitly consider the impact of environmental variables such as water temperature and assumes spatiotemporal variabilities in the lobster environment as random background noises. Furthermore, while climate-induced changes in marine ecosystems continue to impact the productivity of lobster fisheries, studies that model lobster response to altered environmental conditions associated with climate change are lacking. As such, evaluating changes in lobster biogeography and population dynamics, as well as explicitly incorporating quantified lobster response to altered environmental conditions into the specie’s stock assessment will be critical for effective lobster fisheries management in a changing environment. This dissertation research developed a modeling framework to assess and incorporate environmental variability in assessment and management of American lobster stocks in the Gulf of Maine, Georges Bank, and southern New England. This modeling framework consists of: 1) a qualitative bioclimate envelope model to quantify the spatiotemporal variability in availability of suitable lobster habitat; 2) a statistical climate-niche model to quantify spatiotemporal variability of lobster distribution; and 3) a process-based population size-structured assessment model to incorporate the effect of environmental variable such as water temperature in lobster population dynamics. The developed modeling framework was used to predict climate-driven changes in lobster habitat suitability and distribution, as well as to determine whether incorporating the environmental effects can better inform historical recruitment especially for years when recruitment was very low or very high. The first component of the framework provides a qualitative bioclimate envelope model to evaluate the spatiotemporal variability of suitable lobster habitat based on four environmental variables (bottom temperature, bottom salinity, depth, and bottom substrate type. The bioclimate envelope model was applied to lobsters in Long Island Sound and inshore Gulf of Maine waters. In the Long Island Sound, an examination of the temporal change in annual median habitat suitability values identified possible time blocks when habitat conditions were extremely poor and revealed a statistically significant decreasing trend in availability of suitable habitat for juveniles during spring from 1978 to 2012. In the Gulf of Maine, a statistically significant increasing trend in habitat suitability was observed for both sexes and stages (juvenile and adult) during the spring (April–June), but not during the fall (September–November). The second component of the framework provides a statistical niche model to quantify the effects of environmental variables on lobster abundance and distribution. The statistical niche model was used to estimate spatiotemporal variation of lobster shell disease in Long Island Sound, and to quantify environmental effects on season, sex- and size-specific lobster distributions in the Gulf of Maine. In the Long Island Sound, the statistical niche model found that spatial distribution of shell disease prevalence was strongly influenced by the interactive latitude and longitude effects, which possibly indicates a geographic origin of shell disease. In the Gulf of Maine, the statistical niche model indicated that bottom temperature and salinity impact on lobster distribution were more pronounced during spring, and predicted significantly higher lobster abundance under a warm climatology scenario. The third component of the framework provides a size-structured population model that can incorporate the environmental effects to inform recruitment dynamics. The size-structured population model was applied to the Gulf of Maine/Georges Bank lobster stock, where climate-driven habitat suitability for lobster recruitments was used to inform the recruitment index. The performance of this assessment model is evaluated by comparing relevant assessment outputs such as recruitment, annual fishing mortality, and magnitude of retrospective biases. The assessment model with an environment-explicit recruitment function estimated higher recruitment and lower fishing mortality in the early 2000s and late 2010s. Retrospective patterns were also reduced when the environmentally-driven recruitment model was used. This dissertation research is novel as it provides the comprehensive framework that can quantify impacts of environmental variability on lobster biogeography and population dynamics at high spatial and temporal scales. The modeling approaches developed in this study facilitate the need to invoke assumptions of environment at non-equilibrium and demonstrate the importance of considering environmental variability in the assessment and management of the lobster fisheries. This dissertation is dedicated to increase the breadth of knowledge about the dynamics of lobster populations and ecosystems and renders a novel first step towards sustainable management of this species given the expected changes in the Northwest Atlantic ecosystem

Contrasting patterns in the occurrence and biomass centers of gravity among fish and macroinvertebrates in a continental shelf ecosystem

The distribution of a group of fish and macroinvertebrates (n = 52) resident in the US Northeast Shelf large marine ecosystem were characterized with species distribution models (SDM), which in turn were used to estimate occurrence and biomass center of gravity (COG). The SDMs were fit using random forest machine learning and were informed with a range of physical and biological variables. The estimated probability of occurrence and biomass from the models provided the weightings to determine depth, distance to the coast, and along-shelf distance COG. The COGs of occupancy and biomass habitat tended to be separated by distances averaging 50 km, which approximates half of the minor axis of the subject ecosystem. During the study period (1978–2018), the biomass COG has tended to shift to further offshore positions whereas occupancy habitat has stayed at a regular spacing from the coastline. Both habitat types have shifted their along-shelf distances, indicating a general movement to higher latitude or to the Northeast for this ecosystem. However, biomass tended to occur at lower latitudes in the spring and higher latitude in the fall in a response to seasonal conditions. Distribution of habitat in relation to depth reveals a divergence in response with occupancy habitat shallowing over time and biomass habitat distributing in progressively deeper water. These results suggest that climate forced change in distribution will differentially affect occurrence and biomass of marine taxa, which will likely affect the organization of ecosystems and the manner in which human populations utilize marine resources.publishedVersio

Influencia de factores ambientales sobre potas oceánicas (Cephalopoda: Ommastrephidae) explotadas comercialmente: un enfoque para la gestión de stocks

Ommastrephid squids are short-lived ecological opportunists and their recruitment is largely driven by the surrounding environment. While recent studies suggest that recruitment variability in several squid species can be partially explained by environmental variability derived from synoptic oceanographic data, assessment of ommastrephid stocks using environmental variability is rare. In thisstudy, we modified asurplus production model to incorporate environmental variability into the assessment of threeommastrephid squids (Ommastrephes bartramii in the northwest Pacific, Illex argentinus in the southwest Atlantic and Dosidicus gigas in the southwest Pacific). We assumed that the key environmental variables—suitable sea surface temperature on spawning grounds during the spawning seasons and feeding grounds during the feeding seasons—have effects on the carrying capacity and the instantaneous population growth rate, respectively, in the surplus production model. For each squid stock, the assessment model with environmental variability had the highest fitting accuracy and the lowest mean squared error and coefficient of variation, and the management reference points based on the optimal model were more precautionary. This study advances our understanding of the interactions between the environment and ommastrephid squid population dynamics and can therefore improve the management of these commercially valuable stocks with a short life cycle.Los miembros de la familia Ommastrephidae (potas) son cefalópodos de vida breve y oportunistas ecológicos, estando sus reclutamientos profundamente influidos por el ambiente circundante. Aunque algunos estudios recientes sugirieron que la variabilidad del reclutamiento en varias especies de esta familia podría explicarse parcialmente por la variabilidad ambiental derivada de datos oceanográficos sinópticos, la gestión de los stocks de omastréfidos empleando factores medioambientales es muy poco frecuente. En el presente trabajo, se ha modificado un modelo de producción generalizada incorporando en él factores ambientales con objeto de ofrecer una herramienta para la gestión y manejo de tres pesquerías: la de Ommastrephes bartramii en el Pacífico Noroeste, la Illex argentinus en el Atlántico sudoeste y la de Dosidicus gigas en el Pacífico sudoeste. Se asumió que los factores ambientales clave: una apropiada temperatura superficial en las áreas de puesta durante las épocas de freza y en las áreas de alimentación durante las estaciones de nutrición, tenían efectos sobre la capacidad de carga y el crecimiento instantáneo de la tasa de crecimiento de la población, respectivamente, en el modelo de producción generalizada. Para el stock de cada especie, el modelo de gestión con las variables ambientales mostró el mayor y más preciso ajuste y el menor error cuadrático y coeficiente de variación; además, los puntos de referencia de manejo basados en el modelo optimizado fueron los más precautorios. El presente estudio significa un avance en nuestro conocimiento sobre las interacciones entre el ambiente y la dinámica de las poblaciones de especies de esta familia de cefalópodos, lo que puede mejorar la gestión de estos stocks de especies de vida breve, cuya importancia comercial es muy grande

Contrasting patterns in the occurrence and biomass centers of gravity among fish and macroinvertebrates in a continental shelf ecosystem

The distribution of a group of fish and macroinvertebrates (n = 52) resident in the US Northeast Shelf large marine ecosystem were characterized with species distribution models (SDM), which in turn were used to estimate occurrence and biomass center of gravity (COG). The SDMs were fit using random forest machine learning and were informed with a range of physical and biological variables. The estimated probability of occurrence and biomass from the models provided the weightings to determine depth, distance to the coast, and along-shelf distance COG. The COGs of occupancy and biomass habitat tended to be separated by distances averaging 50 km, which approximates half of the minor axis of the subject ecosystem. During the study period (1978–2018), the biomass COG has tended to shift to further offshore positions whereas occupancy habitat has stayed at a regular spacing from the coastline. Both habitat types have shifted their along-shelf distances, indicating a general movement to higher latitude or to the Northeast for this ecosystem. However, biomass tended to occur at lower latitudes in the spring and higher latitude in the fall in a response to seasonal conditions. Distribution of habitat in relation to depth reveals a divergence in response with occupancy habitat shallowing over time and biomass habitat distributing in progressively deeper water. These results suggest that climate forced change in distribution will differentially affect occurrence and biomass of marine taxa, which will likely affect the organization of ecosystems and the manner in which human populations utilize marine resources

Cumulative trophic curves elucidate tropical coral reef ecosystems

There are few generalizable patterns in ecology, with widespread observations and predictability. One possible generalizable pattern is the cumulative trophic theory, which consistently exhibits S-curves of cumulative biomass over trophic level (TL) for over 200 different marine ecosystems. But whether those cumulative biomass patterns persist in some of the more distinct marine ecosystems, coral reefs, is unclear. Coral reefs are unique among marine ecosystems, representing global biodiversity hotspots and providing crucial ecosystem services. They are subject to many pressures, including both global (e.g., climate and ocean changes, warming, acidification) and local (e.g., overexploitation/overfishing, increase in turbidity, bleaching, habitat destruction, invasive species) stressors. The analysis of emergent ecosystem features, such as cumulative biomass S-curves, could represent a useful and new analytical option that can also be implemented for coral reefs. The cumulative biomass approach was applied to 42 U.S. Pacific islands (Guam and the Commonwealth of Northern Mariana Islands, American Samoa, the Pacific Remote Islands Areas, and the Northwestern and Main Hawaiian Islands), using data collected from fish surveys. Results show that coral reef ecosystems do indeed follow the S-curve patterns expected from cumulative trophic theory, which is not trivial for tropical reef systems that tend to be less widely examined and strongly dominated by structuring organisms like corals. The curve parameters results are also consistent with both fish assemblage diversity indexes and the benthic substrate ratio, which suggests this measure could serve as a useful ecosystem indicator to measure the ecological status of reefs. Moreover, the curve shape was consistent with what one would expect for different levels of perturbation, with the areas more densely inhabited showing less pronounced S-curves, in contrast to those observed in low human population density islands. All this is reflected in the curve parameters, particularly inflection point of the TL and steepness, generally showing a negative response to both natural and anthropogenic disturbances. Cross-archipelago differences have also been detected with the Hawaiian Island chain tending to have lower inflection points for biomass and TL than other regions. Collectively our findings demonstrate the potential application of the cumulative biomass approach to evaluate coral reef ecosystems

Evaluating the Hatchery Program of a Highly Exploited Shrimp Stock (Fenneropenaeus chinensis) in a Temperate Marine Ecosystem

Hatchery programs are commonly used to enhance fishery stocks, while the efforts to minimize potential negative ecological impacts have grown in recent years. In China, Fenneropenaeus chinensis is a fast-growing, short-lived shrimp species with a high commercial value. F. chinensis fishery is heavily dependent on the hatchery program. We evaluated the trade-off between economic profits and ecological impacts of F. chinensis hatchery program in the Jiaozhou Bay of China. The total length of released individuals was 1.4 cm. The results showed that artificially released F. chinensis individuals experienced high predation pressure during the first 2 weeks. The economic profit peaked when 198 million individuals were released. The modeled hatchery program yielded a lower proportion of individuals with the increasing amount of F. chinensis release. The temporally uniform hatchery release was more efficient than other hatchery release scenarios (e.g., increasing the released amount year by year) in a long-term hatchery program. F. chinensis had the negative impacts on two large predatory fishes. Large fishes recovered at a slower rate than small fishes after the F. chinensis release stopped. Reducing fishing pressure could offset negative impacts of F. chinensis release on large fishes. The study indicates that the effectiveness of F. chinensis release cannot be enhanced by simply increasing the released amount. A long-term F. chinensis hatchery program with a large released amount may present additional challenges for managing natural resources in an ecosystem context

Data and Code from: Coastal sharks supply the global shark fin trade

ABSTRACT from Biology Letters manuscript: Progress in global shark conservation has been limited by constraints to understanding the species composition and geographic origins of the shark fin trade. Previous assessments that relied on earlier genetic techniques and official trade records focused on abundant pelagic species traded between Europe and Asia. Here we combine recent advances in DNA barcoding and species distribution modeling to identify the species and source the geographic origin of fins sold at market. Derived models of species environmental niches indicated that shark fishing effort was concentrated within Exclusive Economic Zones (EEZs), mostly in coastal Australia, Indonesia, the United States, Brazil, Mexico, and Japan. By coupling two distinct tools, barcoding and niche modeling, our results provide new insights for monitoring and enforcement. They suggest stronger local controls of coastal fishing may help regulate the unsustainable global trade in shark fins

Long-term assessment of California kelp forests, drivers, and resiliency

Kelp deforestation threatens life-sustaining services to coastal communities worldwide. Reversing this trend requires an understanding of long-term anthropogenic stressors from global warming, shoreline development, and trophic loss. By georeferencing early 20th century kelp canopy surveys along the eastern US Pacific, we extend reference timelines for the entire mainland coast of California by 60+ years (1911-2016) to discover a nearly 80% overall decline. Using Random Forest models, we find climate warming outweighed all key drivers of regional century-scale losses, but recovery of sea otters as predators of kelp grazing invertebrates corresponded with the only absolute gains in surface canopy. This century-scale perspective identifies staggering alterations of California’s coastline, stressing the urgency of adopting kelp forests into blue carbon initiatives. Additionally, our results demonstrate the role of otters in increasing natural climate resiliency, underscoring the potential for trophic rewilding to support climate mitigation. Together these findings show the importance of innovative and multifaceted strategies to address climate change – including ocean gardening and wildlife reintroductions – to prevent further broad scale losses in ecosystem benefits to coastal communities