ITR: A Computational Framework for Observational Science: Data Assimilation Methods and their Application for Understanding North Atlantic Zooplankton Dynamics

This project will develop a modular data assimilation system, investigate several algorithms to make data assimilation more efficient, and will apply this system to investigate zooplankton dynamics in the North Atlantic. The goal of data assimilation is to find the value of the control variables (typically, the initial conditions or boundary conditions or model parameters) producing the best agreement between the model and the data. A data assimilation system consists of a forward model representing known dynamics. This model is integrated and the deviation between its predictions and available observations are quantified by a cost function. An adjoint model, representing the inverse of the known dynamics, is then run to determine the dependence of the cost function on the control variables. From the results of the adjoint model, the control variables are adjusted and the entire procedure repeats until the system converges on an answer. Because of the many iterations of the forward/adjoint system are required to find an answer, data assimilation is a computationally intensive process. The proposed data assimilation system will attempt to improve the effciency through parallelization and algorithmic improvements. Specifically, this project will evaluate three standard minimization algorithms and a new algorithm based on multigrid techniques. Using this system, data from the Continous Plankton Recorder survey, the only ongoing basin-wide plankton survey, will be assimilated to provide an accurate, quantitative description of the seasonal and interannual changes of North Atlantic zooplankton populations (especially, Calanus finmarchicus) in the Gulf of Maine and across the entire North Atlantic. This description will provide a better mechanistic understanding of the processes responsible for observed patterns in these populations. Such an understanding is prerequisite for predicting the impact of climate variability and change on zooplankton populations and the ecosystems they support.Broader Impacts: The proposed data assimilation system is a general model for many data assimilation problems including operational oceanography and numerical weather prediction. This project\u27s association with the Cornell Theory Center (CTC) allows a unique opportunity to share its data assimilation system to a wide audience. With the help of CTC staff, a web interface to the system running on CTC\u27s .NET cluster will be built. This interface will allow researchers and students across the world to access a high-performance data assimilation system. The development of the data assimilation system will be integrated into a series of computational tools courses offered at Cornell. This project will also provide research opportunities for both graduate students and undergraduates

Collaborative Research: Life Histories of Species in the Genus Calanus in the North Atlantic and North Pacific Oceans and Responses to Climate Forcing

Species in the genus Calanus are predominant in the mesozooplankton of the North Atlantic and North Pacific Oceans. Their key role in marine food web interactions has been recognized in GLOBEC programs, both in the U.S. and internationally. Considerable knowledge of life history characteristics, including growth, reproduction, mortality, diapause behavior and demography has been acquired from both laboratory experiments and measurements at sea. This project reviews and synthesizes this knowledge and uses it to develop an Individual Based Life Cycle model for sibling species in two sympatric species pairs, C.marshallae and C. pacificus in the North Pacific Ocean and C. finmarchicus and C.helgolandicus in the North Atlantic, that have been the particular focus of GLOBEC programs and other recent research projects in the U.S., Canada and Europe. The IBLC model is then applied to make predictions about the life history response of each species to forcing under reasonable climate change scenarios for ambient food and temperature. The project involves training of a graduate student and two postdoctoral researchers in evaluation and prediction of effects of climate change on marine plankton populations. It fosters international collaboration with Canadian and European researchers, including participation in a workshop in Europe. Outreach to the broader fishing and management community is through seminars, information exchange sessions with fishermen managers, including the Maine Fisherman?s Forum, collaboration in affiliated projects with colleagues involved in herring and tuna research in the Gulf of Maine and in climate and fisheries interactions within NOAA

Collaborative Proposal: CAMEO: Using interdecadal comparisons to understand trade-offs between abundance and condition in fishery ecosystems

The investigators will conduct a model-based investigation of the dynamics of a productive pelagic ecosystems in the Gulf of Maine. The middle trophic levels in highly productive marine ecosystems are typically dominated by a few species of pelagic fish, such as sardines and anchovies in upwelling environments or herring and/or capelin in temperate and subpolar regions. These species act as important conduits for energy to higher trophic levels, including larger fish, seabirds, and cetaceans. When abundant, small pelagics can exert significant pressure on their prey, typically large mesozooplankton. Small pelagic fish exhibit complex dynamics and managing these species under an ecosystem approach is challenging. This modeling study will track both the abundance and condition of representative copepods (Calanus finmarchicus, Centropages typicus), herring, and bluefin tuna. The investigators will use a rigorous comparison of conditions from the 1980s and 1990s to develop the model. They will examine the sensitivity of this ecosystem to changes in fishing pressure on the middle trophic levels and to changes in the magnitude and timing of primary production. They will also consider the impact of increased temperature on the ability of C. finmarchicus to accumulate lipids and alter the condition of herring and tuna.The project will lead to improved knowledge of ecosystems with productive food webs. It will also directly impact address issues related to the management of the herring resource in the Gulf of Maine. The investigators will examine the consequences of ignoring condition of zooplankton and fish, as is the case with the current stock assessment. They will also explore the dynamical properties of the model ecosystem and consider under what conditions it is possible to have both abundant and well conditioned herring

Understanding Copepod Life-history and Diversity Using a Next-generation Zooplankton Model

Evolution has shaped the physiology, life history, and behavior of a species to the physical conditions and to the communities of predators and prey within its range. Within a community, the number of species is determined by both physical properties such as temperature and biological properties like the magnitude and timing of primary productivity, and ecological interactions such as predation. Despite well-known correlations between diversity and properties such as temperature, the mechanisms that drive these correlations are not well-described, especially in the oceans. The investigators will conduct a model-based investigation of diversity patterns in marine ecosystems, focusing on calanoid copepods. Diversity changes on both sides of the Atlantic suggest three main hypotheses, relating copepod diversity to environmental stability, productivity, and size-based predation. To test these, the investigators will develop a novel model of copepod population dynamics. The model treats developmental stage and mass as continua, leading to a single partial differential equation for abundance as a function of stage and mass. This approach facilitates the use of algorithms from computational fluid mechanics to resolve numerical dispersion problems that characterize many copepod abundance models. This new modeling framework will be tested by building a model for the species Calanus finmarchicus and Pseudocalanus newmani to compare the results of the model with prior observations and models for two contrasting ecosystems, the Gulf of Maine and Gulf of St. Lawrence. The model formalizes trade-offs between temperature-dependent development, mass-dependent and temperature-dependent growth, and mass-dependent mortality. A series of 1-D simulations will be conducted, encompassing a range of environmental conditions. Each simulation will be initialized with many distinct species, where a species is described by a set of parameters specifying key physiological and life history parameters. These will be coupled to a nutrient-phytoplankton-microzooplankton model and integrated for many years. This procedure will produce a community of copepods adapted to conditions in each simulated environment. By studying how the modeled copepod communities respond to changes in physical conditions, productivity, and predation, mechanisms accounting for copepod diversity patterns will be tested.The project will lead to improved models for important copepod species that can be incorporated into ongoing and future ecosystem forecasts. The information on copepod biogeographic limits developed by this study could support estimates of copepod distributions under climate change. The model will be designed to work in a basin-scale model. By allowing adaption to physical and biological conditions, the emergent copepod communities should provide more realistic estimates of the impact of climate change. The project will support the professional development of one graduate student and one postdoctoral associate. It will also engage one undergraduate summer intern each year. Concepts related to this project will be communicated to the wider public on a blog at SeascapeModeling.org

CNH: Collaborative Research: Direct and Indirect Coupling of Fisheries Through Economic, Regulatory, Environmental, and Ecological Linkages

The productivity and resilience of fisheries are subject to a multitude of dynamic and interrelated influences that arise from complex coupling of fish populations with the natural and human systems of which they are a part. With few exceptions, fisheries currently are managed independently, ignoring important natural and human linkages among them. The biological productivity, sustainability, and consequently human benefits of complex fishery systems may be substantially increased if these linkages are better understood and if this understanding is applied to management. The American lobster (Homarus americanus), Atlantic herring (Clupea harengus) and Northeast multispecies groundfish fisheries in the Gulf of Maine are of major ecological, economic, social, and cultural importance to the New England region. They are subject to an array of natural and human linkages that have not yet been systematically studied. This interdisciplinary research project will examine key natural and human linkages among these fisheries and integrate them into a quantitative framework, using numerical modeling to explore how improved understanding of complexity can improve sustainability and increase the flow of human benefits. An important component of the research is the translation of concepts and results into an educational program that will teach a new generation of students about the human and natural complexity of the Gulf of Maine ecosystem and create a sustained interest in marine science. The research is organized by themes. Theme 1 focuses on management of the coupled fishery system. Numerical models will be used to integrate research undertaken in themes 2,3, and 4 and to explore how information regarding interrelated natural and human processes can be used to improve management of these resources. Theme 2 will use econometric estimation and bioeconomic modeling to investigate the human connections between these fisheries that arise through movement of labor and capital between fisheries, regulatory interventions and markets for inputs and outputs, such as herring used as an input to lobster harvest. Theme 3 will synthesize and analyze existing data to characterize variability in transport and survival of early life stages to identify exogenous processes (especially climate-related processes) that drive variability in recruitment. Theme 4 will combine new field studies with analysis of existing data to examine the impact of natural and human-induced trophic interactions among lobster, herring, and groundfish on the population dynamics of these species. Theme 5 will focus on translating research findings into an interactive marine science education program, based at the Gulf of Maine Research Institute, which serves fifth and sixth graders throughout the state of Maine.The project will make important contributions to science by improving basic understanding of the dynamic interrelationships of physical, ecological, and human-economic processes that determine the productivity and variability of the Gulf of Maine lobster, herring, and groundfish fisheries. It also will help develop concepts, research methodologies, and models relevant to fishery systems around the world. There is general agreement on the need to take an ecosystem approach to managing fisheries, but little concrete progress has been made in doing so. This project will develop concepts and methodologies needed to implement an ecosystem approach to fishery management. The project brings together a team of researchers from a broad range of disciplines and will demonstrate the benefits of an integrated interdisciplinary approach to investigating natural-human systems. The research will develop new understanding and approaches for management of important Northeast U.S. fisheries. The new information and insights will be conveyed to fishery managers through seminars, participation in the management process, and publications. The research will be coordinated with an ongoing, interactive marine education activity. A broader goal of that education program is to increase the number of students pursuing education and informed careers in the sciences by generating interest and excitement about science at a critical age. The project also will provide training for graduate students and undergraduate assistants in quantitative, multidisciplinary approaches to the study and management of coupled natural-human systems. This project is supported by an award resulting from the NSF competition focusing on the Dynamics of Coupled Natural and Human Systems

Understanding Copepod Life-History and Diversity using a Next-Generation Zooplankton Model

The main goal of our project is to understand the patterns of diversity and biogeography in marine copepods. To achieve this goal, we developed a unique modeling framework to simulate the trade-offs between growth, development, and fecundity in marine copepods. We developed a new approach to modeling growth and development in metazoans. We applied this approach to marine copepods, and used it to understand relationships between copepod body size and temperature, copepod biodiversity patterns, and copepod biogeography. This project also provided support for experiments to look at how copepod body size impacts the particle size spectrum. We used our model to explain why marine copepods and other organisms with strong associations between body size and temperature should be expected to deviate from the temperature-diversity relationship that emerges from classic metabolic theory. We also used a novel emergent modeling approach to explore how temperature and chlorophyll cycles influence copepod biogeography

Forecasting the seasonal timing of Maine's lobster fishery

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Marine Science 4 (2017): 337, doi:10.3389/fmars.2017.00337.The fishery for American lobster is currently the highest-valued commercial fishery in the United States, worth over US$620 million in dockside value in 2015. During a marine heat wave in 2012, the fishery was disrupted by the early warming of spring ocean temperatures and subsequent influx of lobster landings. This situation resulted in a price collapse, as the supply chain was not prepared for the early and abundant landings of lobsters. Motivated by this series of events, we have developed a forecast of when the Maine (USA) lobster fishery will shift into its high volume summer landings period. The forecast uses a regression approach to relate spring ocean temperatures derived from four NERACOOS buoys along the coast of Maine to the start day of the high landings period of the fishery. Tested against conditions in past years, the forecast is able to predict the start day to within 1 week of the actual start, and the forecast can be issued 3–4 months prior to the onset of the high-landings period, providing valuable lead-time for the fishery and its associated supply chain to prepare for the upcoming season. Forecast results are conveyed in a probabilistic manner and are updated weekly over a 6-week forecasting period so that users can assess the certainty and consistency of the forecast and factor the uncertainty into their use of the information in a given year. By focusing on the timing of events, this type of seasonal forecast provides climate-relevant information to users at time scales that are meaningful for operational decisions. As climate change alters seasonal phenology and reduces the reliability of past experience as a guide for future expectations, this type of forecast can enable fishing industry participants to better adjust to and prepare for operating in the context of climate change.This forecast was initiated with support from NSF Coastal SEES (OCE 1325484) and was developed with funds from NASA EPSCoR through Maine Space Grant Consortium (EP-15-03)

The relation between productivity and species diversity in temperate-arctic marine ecosystems

Energy variables, such as evapotranspiration, temperature, and productivity explain significant variation in the diversity of many groups of terrestrial plants and animals at local to global scales. Although the ocean represents the largest continuous habitat on earth with a vast spectrum of primary productivity and species richness, little is known about how productivity influences species diversity in marine systems. To search for general relationships between productivity and species richness in the ocean, we analyzed data from three different benthic marine ecosystems (epifaunal communities on subtidal rock walls, on navigation buoys in the Gulf of St. Lawrence, and Canadian Arctic macrobenthos) across local to continental spatial scales (1000 km) using a standardized proxy for productivity, satellite-derived chlorophyll a. Theoretically, the form of the function between productivity and species richness is either monotonically increasing or decreasing, or curvilinear (hump- or U-shaped). We found three negative linear and three hump-shaped relationships between chlorophyll a and species richness out of 10 independent comparisons. Scale dependence was suggested by more prevalent diversity-productivity relationships at smaller (local, landscape) than larger (regional, continental) spatial scales. Differences in the form of the functions were more closely allied with community type than with scale, as negative linear functions were restricted to sessile epifauna while hump-shaped functions occurred in Arctic macrobenthos (mixed epifauna, infauna). In two of the data sets, (St. Lawrence epifauna and Arctic macrobenthos) significant effects of chlorophyll a co-varied with the effects of salinity, suggesting that environmental stress as well as productivity influences diversity in these marine systems. The co-varying effect of salinity may commonly arise in broad-scale studies of productivity and diversity in marine ecosystems when attempting to sample the largest range of productivity, often encompassing a coastal-oceanic gradient

Rapid Climate-Driven Circulation Changes Threaten Conservation of Endangered North Atlantic Right Whales

As climate trends accelerate, ecosystems will be pushed rapidly into new states, reducing the potential efficacy of conservation strategies based on historical patterns. In the Gulf of Maine, climate-driven changes have restructured the ecosystem rapidly over the past decade. Changes in the Atlantic meridional overturning circulation have altered deepwater dynamics, driving warming rates twice as high as the fastest surface rates. This has had implications for the copepod Calanus finmarchicus, a critical food supply for the endangered North Atlantic right whale (Eubalaena glacialis). The oceanographic changes have driven a deviation in the seasonal foraging patterns of E. glacialis upon which conservation strategies depend, making the whales more vulnerable to ship strikes and gear entanglements. The effects of rapid climate-driven changes on a species at risk undermine current management approaches