Posts Tagged 'communitymodeling'

Modeling climate-dependent larval growth rate and duration of Olympia oysters in the Salish Sea

Most invertebrates in the ocean begin their lives with a planktonic larval phase that is of utmost importance for dispersal and distribution of these species, especially for organisms that are sessile or otherwise mobility-limited during adult life. As larvae are particularly vulnerable to environmental change, holistic understanding of interacting climate stressors on larval life is important to predict population persistence and vulnerability of species. However, traditional experimental designs are often limited by resolution in understanding multiple stress relationships, as environmental variables in the ocean do not occur in discrete interacting levels. Here, I use a novel experimental approach to model growth rate and duration of Olympia oyster larvae and predict the suitability of habitats for larval survival in interacting gradients of temperature, salinity, and ocean acidification. I find that temperature and salinity are closely linked to larval growth and larval habitat suitability, but larvae are resistant to acidification. Olympia oyster larvae from populations in the Salish Sea exhibit higher growth rate and greater tolerance to habitats in near-future climate change conditions compared to present-day conditions in the Salish Sea, suggesting that this species will benefit from some degree of global ocean change. Using generalized linear modeling, I predict larval growth and duration in present-day and future oceanographic conditions in the Salish Sea, finding a vast decrease in mean pelagic larval duration by the year 2095. Using these data, I explore implications of these relationships for Olympia oysters across their range now and in the future.

Continue reading ‘Modeling climate-dependent larval growth rate and duration of Olympia oysters in the Salish Sea’

Spatial patterns in aragonite saturation for the north central California shelf

Ocean acidification is exacerbated along the California shelf due to the upwelling of deep CO2 rich waters. This process of upwelling is driven by along-shore winds, which vary in strength by season. We present the relationship between along-shore wind and aragonite undersaturation utilizing an empirical formula to determine aragonite saturation from salinity, temperature, and dissolved oxygen. Our models show that stronger along-shore winds are correlated with a higher percentage of the water column undersaturated in aragonite. In addition, pteropod and juvenile krill density decrease in upwelled water which is cold, salty, and low in aragonite. With a predicted increase in along-shore winds, California shelf waters will become more undersaturated in aragonite and lead to a decrease in pteropod and krill density.

Continue reading ‘Spatial patterns in aragonite saturation for the north central California shelf’

Effects of an aquaculture pesticide (diflubenzuron) on non-target shrimp populations: extrapolation from laboratory experiments to the risk of population decline


• Diflubenzuron (DFB) in salmon lice treatment can kill non-target crustaceans.

• We developed an age-structured model to assess effects of DFB on shrimp populations.

• The model predicts decline in shrimp abundance by 8%–99%, depending on DFB scenario.

• Environmental fluctuations contribute to the risk of shrimp population decline.

• Future environmental warming and ocean acidification may further impact populations.


Marine aquaculture production has lately experienced high economic growth, but also concerns related to production and environmental contamination. For the Atlantic salmon aquaculture industry, the ectoparasitic crustacean salmon louse (Lepeophtheirus salmonis) has become a major problem. A common method to control populations of salmon lice within farm cages is treatment by various pharmaceuticals. One of the pesticides used in medicated feed for salmon is diflubenzuron (DFB), which acts as a chitin synthesis inhibitor and thereby interferes with the moulting stages during the development of this crustacean. However, DFB from fish feed may also affect non-target crustaceans such as the northern shrimp (Pandalus borealis), which is an economically and ecologically important species. Nevertheless, the actual risk posed by this chemical to shrimp populations in nature is largely unknown. Laboratory experiments have demonstrated that both larval and adult shrimp exposed to DFB through medicated fish feed have reduced survival compared to control. Moreover, the effects of DFB exposure are more severe under conditions of higher temperature and reduced pH (ocean acidification), which can be expected in a future environment. The aim of this study is to make the individual-level information from laboratory studies more relevant for risk assessment at the population level. We have developed a density-dependent age-structured population model representing a northern shrimp population located in a hypothetical Norwegian fjord containing a fish farm, under both ambient and future environments. Our model is based on thorough documentation of shrimp biology and toxicological effects from the laboratory experiments. Nevertheless, extrapolating the reported individual-level effects of DFB to the population level poses several challenges. Relevant information on shrimp populations in Norwegian fjords is sparse (such as abundances, survival and reproductive rates, and density-dependent processes). The degree of exposure to DFB at different distances from aquaculture farms is also uncertain. We have therefore developed a set of model scenarios representing different DFB application schemes and different degrees of exposure for the shrimp populations. The model predicts effects of DFB exposure on population-level endpoints such as long-term abundance, age structure and the probability of population decline below threshold abundances. These model predictions demonstrate how the risk of DFB to shrimp populations can be enhanced by factors such as the timing (season) of DFB applications, the percentage of the population affected, future environmental conditions and environmental stochasticity.

Continue reading ‘Effects of an aquaculture pesticide (diflubenzuron) on non-target shrimp populations: extrapolation from laboratory experiments to the risk of population decline’

Building tools to model the effects of ocean acidification and how it scales from physiology to fisheries

Ocean acidification is a direct consequence of elevated atmospheric carbon dioxide caused by anthropogenic fossil fuel burning and is one of multiple climate-related stressors in marine environments. Understanding of how these stressors will interact to affect marine life and fisheries is limited. In this thesis, I used integrated modelling approaches to scale the effects of biophysical drivers from physiology to population dynamics and fisheries. I focused on ocean acidification and how it interacts with other main drivers such as temperature and oxygen. I used a dynamic bioclimatic envelope model (DBEM) to project the effects of global environmental change on fisheries under two contrasting scenarios of climate change—the low optimistic climate change scenario in line with the 2015 Paris Agreement to limit global warming to 1.5˚ C, and the high climate change scenario on par with our current ‘business-as-usual’ trajectory. First, I developed an ex-vessel fish price database and explored methods using various ocean acidification assumptions. Ex-vessel fish prices are essential for fisheries economic analyses, while model development of ocean acidification effects are important to better understand the uncertainties surrounding acidification and the sensitivity of the model to these uncertainties. These tools and methods were then used to project the impacts of ocean acidification, in the context of climate change, on global invertebrate fisheries—the species group most sensitive to acidification. My results showed that areas with greater acidification have greater negative responses to climate change, e.g. polar regions. However, ocean warming will likely be a greater driver in species distributions and may overshadow direct effects of acidification. While greater climate change will generally have negative consequences on fisheries, Arctic regions may see increased fisheries catch potential as species shift poleward. Canada’s Arctic remains one of the most pristine marine regions left in the world and climate-driven increases in fisheries potential will have major implications for biodiversity and local indigenous reliance on marine resources. In the face of global environmental change, my thesis provides databases, modelling approaches, scenario development, and assessments of global change necessary for adaptation and mitigation of climate-related effects on marine fisheries.

Continue reading ‘Building tools to model the effects of ocean acidification and how it scales from physiology to fisheries’

Comparison of two carbon-nitrogen regulatory models calibrated with mesocosm data


• OBM is more skilful than CN-REcoM when calibrated and validated with mesocosm data.

• OBM suggests that ocean acidification (OA) may stimulate carbon fixation rates in algae.

• Also, OA may elevate metabolic stress in phytoplankton, according to OBM.

• CN-REcoM imposes weak constraints on parameter values, hence solutions are flexible.

• As OBM is constrained by the physiological trade-offs, solutions are rigid and robust.


Marine phytoplankton can regulate their stoichiometric composition in response to variations in the availability of nutrients, light and the pH of seawater. Varying elemental composition of photoautotrophs affects several important ecological and biogeochemical processes, e.g., primary and export production, nutrient cycling, calcification, and grazing. Here we compare two plankton ecosystem models that consider regulatory mechanisms of cellular carbon and nitrogen, driving the physiological acclimation of photoautotrophs. The Carbon:Nitrogen Regulated Ecosystem Model (CN-REcoM) and the optimality-based model (OBM) differ in their representation of phytoplankton dynamics, i.e. nutrient acquisition, synthesis of chlorophyll a, and growth. All other model compartments (zooplankton, detritus, dissolved inorganic and organic matter) and processes (grazing, aggregation, remineralisation) remain identical in both models.

We assess the skills of the two models against data from an ocean acidification mesocosm experiment with three CO2 treatments. Neither model accounts for any carbon dioxide (CO2) effects explicitly. Instead, we assimilate data of the different CO2 treatments separately into the models. Thereby we aim at identifying optimal model parameter values that might correlate with differences in CO2 conditions. For the OBM, optimal parameter estimates of Qmin (subsistence N:C ratio) and V (maximum potential photosynthesis rate of photoautotrophs) turned out to be higher for mesocosms exposed to high CO2 compared to those with low CO2 concentrations. By contrast, a similar correlation is not observed for the CN-REcoM. A possible physiological interpretation of higher estimates of Qmin and V according to the OBM is that phytoplankton may experience environmental stress under more acidic conditions, and hence must invest more energy/resources for maintaining basic cellular functions. Our data assimilation reveals that the parameters of the OBM are better constrained by the data than those of the CN-REcoM. Furthermore, the OBM is better able than CN-REcoM to reproduce data that were not used for parameter optimization.

Continue reading ‘Comparison of two carbon-nitrogen regulatory models calibrated with mesocosm data’

Modelling the environmental niche space and distributions of cold-water corals and sponges in the Canadian northeast Pacific Ocean


• We present the first comparison of realized niche space among six major, habitat-forming cold-water coral and sponge (CWCS) groups (sponge classes: Hexactinellida, Demospongiae; coral orders: Alcyonacea, Scleractinia, Antipatharia, Pennatulacea) occurring in the Northeast Pacific region of Canada (NEPC).
• The environmental gradients influencing CWCS niche space and breadth is driven by dissolved inorganic carbon, total alkalinity, and dissolved oxygen.
• Significant niche separation occurs among CWCS groups; high tolerance and marginality generally identify CWCS as specialists occurring in uncommon habitat conditions within the NEPC.
• Species distribution models developed for each CWCS group all share severely low dissolved oxygen ([O2] < 0.5 ml L−1) as a major predictor of habitat.
• Areas that are predicted to be suitable habitat for multiple CWCW groups primarily occurs primarily within 500–1400 m bottom depths on the continental slope and at offshore seamounts that have summits that reach into this depth range.


Cold water coral and sponge communities (CWCS) are important indicators of vulnerable marine ecosystems (VMEs) and are used to delineate areas for marine conservation and fisheries management. Although the Northeast Pacific region of Canada (NEPC) is notable for having unique CWCS assemblages and is the location of >80% of Canadian seamounts, the extent of potential CWCS-defined VMEs in this region is unknown. Here, we used a diverse set of environmental data layers (n=30) representing a range of bathymetric derivatives, physicochemical variables, and water column properties to assess the primary factors influencing the niche separation and potential distributions of six habitat-forming groups of CWCS in the NEPC (sponge classes: Hexactinellida, Demospongiae; coral orders: Alcyonacea, Scleractinia, Antipatharia, Pennatulacea). The primary environmental gradients that influence niche separation among CWCS are driven by total alkalinity, dissolved inorganic carbon, and dissolved oxygen. Significant niche separation among groups indicates CWCS to be primarily specialists occurring in rare habitat conditions in the NEPC. Species distribution models (SDMs) developed for each CWCS group shared severely low dissolved oxygen levels ([O2] < 0.5 ml L−1) as a top predictor for habitat suitability in the NEPC. Niche separation is further emphasized by differences in the model-predicted areas of suitable habitat among CWCS groups. Although niches varied among taxa, the general areas of high habitat suitability for multiple CWCS groups in the NEPC occurred within the 500–1400 m bottom depth range which is strongly associated with the extensive oxygen minimum zone (OMZ) characterizing this region. As a result, the largest continuous area of potential CWCS habitat occurred along the continental slope with smaller, isolated patches also occurring at several offshore seamounts that have summits that extend into OMZ depths. Our results provide insight into the factors that influence the distributions of some of the most important habitat-forming taxa in the deep ocean and create an empirical foundation for supporting cold-water coral and sponge conservation in the NEPC.

Continue reading ‘Modelling the environmental niche space and distributions of cold-water corals and sponges in the Canadian northeast Pacific Ocean’

Impacts of the changing ocean-sea ice system on the key forage fish Arctic cod (Boreogadus saida) and subsistence fisheries in the Western Canadian Arctic—evaluating linked Climate, Ecosystem and Economic (CEE) models

This study synthesizes results from observations, laboratory experiments and models to showcase how the integration of scientific methods and indigenous knowledge can improve our understanding of (a) past and projected changes in environmental conditions and marine species; (b) their effects on social and ecological systems in the respective communities; and (c) support management and planning tools for climate change adaptation and mitigation. The study links climate-ecosystem-economic (CEE) models and discusses uncertainties within those tools. The example focuses on the key forage species in the Inuvialuit Settlement Region (Western Canadian Arctic), i.e., Arctic cod (Boreogadus saida). Arctic cod can be trophically linked to sea-ice algae and pelagic primary producers and are key vectors for energy transfers from plankton to higher trophic levels (e.g., ringed seals, beluga), which are harvested by Inuit peoples. Fundamental changes in ice and ocean conditions in the region affect the marine ecosystem and fish habitat. Model simulations suggest increasing trends in oceanic phytoplankton and sea-ice algae with high interannual variability. The latter might be linked to interannual variations in Arctic cod abundance and mask trends in observations. CEE simulations incorporating physiological temperature limits data for the distribution of Arctic cod, result in an estimated 17% decrease in Arctic cod populations by the end of the century (high emission scenario), but suggest increases in abundance for other Arctic and sub-Arctic species. The Arctic cod decrease is largely caused by increased temperatures and constraints in northward migration, and could directly impact key subsistence species. Responses to acidification are still highly uncertain, but sensitivity simulations suggests an additional 1% decrease in Arctic cod populations due to pH impacts on growth and survival. Uncertainties remain with respect to detailed future changes, but general results are likely correct and in line with results from other approaches. To reduce uncertainties, higher resolution models with improved parameterizations and better understanding of the species’ physiological limits are required. Arctic communities should be directly involved, receive tools and training to conduct local, unified research and food chain monitoring while decisions regarding commercial fisheries will need to be precautionary and adaptive in light of the existing uncertainties.

Continue reading ‘Impacts of the changing ocean-sea ice system on the key forage fish Arctic cod (Boreogadus saida) and subsistence fisheries in the Western Canadian Arctic—evaluating linked Climate, Ecosystem and Economic (CEE) models’

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Ocean acidification in the IPCC AR5 WG II

OUP book