Extending process and understanding for the development of complex ecosystem models, with application to the Chatham Rise Atlantis model

<p>The Chatham Rise is a highly productive deep-sea ecosystem that supports numerous substantial commercial fisheries, and is therefore a likely candidate for an ecosystem based approach to fisheries management in New Zealand. This thesis describes model construction, calibration and validation, for the first end-to-end ecosystem model of the Chatham Rise, New Zealand. The work extends beyond what has previously been done for validating such models, and explores uncertainty analyses through bootstrapping the oceanographic variables, perturbing the model's initial conditions, and analysing species interaction effects, with the results further analysed with respect to known data gaps. This enables the inclusion of uncertainty in simulated scenarios using the Chatham Rise Atlantis model, thus providing an envelope of results with which to analyse and understand the likely responses of the Chatham Rise ecosystem. The model was designed with 24 dynamic polygons, 5 water column depth bins, 55 species functional groups, and used 12-hour timesteps. The transfer of energy was tracked throughout the system using nitrogen as the model's main currency. The model simulated the system from 1900–2015, preceded by a 35 year burn-in period. The model produced very similar biomass trajectories in response to historical fishing to corresponding fisheries stock assessment models for key fisheries species. Population dynamics and system interactions were considered realistic with respect to growth rates, mortality rates, diets and species group interactions. The model was found to be generally stable under perturbations to the initial conditions, with lower trophic level species groups having the most variability. The specification of the Spawning Stock Recruitment curve was explored, as it relates to the multi-species and ecosystem models within which it is now applied. Close attention needs to be given to population dynamics specific to multi-species interactions such as predation-release, in particular the Spawning Stock Recruitment curve. Potentially misleading dynamics under predation-release were identified, and the simple solution of applying a cap to recruitment when biomass exceeds virgin levels was explored. The population dynamics of myctophids under fishing induced predation release were analysed with and without limiting recruitment to virgin levels. The effects were evident in several ecosystem indicators, suggesting unintentional mis-specification could lead to erroneous model results. It raises several questions around the specification of the Spawning Stock Recruitment relationship for multispecies models, and more generally, whether the concept of ‘virgin’ (or ‘unfished’) biomass should be reconsidered to reflect dynamic natural mortality and potentially changing unfished states. The model components that had knowledge gaps and were found to most likely to influence model results were the initial conditions, oceanographic variables, and the aggregate species groups ‘seabird’ and ‘cetacean other’. It is recommended that applications of the model, such as forecasting biomasses under various fishing regimes, should include alternatives that vary these components, and present appropriate levels of uncertainty in results. Initial conditions should be perturbed, with greater variability applied to species groups modelled as biomass-pools, and age-structured species groups that have little data available from the literature.</p>

Extending process and understanding for the development of complex ecosystem models, with application to the Chatham Rise Atlantis model

<p>The Chatham Rise is a highly productive deep-sea ecosystem that supports numerous substantial commercial fisheries, and is therefore a likely candidate for an ecosystem based approach to fisheries management in New Zealand. This thesis describes model construction, calibration and validation, for the first end-to-end ecosystem model of the Chatham Rise, New Zealand. The work extends beyond what has previously been done for validating such models, and explores uncertainty analyses through bootstrapping the oceanographic variables, perturbing the model's initial conditions, and analysing species interaction effects, with the results further analysed with respect to known data gaps. This enables the inclusion of uncertainty in simulated scenarios using the Chatham Rise Atlantis model, thus providing an envelope of results with which to analyse and understand the likely responses of the Chatham Rise ecosystem. The model was designed with 24 dynamic polygons, 5 water column depth bins, 55 species functional groups, and used 12-hour timesteps. The transfer of energy was tracked throughout the system using nitrogen as the model's main currency. The model simulated the system from 1900–2015, preceded by a 35 year burn-in period. The model produced very similar biomass trajectories in response to historical fishing to corresponding fisheries stock assessment models for key fisheries species. Population dynamics and system interactions were considered realistic with respect to growth rates, mortality rates, diets and species group interactions. The model was found to be generally stable under perturbations to the initial conditions, with lower trophic level species groups having the most variability. The specification of the Spawning Stock Recruitment curve was explored, as it relates to the multi-species and ecosystem models within which it is now applied. Close attention needs to be given to population dynamics specific to multi-species interactions such as predation-release, in particular the Spawning Stock Recruitment curve. Potentially misleading dynamics under predation-release were identified, and the simple solution of applying a cap to recruitment when biomass exceeds virgin levels was explored. The population dynamics of myctophids under fishing induced predation release were analysed with and without limiting recruitment to virgin levels. The effects were evident in several ecosystem indicators, suggesting unintentional mis-specification could lead to erroneous model results. It raises several questions around the specification of the Spawning Stock Recruitment relationship for multispecies models, and more generally, whether the concept of ‘virgin’ (or ‘unfished’) biomass should be reconsidered to reflect dynamic natural mortality and potentially changing unfished states. The model components that had knowledge gaps and were found to most likely to influence model results were the initial conditions, oceanographic variables, and the aggregate species groups ‘seabird’ and ‘cetacean other’. It is recommended that applications of the model, such as forecasting biomasses under various fishing regimes, should include alternatives that vary these components, and present appropriate levels of uncertainty in results. Initial conditions should be perturbed, with greater variability applied to species groups modelled as biomass-pools, and age-structured species groups that have little data available from the literature.</p>

Oceanographic Drivers of Cuvier’s (Ziphius cavirostris) and Sowerby’s (Mesoplodon bidens) Beaked Whales Acoustic Occurrence along the Irish Shelf Edge

Cuvier’s and Sowerby’s beaked whales occur year-round in western Irish waters, yet remain some of the most poorly understood cetaceans in the area. Considering the importance of the area for anthropogenic activities and the sensitivity of beaked whales to noise, understanding their ecology is essential to minimise potential overlaps. To this end, fixed bottom-mounted autonomous acoustic recorders were deployed at 10 stations over four recording periods spanning from May 2015 to November 2016. Acoustic data were collected over 1934 cumulative days, for a total of 7942 h of recordings. To model the probability of presence of Cuvier’s and Sowerby’s beaked whales in the area as a function of oceanographic predictors, we used Generalised Additive Models, fitted with Generalised Estimating Equations to deal with temporal autocorrelation. To reflect prey availability, oceanographic variables acting as proxies of primary productivity and prey aggregation processes such as upwelling events and thermal fronts were selected. Our results demonstrated that oceanographic variables significantly contributed to the occurrence of Cuvier’s and Sowerby’s beaked whales (p-values between <0.001 and <0.05). The species showed similar preferences, with the exception of sdSST. The inclusion of a parameter accounting for the recorders location confirmed the existence of a latitudinal partitioning for those species in the area. This study provides a point of comparison for future research and represents an important step towards a better understanding of those elusive species.

The Distribution Pattern of Marine Bivalve Death Assemblage From the Western Margin of Bay of Bengal and Its Oceanographic Determinants

The global pattern of shallow marine biodiversity is constructed primarily using the data from extra-tropical sites. A severe knowledge gap in the shallow benthic diversity exists for the tropical Indian Ocean, especially along the coastline of peninsular India. Latitudinal biodiversity gradient (LBG)—a poleward decrease in diversity, even though accepted as a pervasive global pattern, often differs from regional trends. Although several oceanographic variables are known to influence regional patterns, their relative effect in shaping the shallow benthic community in tropical seas remains unclear. The east coast of India bordering the Bay of Bengal (BoB) presents a 2,500 km stretch (8–22°N) of tropical coastline with a spatial variation in oceanographic parameters including freshwater mixing, primary productivity, temperature, and shelf area. Here, we documented the marine bivalve distribution using spatially-temporally averaged beach samples and evaluated their relationship with the oceanographic variables. Our data reveal the existence of a highly diverse fauna, comparable to other tropical shallow marine sites. Overall species composition reflects a typical assemblage of the Indian Ocean, dominated by Veneridae but shows an uncharacteristically low proportion of Tellinidae and Lucinidae. The latitudinal variation in diversity shows a mid-latitude drop at around 14°N—a pattern inconsistent with the prediction of latitudinal biodiversity gradient (LBG). The functional groups are dominated by infauna (65%), unattached groups (69%), and suspension feeders (87%). There is only a slight difference in species composition between southern and the northern sites pointing to a predominantly continuous circulation and considerable mixing within the BoB. Productivity range, shelf area, and salinity emerge as best predictors of the species richness. All environmental variables together explain the species composition across the latitudinal bins satisfactorily. The species composition of the east coast shows no distinct nature in comparison to the Indo-Malayan biodiversity hotspot; the proximity to this hotspot and biological exchange with it may have contributed to the high diversity of the east coast fauna. Our study highlights the complex interplay between multiple oceanographic variables in determining the distribution and diversity of tropical shallow marine benthos at a regional scale generating biodiversity patterns that are at odds with global trends such as LBG.

Substrate-dependent fish have shifted less in distribution under climate change

Analyses of the impacts of climate change on fish species have primarily considered dynamic oceanographic variables that are the output of predictive models, yet fish species distributions are determined by much more than just variables such as ocean temperature. Functionally diverse species are differentially influenced by oceanographic as well as physiographic variables such as bottom substrate, thereby influencing their ability to shift distributions. Here, we show that fish species distributions that are more associated with bottom substrate than other dynamic environmental variables have shifted significantly less over the last 30 years than species whose distributions are associated with bottom salinity. Correspondingly, species whose distributions are primarily determined by bottom temperature or ocean salinity have shifted their mean centroid and southern and northern range boundaries significantly more than species whose distributions are determined by substrate or depth. The influence of oceanographic versus static variables differs by species functional group, as benthic species distributions are more associated with substrate and they have shifted significantly less than pelagic species whose distributions are primarily associated with ocean temperatures. In conclusion, benthic fish, that are more influenced by substrate, may prove much less likely to shift distributions under future climate change.