Modelling diet composition dynamics among North Sea predatory fish using a length-structured partial ecosystem model

Multispecies fisheries management approaches must take account of the array of trophic interactions within the ecosystem. Studies of the gut contents of fish stocks in the North Sea show decadal changes in diet composition, as might be expected when the relative abundances of prey species change. In this paper we explore the extent to which a simple model of prey consumption deployed within a dynamic multi-species population model is able to capture those changes. We make use of a length-structured partial-ecosystem model (FishSUMS) in which the relative preferences of predators for prey are set by a combination of species weightings and predator-to-prey length ratios. The model allows for diets to evolve over the lifetime of the predator species as well as in response to changes in the available prey. Eleven commercially important North Sea species were included in the model with full length structure, together with other trophic resources represented in less detail. The model was simultaneously tuned to various sources of data, including time series of stock biomass and landings. We show that, despite the simplicity of the representation of the predation process, it is capable of capturing some of the large observed changes in diet in four predator species that were sampled during the Year of the Stomach projects in 1981 and 1991: cod, haddock, whiting and saithe. We also quantify how much of the biomass is lost to the fishery, to predation by explicitly-modelled species, and to unspecified mortality

Characterising soil structural stability and form of sodic soil used for cotton production

In eastern Australia, Vertosols are widely utilised for the production of irrigated cotton (Gossypium hirsutum) due to their inherent fertility and large water–holding capacity. However, irrigated agriculture in eastern Australia is faced with a decline in the availability of good quality irrigation water sources i.e. waters with low electrolyte concentrations and small Na+ contributions. Consequently, alternative water resources that contain larger contributions of Na+ are becoming increasingly relevant as potential irrigation sources. It is known that the application of Na+ rich waters as irrigation has the potential to increase the Na+ content of the soil, and that this will affect the structural condition of Vertosols. However, the extent to which these poor quality water resources will influence the structural characteristics of different Vertosols is unknown. In addition to this knowledge gap, there is currently no suitable predictor of dispersive behaviour for this soil type, particularly where Vertosols are irrigated with different water quality solutions. The research conducted in this study aimed to characterise the impact of different increments of water quality on the structural stability of different Vertosols. Once this was concluded, the study looked to assess the impact of irrigation water quality on the structural stability, structural form and soil water retention properties of intact soil columns. Knowledge of the structural stability of the soils investigated was then used to derive a model describing the impact of water quality on the structural stability of different cotton producing soils. To achieve the aims nine different soil profiles were sampled from the Bourke, lower Gwydir, Hillston and lower Namoi cotton–producing regions. Eight of these soils are Grey and Black Vertosols with clay phyllosilicate suites dominated to different extents by 2:1 expanding clays, and the ninth soil is an illitic Red Vertosol containing small contributions of 2:1 expanding clays. The soils investigated have ESPs that range between 1 and 10, ECs of 0.1 to 1.2 dS m-1 and CECeff values that are largest for those soils that contain more 2:1 expanding clays. This study shows that the clay phyllosilicate suite of different Vertosols is the primary determinant of structural stability, structural form and soil water retention properties. For example, the Gwydir and Namoi soils contain more 2:1 expanding lattice phyllosilicate clays, have the largest CECeff values of all nine soils and are the most dispersive after all applied immersion treatments. The Bourke and Hillston soils contain less 2:1 expanding lattice clay, have smaller CECeff values and are generally more stable. Irrigation of structurally–intact soils with solutions of larger SARw resulted in larger exchangeable Na+ contents for each soil (and larger ESPs) and smaller contributions of exchangeable Ca2+ and Mg2+. For each soil, larger ESPs are reflected by decreased stability, but generally the soils dominated by 2:1 expansive clays are much less stable than the soils containing smaller contributions of these clay mineral types. Irrigating the structurally–intact Vertosols dominated by 2:1 expansive clays generally resulted in structural form attributes that do not indicate any impact of the applied water treatments, but the Vertosols with less of these mineral types tend to have less desirable structural form attributes after irrigation with solutions of larger Na+ content. Similarly, where the water retention properties of two soils were assessed, the illitic Red Vertosol has less structural pore space after treatment using the large SARw solutions, while the other soil (a Black Vertosol dominated by 2:1 expansive clays) does not show any differences between water retention properties that can be linked to irrigation water quality. These results were clarified for the water retention properties by the assessment of pore–solid space relations, which show both these soils to contain less solid space after irrigation with clean water or solutions of large SARw. This is attributed to increased swelling of clays in the presence of larger Na+ contributions, but both soils have different structural arrangements as shown by the water retention properties and structural form assessment. The red illitic Vertosol shows signs of structural collapse, while the black Vertosol maintains its structural arrangement. Finally, a model describing the structural stability of different Vertosols was developed from the stability assessment of soils, both in different water quality treatments and after the irrigation of structurally–intact columns. The model presented uses a surface response function to describe the impact of increased ECw and SARw of irrigation solutions on soil stability after immersion according to specific soil physico–chemical attributes. In this model increased exchangeable Na+, SAR and a larger CECeff (and consequently, an increased proportion of 2:1 swelling clays) are associated with increases in clay dispersion, while a smaller Ca2+:Mg2+ ratio, EC and less total clay are associated with decreases in clay dispersion

Global sensitivity analysis of an end-to-end marine ecosystem model of the North Sea : factors affecting the biomass of fish and benthos

Comprehensive analysis of parameter and driver sensitivity is key to establishing the credibility of models of complex systems. This is especially so for models of natural systems where experimental manipulation of the real-world to provide controlled validation data is not possible. Models of marine ecosystems fall into this category, but despite the interest in these models for evaluating the effects of climate change and fishing on nutrient fluxes and the abundances of flora and fauna, none have yet been subjected to global sensitivity analysis. Here we present results of both local ‘one-at-a-time’ (OAT), and variance based global sensitivity analyses (GSA) of the fish and fishery aspects of StrathE2E, an end-to-end (nutrients to birds and mammals) ecosystem model of the North Sea. The sensitivity of the model was examined with respect to internal biological parameters, and external drivers related to climate and human activity. The OAT Morris method was first used to screen for factors most influential on model outputs. The Sobol GSA method was then used to calculate quantitative sensitivity indices. The results indicated that the fish and shellfish components of the model (demersal and pelagic fish, filter/deposit and scavenge/carnivore feeding benthos) were influenced by different sets of factors. Harvesting rates were directly influential on demersal and pelagic fish biomasses. Suspension/deposit feeding benthos were directly sensitive to changes in temperature, while the temperature acted indirectly on pelagic fish through the connectivity between model components of the food web. Biomass conversion efficiency was the most important factor for scavenge/carnivorous feeding benthos. The results indicate the primacy of fishing as the most important process affecting total fish biomass, together with varying responses to environmental factors which may be relevant in the context of climate change. The non-linear responses and parameter interactions identified by the analysis also highlight the necessity to use global rather than local methods for the sensitivity analysis of ecosystem models

Modelling the Whole-Ecosystem Impacts of Trawling

Trawling has been controversial since its introduction in the 17th century. In 1882 the Fishery Board for Scotland was established and assigned powers to ban beam and otter trawling where necessary to protect traditional static gear fisheries. Under these powers, large parts of the inshore waters off the east and west coasts of Scotland were closed to trawling. The Firth of Clyde remained closed until 1962. More recently, in April 2015 solicitors acting for Greenpeace obtained High Court permission for a judicial review of Defra’s alleged failure to adjust its policy on allocating annual landing quotas to reflect reforms to the CFP. It is claimed the reforms stipulate that greater preference should be given to sustainable low impact fishing methods at the expense of high-impact methods such as trawling. In Scotland, the exclusion of trawling activity from a network of marine protected areas established in July 2015 has also been highly controversial. There is no doubt that some trawl gears can be extremely destructive of fragile habitats and slowly regenerating fauna such as coral. Over expanses of mud or sand, however, it has been claimed that trawling may be a positive factor, akin to ploughing the fields in terrestrial agriculture, and enhancing the productivity of the ecosystem. There have been many scientific studies, both in the field and using mathematical modelling, of the impact of trawling on the seabed. Similarly, we know very well that harvesting of fish and shellfish, whether using trawling or static gear, has consequences for marine food webs. However, there have been few, if any, scientific studies which have put these two aspects of trawling together and then compared the seabed impacts of trawling with the consequences of harvesting. In this project we used a mathematical model to compare and contrast the whole ecosystem effects of harvesting fish and shellfish with the consequences of other aspects of trawling activity, especially the ploughing of seabed habitats. The model is not detailed to the level of individual species or exact locations. Rather it gives results at the level of a whole regional sea area, such as the North Sea or the whole of the west of Scotland. The project had three main components. First, was the extension of an existing mathematical model of a marine ecosystem to include explicit representation of the ploughing effects that different gears have on seabed habitats. Second, an analysis of a large international data set on activity, landings and catches by different fishing gears in northwest European waters, and the mapping of these onto different seabed habitats to generate inputs to the model. Finally, we carried out a series of sensitivity experiments with the model. These experiments investigated the whole ecosystem effects of seabed ploughing by different gears, using food web indicators relevant to the EU Marine Strategy Framework Directive, and compared them with the impact of one scenario for implementing a landing obligation, and the potential impacts of a reduction in overall fishing activity. For the North Sea, the results show that even if all ploughing effects were eliminated, the effects on the whole ecosystem would be equivalent to only a 1% or less change in overall harvesting rate of fish and shellfish. This is a very small effect compared to the changes in effective harvesting rate implied by the improvements in gear selectivity required to achieve the landing obligation. For the west of Scotland region, the model showed that the food web was more sensitive to the effects of ploughing by fishing gears than in the North Sea, but the effect was still small compared to the consequences of activity reduction overall. The greater sensitivity of the west of Scotland to seabed ploughing arose because the disturbance rate of muddy sediments was around 5-times higher than in the North Sea, almost entirely due to the activities of TR2 Nephrops trawling. Despite our conclusion that the regional scale food web effects of seabed ploughing are small compared to the primary consequences of harvesting fish, this is not to say that there are no effects on regional biodiversity, or significant effects at local scales on specific habitats or vulnerable species. In particular the study identifies the TR2 gear fleet as being responsible for the majority of ecosystem-wide consequences of seabed ploughing. This gear has a particularly high ploughing rate and its activity is focussed on muddy sediments where the nutrient chemistry processes are more vulnerable to ploughing than in sandy and coarser sediments

Spatial modelling of Calanus finmarchicus and Calanus helgolandicus : parameter differences explain differences in biogeography

The North Atlantic copepods Calanus finmarchicus and C. helgolandicus are moving north in response to rising temperatures. Understanding the drivers of their relative geographic distributions is required in order to anticipate future changes. To explore this, we created a new spatially explicit stage-structured model of their populations throughout the North Atlantic. Recent advances in understanding Calanus biology, including U-shaped relationships between growth and fecundity and temperature, and a new model of diapause duration are incorporated in the model. Equations were identical for both species, but some parameters were species-specific. The model was parameterized using Continuous Plankton Recorder Survey data and tested using time series of abundance and fecundity. The geographic distributions of both species were reproduced by assuming that only known interspecific differences and a difference in the temperature influence on mortality exist. We show that differences in diapause capability are not necessary to explain why C. helgolandicus is restricted to the continental shelf. Smaller body size and higher overwinter temperatures likely make true diapause implausible for C. helgolandicus. Known differences were incapable of explaining why only C. helgolandicus exists southwest of the British Isles. Further, the fecundity of C. helgolandicus in the English Channel is much lower than we predict. We hypothesize that food quality is a key influence on the population dynamics of these species. The modeling framework presented can potentially be extended to further Calanus species

Investigating trends in the growth of five demersal fish species from the Firth of Clyde and the wider western shelf of Scotland

Demersal fish landings from the Firth of Clyde peaked in 1973, then declined rapidly until the targeted demersal fishery ceased in 2005. The abundance of large fish decreased during this period, and their numbers have not recovered since 2005. We aim to determine whether changing growth rates have con- tributed to the decline in the abundance of large fish. Bottom trawl survey data from 1980–2012 was used to calculate the annual mean length-at-age and time series of von Bertalanffy growth parameters of five demersal species; cod, haddock, whiting, Norway pout and saithe. Two regions were considered: the Firth of Clyde and the neighbouring seas west of Scotland (the western shelf). There have been substantial decreases in the lengths of most age groups of Clyde haddock and whiting due to declines in both asymptotic length and von Bertalanffy growth rate. Lengths-at-age have also declined in western shelf populations, but at markedly slower rates than within the Clyde. Trends in temperature and year class strength tended to contribute little to changes in the growth parameters, so declines in length-at-age have been largely due to other factors. Fishing intensity is greater in the Clyde than western shelf, and the size selectivity of the fisheries differ as more Clyde vessels use Nephrops trawling gear. Since trends in growth were also more extreme in the Clyde, it appears as though size-selective fishing may have caused reductions in the lengths of these fish. If the changes in growth are partially due to fishing induced evolution then it may take many generations for the changes to reverse

The effect of viral plasticity on the persistence of host-virus systems

Phenotypic plasticity plays an important role in the survival of individuals. In microbial host-virus systems, previous studies have shown the stabilizing effect that host plasticity has on the coexistence of the system. By contrast, it remains uncertain how the dependence of the virus on the metabolism of the host (i.e. “viral plasticity”) shapes bacteria-phage population dynamics in general, or the stability of the system in particular. Moreover, bacteria-phage models that do not consider viral plasticity are now recognised as overly simplistic. For these reasons, here we focus on the effect of viral plasticity on the stability of the system under different environmental conditions. We compared the predictions from a standard bacteria-phage model, which neglects plasticity, with those of a modification that includes viral plasticity. We investigated under which conditions viral plasticity promotes coexistence, with or without oscillatory dynamics. Our analysis shows that including viral plasticity reveals coexistence in regions of the parameter space where models without plasticity predict a collapse of the system. We also show that viral plasticity tends to reduce population oscillations, although this stabilizing effect is not consistently observed across environmental conditions: plasticity may instead reinforce dynamic feedbacks between the host, the virus, and the environment, which leads to wider oscillations. Our results contribute to a deeper understanding of the dynamic control of bacteriophage on host populations observed in nature

Projected impacts of 21st century climate change on diapause in Calanus finmarchicus

Diapause plays a key role in the life cycle of high latitude zooplankton. During diapause animals avoid starving in winter by living in deep waters where metabolism is lower and met by lipid reserves. Global warming is therefore expected to shorten the maximum potential diapause duration by increasing metabolic rates and by reducing body size and lipid reserves. This will alter the phenology of zooplankton, impact higher trophic levels and disrupt biological carbon pumps. Here we project the impacts of climate change on the key North Atlantic copepod Calanus finmarchicus under IPCC RCP 8.5. Potential diapause duration is modelled in relation to body size and overwintering temperature. The projections show pronounced geographic variations. Potential diapause duration reduces by more than 30% in the Western Atlantic, whereas in the key overwintering centre of the Norwegian Sea it changes only marginally. Surface temperature rises, which reduce body size and lipid reserves, will have a similar impact to deep water changes on diapause in many regions. Because deep water warming lags that at the surface, animals in the Labrador Sea could offset warming impacts by diapausing in deeper waters. However, the ability to control diapause depth may be limited

Modelling sea level surges in the Firth of Clyde, a fjordic embayment in south-west Scotland

Storm surges are an abnormal enhancement of the water level in response to weather perturbations. They have the capacity to cause damaging flooding of coastal regions, expecially when they coincide with astronomical high spring tides. Some areas of the UK have suffered particularly damaging surge events, and the Firth of Clyde is a region with high risk due to its location and morphology. Here we use a three-dimensional high spatial resolution hydrodynamic model to simulate the local bathymetric and morphological enhancement of surge in the Clyde, and disaggregate the effects of far-field atmospheric pressure distribution and local scale wind forcing of surges. A climatological analysis, based on 30 years of data from Millport tide gauges is also discussed. The results suggest that floods are not only caused by extreme surge events, but also by the coupling of spring high tides with moderate surges. Water level is also enhanced by a funnelling effect due to the bathymetry and the morphology of fjordic sealochs and the River Clyde estuary. In a world of rising sea level, studying the propagation and the climatology of surges and high water events is fundamental. In addition, high-resolution hydrodynamic models are essential to forecast extreme events and prevents the loss of lives, or to plan coastal defences solutions