Limitations of grazing rate equations: the case for time-series measurements

The limitations of traditional zooplankton grazing rate equations were analysed, and the relative advantages of taking time-series measurements or single end-point measurements of grazing rate examined. For zooplankters with variable feeding rates, the time-series approach is the only acceptable method. Use of end-point measurements to calculate feeding rates results in significant error if clearance rate changes or feeding ceases during the experiment, i.e. when the grazing coefficient is not constant, as is assumed in the clearance rate equations. The use of timeseries measurements is particularly important above the critical concentration for saturated ingestion rate. The functional response plot of ingestion rate versus mean cell concentration is inappropriate statistically and should be modified to avoid compounding variables appearing on both axes of the plot.     

Stratification and Circulation in a Shallow Turbid Waterbody

Shallow waterbodies are often assumed to be well mixed in the vertical. However, when they are characterised by high turbidity levels, absoption of solar heating within a relatively thin surface layer can produce thermal stratification. Results from an intensive monitoring program have been combined with three-dimensional circulation modelling to examine the diurnal stratification cycles in a small turbid waterbody. The waterbody, known as Rushy Billabong, is located in southeastern Australia and its high turbidity coupled with forcing by wind and solar radiation resulted in regular diurnal cycles of stratification and overturning. Under conditions of light wind and high solar radiation, the model results were generally consistent with the observed temperature field. However, under stronger winds, preferential cooling and sinking of shallow water around the edge of the lake began to contribute significantly to the interior stratification. Model estimates then became more sensitive to the detailed bathymetry and the choice of turbulence parameterisation. The level of stratification is also shown to influence the circulation in the billabong by trapping the wind-driven flow near the surface. Insights provided by the observations and modelling may have broader implications for the management of small turbid systems such as settling ponds, aquaculture ponds, and some natural wetlands.     

Ecological degradation and hydraulic dispersion of contaminant in wetland

For the typical case of a pulsed contaminant emission into a free surface wetland flow, a theoretical analysis is presented in this paper for the decay of the depth-averaged concentration under the combined action of ecological degradation and hydraulic dispersion. Based on a first-order reaction model extensively employed in related ecological risk assessment and environmental hydraulic design, the effect of ecological degradation is separated from the hydraulic effect via an exponential transformation for the general formulation for contaminant transport. The speed profile of a fully developed steady flow through the wetland is obtained. A hydraulic dispersion model for the depth-averaged concentration is devised as an extension of Taylor’s classical analysis on dispersion, and corresponding hydraulic dispersivity is obtained by Aris’s method of moments. Analytical solution of depth-averaged concentration is rigorously derived and characterized. For typical pollutant constituents in wastewater emission, the evolution of contaminant cloud in the wetland flow is illustrated by critical length and duration of influenced region with contaminant concentration beyond given environmental standard level, with essential implications for ecological risk assessment and environmental management.     

Mixing dynamics of turbidity currents interacting with complex seafloor topography

Direct Numerical Simulations are employed to investigate the mixing dynamics of turbidity currents interacting with seamounts of various heights. The mixing properties are found to be governed by the competing effects of turbulence amplification and enhanced dissipation due to the three-dimensional topography. In addition, particle settling is seen to play an important role as well, as it affects the local density stratification, and hence the stability, of the current. The interplay of these different mechanisms results in the non-monotonic dependence of the mixing behavior on the height of the seamount. Regions of dilute lock fluid concentration generally mix more intensely as a result of the seafloor topography, while concentrated lock fluid remains relatively unaffected. For long times, the strongest mixing occurs for intermediate bump heights. Particle settling is seen to cause turbidity currents to mix more intensely with the ambient than gravity currents.     

Modelling the biochemical oxidation processes in artificial conditions of waste treatment plants

For natural water bodies there are many models of biochemical oxidation of organic pollutants, from simple to complicated ones. For the artificial conditions of waste water treatment plants there are numerous models of oxidation processes too. The authors believe that a better understanding of these processes in nature would be gained if the oxidation processes in more simple artificial conditions were understood.An attempt has been made to explain the variety of types of models of waste treatment in an activated sludge system or a biofilm reactor by the diffusion mechanism of oxidation of single substrates on the one hand, and by superposition of the kinetics of oxidation of single substrates in measurements of the dynamics of oxidation of a complex pollutant on the other hand.The conditions in which zero- and first-order models are valid in the oxidation of single substrates are derived. Respective formulae for rate constants are given. Monod's model is valid in a broader range of substrate concentration variations. An approximate formula for the half-saturation constant is proposed. Satisfactory agreement with experimental data for glucose and ammonia substrates is shown.The formal character of models being used at present is claimed for multicomponent substrates. The accuracy of the calculation is largely governed by the number of model coefficients. Similar results obtained by Monod's and Grau's models, often used in practice, are emphasized.     

A Bayesian approach to retransformation bias in transformed regression

Ecological data analysis often involves fitting linear or nonlinear equations to data after transforming either the response variable, the right side of the equation, or both, so that the standard suite of regression assumptions are more closely met. However, inference is usually done in the natural metric and it is well known that retransforming back to the original metric provides a biased estimator for the mean of the response variable. For the normal linear model, fit under a log-transformation, correction factors are available to reduce this bias, but these factors may not be generally applicable to all model forms or other transformations. We demonstrate that this problem is handled in a straightforward manner using a Bayesian approach, which is general for linear and nonlinear models and other transformations and model error structures. The Bayesian framework provides a predictive distribution for the response variable so that inference can be made at the mean, or over the entire distribution to incorporate the predictive uncertainty.     

Sustained dynamic transience in a Lotka-Volterra competition model system for grassland species

Theoretical approaches, such as the Lotka-Volterra framework, enable predictions about long term species coexistence based on stability criteria, but generally assume temporal constancy of system equations and parameters. In real world systems, temporal variability may interfere with the attainment of stable states. Managed grassland ecosystems in Northwestern Europe experience structural periodic fluctuations in environmental conditions: the seasons. In addition, periodic disturbances such as cutting are very common. Here we show, using a Lotka-Volterra system applied to grassland species with empirically derived parameters, that seasonal variability can result in a time dependent equilibrium and redirection of displacement processes.Parameter estimates differed between species and - in most cases - between the seasons. As a result, five of the fifteen tested species combinations had different outcomes of species interactions between seasons. This indicates that systems remain in dynamic transience over the year as the equilibrium changes and the species composition of the system follows the equilibrium without ever attaining it. The non-attainment of the steady state enables coexistence of species even if there is competitive exclusion in one of the seasons. For three of the fifteen species combinations, cutting frequency affected the long-term coexistence patterns. Cutting resets the biomass of competing species and favours during regrowth those species that have a high growth rate, which can alter species coexistence in comparison to a Lotka-Volterra model without cutting. The Lotka-Volterra framework with seasonally changing empirical parameters predicts coexistence as a possible outcome of systems that in component seasons are characterised by exclusion, and vice versa.     

Physiological effects of the detergent linear alkylbenzene sulphonate on blue mussel larvae (Mytilus edulis) in laboratory and mesocosm experiments

A series of laboratory (short-term exposure in small beakers) studies and a 19 d mesocosm (6 m³ polyethylene bags filled with fjord water) study were conducted on blue mussel, Mytilus edulis, larvae and plantigrades exposed to a concentration gradient of the detergent linear alkylbenzene sulphonate (LAS, 0 to 39 mg l⁻¹). LAS is increasingly found in nearshore environments receiving wastewater from urban treatment plants. The aims were to observe physiological effects on swimming, grazing and growth in the laboratory and effects on settling and population development at in situ conditions (in field mesocosms) in order to evaluate the damages on ciliated meroplankton caused by LAS. In the laboratory the larvae showed a 50% mortality at 3.8 mg LAS l⁻¹ after 96 h exposure whether or not food was provided. Additionally the swimming behaviour was affected at 0.8 mg LAS l⁻¹ (i.e. a more compact swimming track, a smaller diameter of the swimming tracks, and reduced swimming speed). The larval particle grazing was reduced 50% at 1.4 mg LAS l⁻¹. The specific growth rate of the larvae was reduced to half at 0.82 mg LAS l⁻¹ over 9 d. During the mesocosm experiment, the larval population showed a dramatic decrease in abundance within 2 d at concentrations as low as 0.08 mg LAS l⁻¹, both due to a significantly increased mortality, but also due to settling. The settling success was reduced at the same LAS concentration as that at which mortality was observed to increase significantly. In addition to reduced settling rate, the larvae showed delayed metamorphosis and reduced shell growth as a response to LAS. Our hypothesis that the larval ciliary apparatus, crucial for normal swimming, orientation, and settling behaviours and for particle uptake, was damaged due to LAS exposure is supported by our results. This is confirmed by the physiological data (grazing, growth) and in the direct video-based observations of larval performance (swimming) and provides a reasonable explanation for what was observed in the bags (abundance, settling, mortality). These physiological effects on blue mussel larvae/plantigrades occurred at LAS concentrations reported to occur in estuarine waters. Received: 15 January 1997 / Accepted: 12 February 1997     

Spatial elements of mortality risk in old-growth forests

For many species of long-lived organisms, such as trees, survival appears to be the most critical vital rate affecting population persistence. However, methods commonly used to quantify tree death, such as relating tree mortality risk solely to diameter growth, almost certainly do not account for important spatial processes. Our goal in this study was to detect and, if present, to quantify the relevance of such processes. For this purpose, we examined purely spatial aspects of mortality for four species, Abies concolor, Abies magnifica, Calocedrus decurrens, and Pinus lambertiana, in an old-growth conifer forest in the Sierra Nevada of California, USA. The analysis was performed using data from nine fully mapped long-term monitoring plots. In three cases, the results unequivocally supported the inclusion of spatial information in models used to predict mortality. For Abies concolor, our results suggested that growth rate may not always adequately capture increased mortality risk due to competition. We also found evidence of a facilitative effect for this species, with mortality risk decreasing with proximity to conspecific neighbors. For Pinus lambertiana, mortality risk increased with density of conspecific neighbors, in keeping with a mechanism of increased pathogen or insect pressure (i.e., a Janzen-Connell type effect). Finally, we found that models estimating risk of being crushed were strongly improved by the inclusion of a simple index of spatial proximity. Not only did spatial indices improve models, those improvements were relevant for mortality prediction. For P. lambertiana, spatial factors were important for estimation of mortality risk regardless of growth rate. For A. concolor, although most of the population fell within spatial conditions in which mortality risk was well described by growth, trees that died occurred outside those conditions in a disproportionate fashion. Furthermore, as stands of A. concolor become increasingly dense, such spatial factors are likely to become increasingly important. In general, models that fail to account for spatial pattern are at risk of failure as conditions change.     

Biological parameters used in setting captive‐breeding quotas for Indonesia's breeding facilities

The commercial captive breeding of wildlife is often seen as a potential conservation tool to relieve pressure on wild populations, but laundering of wild‐sourced specimens as captive bred can seriously undermine conservation efforts and provide a false sense of sustainability. Indonesia is at the center of such controversy; therefore, we examined Indonesia's captive‐breeding production plan (CBPP) for 2016. We compared the biological parameters used in the CBPP with parameters in the literature and with parameters suggested by experts on each species and identified shortcomings of the CBPP. Production quotas for 99 out of 129 species were based on inaccurate or unrealistic biological parameters and production quotas deviated more than 10% from what parameters in the literature allow for. For 38 species, the quota exceeded the number of animals that can be bred based on the biological parameters (range 100–540%) calculated with equations in the CBPP. We calculated a lower reproductive output for 88 species based on published biological parameters compared with the parameters used in the CBPP. The equations used in the production plan did not appear to account for other factors (e.g., different survival rate for juveniles compared to adult animals) involved in breeding the proposed large numbers of specimens. We recommend the CBPP be adjusted so that realistic published biological parameters are applied and captive‐breeding quotas are not allocated to species if their captive breeding is unlikely to be successful or no breeding stock is available. The shortcomings in the current CBPP create loopholes that mean mammals, reptiles, and amphibians from Indonesia declared captive bred may have been sourced from the wild.     

Analytical expression for predicting the reduced settling velocity of small particles in turbulence

The influence of turbulence on the settling velocity of small particles remains an inconclusive research subject. Both enhanced and retarded particle settling compared to quiescent settling have been reported in previous literature, and several theories have been proposed. Among the mechanisms that account for reduced settling velocities in turbulence, the loitering effect is an important one that generally exists in various conditions. This study focuses on an analytical prediction of reduced particle settling velocities due to the loitering effect. By considering the velocity autocorrelation function as a step function analogous to the free path theory, and using a modified integral time scale to capture the essence of the loitering effect, an analytical expression is derived for predicting the reduction in particle settling velocities in turbulent flows. Calculation results of the expression are then examined by comparing with the results of a random walk model, direct numerical simulations that conditionally captured the reduction of particle settling velocities due to the loitering effect, and several representative experiments. Major possible influencing factors on the prediction of the analytical expression and applicable conditions of the expression are then further discussed. The proposed analytical expression is shown to be suitable for predicting the reduced settling velocities of small particles with relatively weak inertia in turbulent flows and could provide a reasonable explanation for reported cases in which small to moderate reductions in particle settling velocities were observed.

     

A stochastic model for estimating sustainable limits to wildlife mortality in a changing world

Human-caused mortality of wildlife is a pervasive threat to biodiversity. Assessing the population-level impact of fisheries bycatch and other human-caused mortality of wildlife has typically relied upon deterministic methods. However, population declines are often accelerated by stochastic factors that are not accounted for in such conventional methods. Building on the widely applied potential biological removal (PBR) equation, we devised a new population modeling approach for estimating sustainable limits to human-caused mortality and applied it in a case study of bottlenose dolphins affected by capture in an Australian demersal otter trawl fishery. Our approach, termed sustainable anthropogenic mortality in stochastic environments (SAMSE), incorporates environmental and demographic stochasticity, including the dependency of offspring on their mothers. The SAMSE limit is the maximum number of individuals that can be removed without causing negative stochastic population growth. We calculated a PBR of 16.2 dolphins per year based on the best abundance estimate available. In contrast, the SAMSE model indicated that only 2.3–8.0 dolphins could be removed annually without causing a population decline in a stochastic environment. These results suggest that reported bycatch rates are unsustainable in the long term, unless reproductive rates are consistently higher than average. The difference between the deterministic PBR calculation and the SAMSE limits showed that deterministic approaches may underestimate the true impact of human-caused mortality of wildlife. This highlights the importance of integrating stochasticity when evaluating the impact of bycatch or other human-caused mortality on wildlife, such as hunting, lethal control measures, and wind turbine collisions. Although population viability analysis (PVA) has been used to evaluate the impact of human-caused mortality, SAMSE represents a novel PVA framework that incorporates stochasticity for estimating acceptable levels of human-caused mortality. It offers a broadly applicable, stochastic addition to the demographic toolbox to evaluate the impact of human-caused mortality on wildlife.     

Study on the concentration distribution in a trapezoidal open-channel flow with a side discharge

The number and distribution of pollutant concentration in a trapezoidal open channel flow with a side discharge is calculated and effects of the bank gradient are investigated in this paper. A sigma-coordinate water quality numerical model is used to simulate the process of both water and pollutant transportation in the trapezoidal channel open flow. The diffusion coefficient used in the prediction is determined by two methods including constant coefficient and the depth-averaged k-epsilon turbulence closure model. The change of the concentration with the bank gradient is acquired based on the simulation of cases with different bank gradients. An analytical formula is derived by using the mirror image method and related diffusion theories, ignoring the discharge momentum and the influence of the opposite bank. The formula can predict the number and distribution of pollutant concentration with some acceptable errors. The results demonstrate that the bank gradient has great influence on the concentration distribution which will decrease with the increase of the bank gradient approximately following a hyperbolic law.     

A model of vertical distribution of suspended matter in an open channel flow

A quasi-stationary model of vertical distribution of concentration of suspended particular matter in the bottom layer of 1D open channel with a sloped bottom and varying free surface slope is discussed. The model proceeds from the balance between the turbulent diffusion and settling with the buoyancy flux effects on the medium turbulence neglected. The model outcome is formulated in the form of an analytic formula for the vertical distribution of concentration. It is shown that the derived formula embraces two basic types of vertical distribution of concentration, one with a monotonic decrease of concentration gradient and the other with a gradient maximum (lutocline) located at some distance from the bottom. The first distribution type realizes for a relatively large settling velocity or low intensity of turbulence and the second type for a small settling velocity or high intensity of turbulence. The skill of the model to mimic realistic situations is demonstrated on data measured in the Jiaojiang Estuary (China).     

Improved formulae of velocity distributions along the vertical and transverse directions in natural rivers with the sidewall effect

The distribution of flow velocity is a basis for the research into the transport of flow and sediment in natural rivers. Characteristics of velocity distribution in narrow-deep natural rivers are different from those in wide-shallow open channels, and the effect of sidewalls on the distribution of flow velocity is considerable, which leads to a large transverse gradient of the depth-averaged velocity, with the maximum velocity occurring below the water surface. Based on the Reynolds equation of turbulence flow and the analysis of the features of velocity distribution in natural rivers, improved formulae with two empirical parameters α and β have been proposed for the velocity distributions along the vertical and transverse directions, with the effect of sidewalls being considered, through solving the definite solution problem by the method of variable separation. The proposed formulae were validated fully through comparisons between the calculated and measured velocity profiles and depth-averaged velocities at several sections in the Yangtze and Baitarani Rivers, with close agreement between them being obtained. The formula of velocity distribution along the transverse direction in natural rivers with the sidewall effect was also compared with previous studies, and the calculation accuracy of this formula at a section with a narrow-deep geometry was higher than the accuracy of the previous equations. It is confirmed that the proposed formulae can reproduce well the distribution characteristics of flow velocity along the vertical and transverse directions in narrow-deep natural rivers, with a more wide application in practice.     

Aerial surveys of manatees (<Emphasis Type="Italic">Trichechus manatus)</Emphasis> in Lee County,Florida<Emphasis Type="Italic">,</Emphasis> provide insights regarding manatee abundance and real time information for managers and enforcement officers

Conservation and management of the endangered Florida manatee is often centered on reducing mortality caused by watercraft collisions. Lee County, Florida, has led the state in watercraft-related mortality for eight of the last 10 years. This county is of particular concern as it contains important habitat for manatees, including extensive feeding grounds and an artificial warm-water refuge where more than 900 manatees have been recorded on a single day. Distributional aerial surveys were conducted from April 2007 through April 2009 over Lee County waters. Surveys yielded higher numbers of manatees than previously observed in this area. Using GIS methodology, kernel density analysis illustrated seasonal changes in distribution patterns and highlighted areas where manatees were most densely clustered. For example, during summer months, manatees were widely distributed throughout the survey area, with high-density areas associated with seagrass beds. During winter months, manatees were densely clustered at warm-water sites and over feeding grounds within close distance of these sites. These seasonal distribution patterns coincide well with speed zone designations. Counts and distributions of manatees were made available, almost immediately if necessary, to local marine law enforcement in an attempt to focus resources toward reducing manatee-watercraft collisions. Future studies should implement similar communication strategies to improve conservation efforts.     

The Residence Time of Settling Particles in the Surface Mixed Layer

The transport from the upper mixed layer into the pycnocline of particles with negative buoyancy is considered. Assuming the hydrodynamic parameters to be time- independent, an adjoint model is resorted to that provides a general expression of the residence time in the mixed layer of the constituent under study. It is seen that the residence time decreases as the settling velocity increases or the diffusivity decreases. Furthermore, it is demonstrated that the residence time must be larger than z/w and smaller than h/w, where z, h and w denote the distance to the pycnocline, the thickness of the mixed layer and the sinking velocity. In the vicinity of the pycnocline, the residence time is not necessarily zero; its behaviour critically depends on the eddy diffusivity profile in this region. Closed-form solutions are obtained for constant and quadratic diffusivity profiles, which allows for an analysis of the sensitivity of the residence time to the Peclet number. Finally, an approximate value is suggested of the depth-averaged value of the residence time.     

The Value of Species and the Ethical Foundations of Assisted Colonization

Abstract: Discourse around assisted colonization focuses on the ecological risks, costs, and uncertainties associated with the practice, as well as on its technical feasibility and alternative approaches to it. Nevertheless, the ethical underpinnings of the case for assisted colonization are claims about the value of species. A complete discussion of assisted colonization needs to include assessment of these claims. For each type of value that species are thought to possess it is necessary to determine whether it is plausible that species possess the type of value and, if so, to what extent their possessing it justifies assisted colonization. I conducted such an assessment for each of the predominant types of value ascribed to species: ecological, instrumental (including option value), existence, and intrinsic value (including interest‐based, objective, and valuer‐dependent intrinsic value). The vast majority of species, including several that have been proposed as candidates for assisted colonization, have much less value than is often presumed. Moreover, with respect to some types of value, assisted colonization would not fully preserve the value of the target species even if it were to keep the target species in existence. Therefore, the case for assisted colonization is significantly weaker and more qualified than its advocates often suppose. There may be exceptional species for which assisted colonization is well justified—and for this reason, case‐by‐case assessment is necessary—but in general the burden of justification generated by the ecological risks associated with assisted colonization is not met by the value potentially preserved by assisted colonization. This suggests that assisted colonization ought to have, at most, a very minor role in the portfolio of ecosystem management practices, even as it pertains to species conservation under conditions of rapid climate change.     

Similarity theory and parameterization of mixing in the upper ocean

Boundary layers with small thermal and mechanical inertia are close to steady-state conditions. This underlies the Monin-Obukhov similarity theory and explains why the surface values of the fluxes can be chosen as external parameters. For fluids with large thermal inertia, such as the ocean, the thermal time scale is relatively large, and the density flux is a complex function of depth; thus, the external thermal forcing is no longer a governing parameter. However, the mechanical inertia of the upper ocean is about three orders of magnitude smaller than the thermal inertia. Consequently, the upper ocean can be considered as steady-state in the dynamic sense, to any dynamic property depends primarily on the depth, the surface momentum flux, and the vertical density structure. This property allows us to suggest an alternative formulation of the similarity theory for the stratified boundary layers through specification of a new stratification parameter which characterizes the internal density structure instead of the external density flux. The turbulent mixing coefficient is derived as dependent on the stratification parameter. The latter includes the surface stress and the integral density deficit for the entire layer above. The general form and the asymptotic behavior of the nondimensional turbulent mixing coefficient as a function of the stratification parameter are obtained using dimensional considerations. Determination of numerical parameters is based on 8 years of temperature profiles acquired at the Ocean Weather Ship (OWS) PAPA. Finally, a method for calculating the profile of the turbulent mixing coefficient is obtained. This approach reproduces the 8-year evolution of the upper ocean with the maximum rms difference of approximately 1C and the bias of 1C over the depth range 0–150 m. Additional 1-year simulation of the upper ocean at OWS CHARLEY and 9-year simulation at OWS NOVEMBER confirms reasonable applicability of this approach. The proposed simple turbulent mixing scheme reproduces the evolution of the upper ocean with accuracies similar to those obtained using much more complicated models.     

A test of two models of different levels of complexity for predicting changes of phosphorus concentration in a lake's outflow

The objective of this investigation is to compare the ability of a one-box model and a two-box model to predict the temporal variations of total phosphorus in the outflow of several lakes. The one-box model considers only total phosphorus and treats the lake as well-mixed, all year round. The two-box model considers two phosphorus fractions and the epilimnion and hypolimnion. For five shallow Canadian Shield lakes, some of the temporal variability in lake phosphorus concentrations can be explained on the basis of changes in hydraulic inflows and phosphorus loadings. Both models give roughly similar predictions for shallow lakes with high hydraulic loadings (1–200 m/year) and small variations in total phosphorus concentrations. In comparing the settling and hydraulic outflow mechanisms, a sensitivity analysis shows that both models are more sensitive to the settling rate if the lake's hydraulic loadings are less than 1 m/year, and more sensitive to the outflow rate if the lake's hydraulic loadings are greater than 100 m/year. This analysis suggests a priority for concentrating economic and other resources in conducting field measurement programs for testing phosphorus models.