Exploitation of a single-cohort fishery under risk: A simulation-optimization approach

A numerical approach involving dynamic programming and computer simulation is used to examine the socially optimal exploitation of a single-cohort fishery under risk, with specific reference to the Exmouth Gulf Prawn Fishery in Western Australia. Best management strategies for given investment levels are sought before optimizing investment. The results for this industry show that time of year is much more important then level of biomass in determining best fishing policies, and that the timing of the catch is sensitive to natural fluctuations in some biological variables. Employing a “closed season” policy for part of the year appears an attractive way of reconciling private and social objectives under commonality. Under or overcapitalization does not reduce benefits markedly.     

Estimating abundance: a non parametric mark recapture approach for open and closed systems

We present a novel, non-parametric, frequentist approach for capture-recapture data based on a ratio estimator, which offers several advantages. First, as a non-parametric model, it does not require a known underlying distribution for parameters nor the associated assumptions, eliminating the need for post-hoc corrections or additional modeling to account for heterogeneity and other violated assumptions. Second, the model explicitly deals with dependence of trials by considering trials to be dependent; therefore, cluster sampling is handled naturally and additional adjustments are not necessary. Third, it accounts for ordering, utilizing the fact that a system with a small population will have a greater frequency of recaptures “early” in the survey work compared to an identical system with a larger population. We provide mathematical proof that our estimator attains asymptotic minimum variance under open systems. We apply the model to a data set of bottlenose dolphins (Tursiops truncatus) and compare results to those from classic closed models. We show that the model has an impressive rate of convergence and demonstrate that there’s an inverse relationship between population size and the proportion of the population that need to be sampled, while achieving the same degree of accuracy for abundance estimates. The model is flexible and can apply to ecological situations as well as other situations that lend themselves to capture recapture sampling.     

A simulation model of management alternatives in a freshwater fishery

A model for investigating management alternatives on the Pyramid Lake-Truckee River system of Nevada and California is presented. Cutthroat trout, Cui-ui, Tahoe Sucker and Tui Chub are modeled with special emphasis on river spawning by trout. Management decision variables include hatchery input, water flow control, and diversion screening. Preliminary results indicate that some hatchery input will be needed to support the trout even with the best river management.     

Estimating an homogeneous series of a population abundance indicator despite changes in data collection procedure: A hierarchical Bayesian modelling approach

Abundance indicators are required both to assess and to manage wild populations. As new techniques are developed and teams in charge of gathering the data change, data collection procedures (DCPs) can evolve in space and time. How to estimate an homogeneous series of abundance indicator despite changes in DCP? To tackle this question a hierarchical Bayesian modelling (HBM) approach is proposed. It integrates multiple DCPs in order to derive a single abundance indicator that can be compared over space and time irrespective of the DCP used. Compared to single DCP models, it takes further advantage for abundance estimation of the joint treatment of a larger set of spatio-temporal units. After presenting the general formulation of our HBM approach, it is applied to the juvenile Atlantic salmon (Salmo salar L.) population of the River Nivelle (France). Posterior model checking, using χ² discrepancy measure, do not reveal any inadequacy between the model and the data. Despite a change in the DCP used (successive removals to catch-per-unit of effort), a unique abundance indicator for the 425 spatio-temporal units (site × year) sampled over twenty-four years (1985-2008) is estimated. The HBM approach allows the assessment of precision of the abundance estimates and shows variation between DCPs: a reduction in precision is observed during the most recent years (2005-2008) when only the catch-per-unit of effort DCP was used. The merits and generality of our HBM approach are discussed. We contend it extends previous single DCP models or inter-calibration of two DCPs, and it could be applied to a wide range of specific situations (taxon and DCPs).     

Assessing competition between Steller sea lions and the commercial groundfishery in Alaska: A bioenergetics modelling approach

In the last three decades the western stock of the Steller sea lion (Eumetopias jubatus) has declined by more than 85%. Nutritional stress resulting in increased juvenile mortality is one of the leading hypotheses to account for this decline. Competition between Steller sea lions and the commercial groundfishery for walleye pollock (Theragra chalcogramma) has been proposed as a mechanism underlying the nutritional stress. In order to examine the competition component of the nutritional stress hypothesis, we developed a bioenergetics-based model to project the population trends of Steller sea lions under various scenarios of continued groundfish harvest. Annual energy budgets were calculated for the Gulf of Alaska population of Steller sea lions, and compared with projected available energy from walleye pollock under a variety of harvest scenarios. Model simulations produced 50-year Steller sea lion population projections consistent with current trends, as well as with published projections for stable and increasing populations from stable age distribution life table models. Model simulations were unable to produce energy deficits sufficient to account for the decline in Steller sea lions, but do suggest areas where existing data need supplementing.     

It takes more than a village: the challenges of co-management in Uganda's fishery and forestry sectors

Decentralisation policies in least developed countries have emerged in response to failed centralised natural resource governance programmes because high-value natural resources are distributed unequally, with central governments often reaping more than local-level users. Current natural resource governance institutions have been created to remedy the problems that central governments formerly posed. Here, we argue that Uganda's forestry and fishery resources are biologically diverse and thus amenable to current decentralised management programmes, provided that there is compromise between market values and local cultural and subsistence values and uses. We observe, however, Uganda's current institutional arrangement favours the former over the latter and determine that successful natural resource decentralisation requires strengthening local-level natural resource institutions with increased fiscal flow, enforcement, monitoring and judicial powers. A strong and reliable partnership between local-level resource users and the central government is necessary for this to occur.     

The fishery in a fluctuating environment: Coexistence of specialist and generalist fishing vessels in a multipurpose fleet

The fishery is a prime example of a common property renewable resource industry. A second prominent feature is the extreme variability of its environment, both biologic and economic. Traditionally fishing vessels have harvested a single species or aggregation, but now powerful multipurpose vessels have been introduced which switch targets as opportunities arise. These vessels represent an adaptation to the fluctuating environment: they give up efficiency of specialized operation for flexibility under changing conditions. We analyze, from the point of view of economic efficiency, the common property operation of a mixed fleet of generalist and specialist fishing vessels in a fluctuating environment.     

Sustainable fishing gear: the case of modified circle hooks in a Costa Rican longline fishery

Our research aims to identify longline fishing gear modifications that can improve fishing selectivity and reduce incidental capture of non-target species. Catch rates and anatomical hook locations (AHL) were compared when using a 14/0 standard ??control?? circle hook with a 0° offset and an experimental ??appendage?? hook in a Costa Rican longline fishery. With the appendage, the maximum dimension of the appendage hook was increased by 10% and the minimum dimension of the hook by 19%. A total of 1,811 marine animals were captured during five fishing trips. By taxonomic groups, sea turtles represented the largest total catch (27%), followed by sharks (26%), rays (25%), mahimahi (Coryphaena hippurus) (12%), and tunas and billfish (10%). Non-target and discard species, such as rays and sea turtles, accounted for over half of the total catch. Catch per unit effort (CPUE; number of individuals per 1,000 hooks) was higher with control hooks compared to appendage hooks for all species?? categories except rays; appendage hooks caught 52% fewer sea turtles and 23% fewer tunas and billfish than standard hooks, which represents a significant reduction in bycatch of endangered and other species. No differences were found in the AHL for sea turtles, suggesting use of the appendage may not incur additional advantages regarding turtles?? post-release survivorship. Despite lower catch rates for marketable species, such as sharks and mahimahi, use of the appendage resulted in dramatic reductions in catch rates of sea turtles. The results suggest that large scale adoption of hooks with a significantly wider hook dimension could be an effective conservation measure to maintain marine biodiversity while allowing for continued fishing.     

Test for independence between marks and points of marked point processes: a subsampling approach

Ecological data often involve measurements taken at irregularly spaced locations (e.g., the heights of trees in a forest). A useful approach for modeling such data is via a marked point process, where the marks (i.e., measurements) and points (i.e., locations) are often assumed to be independent. Although this is a convenient assumption, it may not hold in practice. Schlather et al. (Journal of the Royal Statistical Society Services B, 66, 79–93, 2004) proposed a simulation-based approach to test this assumption. This paper presents a new method for testing the assumption of independence between the marks and the points. Instead of considering a simulation approach, we derive analytical results that allow the test to be implemented via a conventional χ² statistic. We illustrate the use of our approach by applying it to an example involving desert plant data.     

Fish assemblages composition in a natural, then regulated, stream: A quantitative long-term study

This paper tests the hypothesis how effectively fish assemblage composition was shaped by local climate changes and by engineering impact in 1989. This was possible due to the monitoring protocols of the present study, which allowed estimation of the magnitude of anthropogenic changes from changes naturally occurring in nature. Fish were sampled at the end of every growing season (October) for 23 years at five contiguous sites in a stream, before (1979-1988) and after (1989-2001) regulation. In each sample, six successive electrofishing passes were used to calculate the density and mean biomass for assemblage analysis using the Zippin model. During the study, the natural, meandering stream with pools, riffles, and a moderate canopy was modified into a straight stream of uniform width and depth, stripped of all vegetation. The output layer of a self-organizing map (SOM, the artificial neural network algorithm) applied in this study for site similarity analysis was partitioned into six subclusters placed in two main clusters. Subclusters in the upper part of the SOM were occupied chiefly by regulated stream samples and those in the lower part of the SOM by natural stream samples. Subclusters in the middle position, contained both natural (19) and regulated (20) samples in nearly equal proportion. In addition, the SOM contained one subcluster with sites only from the regulated period and another with only natural sites. Differences between subclusters were attributed to differences in climate, with some differences profound. Warming of the local weather, which became most evident in the 1990s, may have resulted in changes in fish assemblages. This is shown in the SOM, in which samples from the 1980s with cold years dominate the bottom of the SOM, whereas those from the 1990s and later are at the top. Subclusters dominated by regulated or natural sites were not always significantly different when the number of species and diversity indices were considered. Clear differences between the regulated and natural samples involved qualitative characteristics and mainly concerned assemblage composition. They were also confirmed by significant IndVal values (indicator species) and neither mixed subcluster contained important species in their assemblages.     

Estimating the objectives of a public firm in a natural resource industry

The purpose of this paper is to understand the behavior of policymakers in a public firm. To accomplish this goal, the objectives of a government-owned firm operating in the Saskatchewan uranium industry are econometrically estimated. The estimates are used to determine the importance policymakers attach to the outcomes resulting from their behavior and to examine how the firm might respond to changes in its economic environment. Empirical results indicate that the public firm is willing to reduce profits in order to increase employment and reserves.     

Sinks for nitrogen inputs in terrestrial ecosystems: a meta-analysis of 15N tracer field studies

Effects of anthropogenic nitrogen (N) deposition and the ability of terrestrial ecosystems to store carbon (C) depend in part on the amount of N retained in the system and its partitioning among plant and soil pools. We conducted a meta-analysis of studies at 48 sites across four continents that used enriched 15N isotope tracers in order to synthesize information about total ecosystem N retention (i.e., total ecosystem 15N recovery in plant and soil pools) across natural systems and N partitioning among ecosystem pools. The greatest recoveries of ecosystem 15N tracer occurred in shrublands (mean, 89.5%) and wetlands (84.8%) followed by forests (74.9%) and grasslands (51.8%). In the short term (< 1 week after 15N tracer application), total ecosystem 15N recovery was negatively correlated with fine-root and soil 15N natural abundance, and organic soil C and N concentration but was positively correlated with mean annual temperature and mineral soil C:N. In the longer term (3-18 months after 15N tracer application), total ecosystem 15N retention was negatively correlated with foliar natural-abundance 15N but was positively correlated with mineral soil C and N concentration and C:N, showing that plant and soil natural-abundance 15N and soil C:N are good indicators of total ecosystem N retention. Foliar N concentration was not significantly related to ecosystem 15N tracer recovery, suggesting that plant N status is not a good predictor of total ecosystem N retention. Because the largest ecosystem sinks for 15N tracer were below ground in forests, shrublands, and grasslands, we conclude that growth enhancement and potential for increased C storage in aboveground biomass from atmospheric N deposition is likely to be modest in these ecosystems. Total ecosystem 15N recovery decreased with N fertilization, with an apparent threshold fertilization rate of 46 kg N x ha(-1) x yr(-1) above which most ecosystems showed net losses of applied 15N tracer in response to N fertilizer addition.     

A three-isotope approach to disentangling the diet of a generalist consumer: the yellow-legged gull in northwest Spain

The widespread omnivory of consumers and the trophic complexity of marine ecosystems make it difficult to infer the feeding ecology of species. The use of stable isotopic analysis plays a crucial role in elucidating trophic interactions. Here we analysed δ¹⁵N, δ¹³C and δ³⁴S in chick feathers, and we used a Bayesian triple-isotope mixing model to reconstruct the diet of a generalist predator, the yellow-legged gull (Larus michahellis) that breeds in the coastal upwelling area off northwest mainland Spain. The mixing model indicated that although chicks from all colonies were fed with a high percentage of fish, there are geographical differences in their diets. While chicks from northern colonies consume higher percentages of earthworms, refuse constitutes a more important source in the diet of chicks from western colonies. The three-isotope mixing model revealed a heterogeneity in foraging habitats that would not have been apparent if only two stable isotopes had been analysed. Moreover, our work highlights the potential of adding δ³⁴S for distinguishing not only between terrestrial and marine prey, but also between different marine species such as fish, crabs and mussels.     

Estimating digestion time in gelatinous predators: a methodological comparison with the scyphomedusa Aurelia aurita

In order to quantify the trophic impact of gelatinous predators, digestion time estimates are commonly applied to counts of prey in the guts. Three primary approaches are used, the Manual-feeding, Natural-feeding and Steady-state methods; these differ in methodology and their underlying assumptions. The criteria used to define the end-point of digestion, and the resolution at which digestion progress is observed, also vary across studies. To understand the impact of such differences, we estimate digestion times of the scyphomedusa Aurelia aurita fed adult females of the copepod Acartia tonsa using these various approaches. We find ~fourfold differences which can be attributed to bias towards the slowest rates of digestion by some end-point criteria, and overestimation from low observation resolution. Artificial manipulation and the degree to which swimming and feeding behaviour are natural may also influence estimates. We provide recommendations for those quantifying digestion times of Aurelia aurita medusae and gelatinous predators.     

Influence of host migration between woodland and pasture on the population dynamics of the tick Ixodes ricinus: A modelling approach

Ticks act as vectors of pathogens that can be harmful to animals and/or humans. Epidemiological models can be useful tools to investigate the potential effects of control strategies on diseases such as tick-borne diseases. The modelling of tick population dynamics is a prerequisite to simulating tick-borne diseases and the corresponding spread of the pathogen. We have developed a dynamic model to simulate changes in tick density at different stages (egg, larva, nymph and adult) under the influence of temperature. We have focused on the tick Ixodes ricinus, which is widespread in Europe. The main processes governing the biological cycles of ticks were taken into account: egg laying, hatching, development, host (small, mainly rodents, or large, like deer and cattle, mammals) questing, feeding and mortality. This model was first applied to a homogeneous habitat, where simulations showed the ability of the model to reproduce the general patterns of tick population dynamics. We considered thereafter a multi-habitat model, where three different habitats (woodland, ecotone and meadow) were connected through host migration. Based on this second application, it appears that migration from woodland, via the ecotone, is necessary to sustain the presence of ticks in the meadow. Woodland can therefore be considered as a source of ticks for the meadow, which in turn can be regarded as a sink. The influence of woodland on surrounding tick densities increases in line with the area of this habitat before reaching a plateau. A sensitivity analysis to parameter values was carried out and demonstrated that demographic parameters (sex ratio, development, mortality during feeding and questing, host finding) played a crucial role in the determination of questing nymph densities. This type of modelling approach provides insight into the influence of spatial heterogeneity on tick population dynamics.     

Description and sensitivity analysis for the LESV model: Water quality variables and the balance of organisms in a fjordic region of restricted exchange

In this paper we describe a new ecological model for Regions of Restricted Exchange (RRE), such as fjords, estuaries, rias and lagoons. The model is intended to simulate the impact of external nutrient input on microplankton (phytoplankton plus pelagic microheterotrophs) in RREs. We have implemented the model with the practical purpose of finding a safe limit to the capacities of RRE to assimilate fish-farm waste. Sea-cage farming of fish is increasing in fjords in northern and southern hemispheres, and its external nutrient input can lead to environmental problems such as eutrophication and deoxygenation. The model includes a physical system of three layers with exchanges driven by tidal movement, freshwater input, wind stirring. The biological part includes two microplankton compartments, each parameterizing a microbial loop and each containing chlorophyll. The first compartment represents diatoms and associated heterotrophs, and the second compartment represents flagellates and associated heterotrophs. As well as the balance of these organisms, the model simulates concentrations of nutrient N, P, and Si, dissolved oxygen, and water transparency. Chlorophyll and nutrient change are linked by yields (q  ). Losses of microplankton to grazing by mesozooplankton or benthos are simulated by a temperature-dependent grazing pressure acting on a mean loss (_L0)$(L_0)$. The model also includes the ability to simulate point source inputs of nutrients or organic matter and a generic tracer with first order decay. Sea-cage fish-farms exemplify such point sources. In order to explore model behaviour, we included inputs from a 1500 tonnes salmon farm multiplied by a factor (γ)$(\gamma )$. We carried out sensitivity analysis to identify the most influential model parameters and forcing variables in the case of the shallow Scottish fjord, Loch Creran, in 1975 before the introduction of salmon farming. We tested the model fit to this pristine state (γ=0)$(\gamma =0)$, using Major Axis Regression of simulated variables on observed variables. The model successfully follows the seasonal cycles of chlorophyll (summer over both microplanktons) and the limiting nutrients (P, N). The sensitivity analysis identified three sets of key parameters: (γ)$(\gamma )$ and other fish-farm coefficients, which control farm waste effects on an RRE; (_L0)$(L_0)$ parameters for each microplankton, which link these to the rest of the ecosystem and which have implications for future inclusion of shellfish farming in the model and, chlorophyll yields from nutrients (q), which are crucial for the predication of eutrophication and the ecological understanding of the model.     

The status of heavy metal levels in a Ramsar site,Kuala Gula bird sanctuary: the impact of the anthropogenic inputs

Distributions of Cd, Cu, Pb, and Zn in the surface sediments from two sites of the Kuala Gula Bird Sanctuary, Malaysia were monitored for a period of 6 months from October 2006 to March 2007. In December 2006, the concentration of Zn in one location was significantly (p??1) than the other metals at both sites, but in the oxidizable organic fraction it was highest at both sites during October; with mean concentrations of 18?mg?kg^?1 at both locations. In the acid-reducible fraction, high concentrations of Pb (2.3?mg?kg^?1) were detected at station 2 in February 2007, being highest among all four metals at both stations. The acid-reducible fraction found in Pb ranged from 0.10% to 3.1% in both stations. Percentages ranging from 51% to 96% were observed for all four metals in the resistant fraction throughout the sampling period. These results indicate low contributions from anthropogenic sources. The findings constitute a baseline data archive for future reference.     

Modeling a spatially restricted distribution in the Neotropics: How the size of calibration area affects the performance of five presence-only methods

We here examine species distribution models for a Neotropical anuran restricted to ombrophilous areas in the Brazilian Atlantic Forest hotspot. We extend the known occurrence for the treefrog Hypsiboas bischoffi (Anura: Hylidae) through GPS field surveys and use five modeling methods (BIOCLIM, DOMAIN, OM-GARP, SVM, and MAXENT) and selected bioclimatic and topographic variables to model the species distribution. Models were first trained using two calibration areas: the Brazilian Atlantic Forest (BAF) and the whole of South America (SA). All modeling methods showed good levels of predictive power and accuracy with mean AUC ranging from 0.77 (BIOCLIM/BAF) to 0.99 (MAXENT/SA). MAXENT and SVM were the most accurate presence-only methods among those tested here. All but the SVM models calibrated with SA predicted larger distribution areas when compared to models calibrated in BAF. OM-GARP dramatically overpredicted the species distribution for the model calibrated in SA, with a predicted area around 10⁶ km² larger than predicted by other SDMs. With increased calibration area (and environmental space), OM-GARP predictions followed changes in the environmental space associated with the increased calibration area, while MAXENT models were more consistent across calibration areas. MAXENT was the only method that retrieved consistent predictions across calibration areas, while allowing for some overprediction, a result that may be relevant for modeling the distribution of other spatially restricted organisms.