Age-structured Simulation Model Research Articles

Examining the performance of alternative harvest regulations for short-lived taxa: A case study of Florida Bay scallop management

The life history schedule of short-lived species compresses the temporal window available for harvest and exacerbates harvest timing decisions. For annual species whose populations are made up of a single year class, it is challenging yet essential to limit harvest to a level that will allow sufficient spawning escapement to sustain the population. Unexpectedly, intense harvest prior to reproduction could extirpate a population in a single season. Larger-scale commercial fisheries for annual or semelparous species are often managed using sophisticated pre-season abundance forecasts or in-season depletion estimates combined with intensive monitoring of catches and enforcement of catch limits. However, sufficient monitoring and harvest control are rarely feasible in recreational fisheries. We demonstrate the use of an age-structured simulation model to identify robust management regulations for recreational harvest season and bag limits applied to the Florida bay scallop fishery. We compared the outcomes of current harvest regulations with a suite of alternative harvest regulations in a recreational fishery for Florida bay scallops. To account for uncertainty in the stock status and dynamics of the fishery, we evaluated alternative harvest options across three levels of initial stock exploitation and two scenarios for future fishing effort. Our results show that biologically-informed regulations which allowed for more bay scallops to spawn prior to harvest, such as a later harvest season and daily harvest limit increasing over the season, performed well across all treatments and outperformed many of the current regulations when the initial stock state was more exploited, as well as when future effort doubled. These results suggest that (1) harvest regulations that more closely match the biology and life history are likely to perform better for short-lived, annual taxa than simpler regulations that may not explicitly consider these factors, and (2) simpler regulations can perform well, but require precise, annual monitoring to prevent potentially catastrophic overharvest or costly underutilization.

Age Structured Simulation Model for the Spread of COVID-19

Age Structured Simulation Model for the Spread of COVID-19

Dynamic factor analysis to reconcile conflicting survey indices of abundance

Abstract Stock-wide trends in fish relative abundance are challenging to obtain when a single, comprehensive survey is unavailable, and multiple, spatially, and/or temporally fragmented surveys must be relied upon instead. Indices of abundance from multiple surveys frequently have differing trends, resulting in obscured true abundance patterns of the resource. We use an age-structured simulation model of two coastal shark species in the southeast United States to explore the performance of dynamic factor analysis (DFA) for reconciling multiple indices of abundance that are in conflict. Survey-specific time-variation in catchability was induced to generate conflicting indices of abundance. Key simulation sensitivities included survey variability, abundance pattern in the resource, and missing years of survey data. We caution against using DFA when there is no contrast in the underlying stock abundance or when trends in catchability in all surveys result in no survey that is representative of stock abundance. When multiple representative surveys were available, DFA proved useful across species in estimating stock-wide trends from conflicting survey indices with different selectivities, catchabilities, variances, and, to a lesser extent, with missing data. Our results suggest that resolving contrasting patterns among multiple time-series of relative abundance can improve understanding of the temporal trend in stock abundance.

Modeling the impact of dam removal on the Formosan landlocked salmon in the context of climate change

Dam removal is analyzed as a conservation strategy for the Formosan landlocked salmon Oncorhynchus masou formosanus, a critically endangered species whose last refuge is the Wuling basin in central Taiwan. In a previous study, a stochastic age-structured simulation model was developed and used to assess the effectiveness of removing four dams in increasing salmon abundance in Kaoshan Stream in the context of climate change. Three check dams remain intact in Chichiawan Stream and one of its tributaries. In this study, the model is recalibrated for these regions and simulates the removal of each of these dams. Model analysis suggests that the combined effect of dam removal and climate change decreases the effectiveness of dam removal while increasing the negative impact of climate change on abundance. A simple graphing technique is presented for comparing the predicted impact of the removal of each dam under consideration. The model predicts that removing the dam in Chichiawan Stream has the largest potential for increasing the 2035 abundance, but only under narrow conditions of climate change and effectiveness of dam removal. The potential benefit from removing one of the tributary dams is smaller, but the conditions for reaching closer to its potential are less restrictive. This type of analysis is useful for dam removal management decisions regarding habitat restoration.

Assessing long-term changes in sex ratios of Pacific herring in Prince William Sound, Alaska

The Pacific herring (Clupea pallasii) population in Prince William Sound, Alaska suffered a sudden collapse in 1993 and has failed to recover. No consensus has been reached for the causes of the collapse, but hypotheses span a range of ecological, environmental, and anthropogenic drivers. During the course of investigations into changes in PWS herring and salmon population dynamics and fisheries we discovered that the observed percentage of male herring in spawning biomass estimates appeared to increase since the mid-1980s. Using available data (1983–2015) we analysed sex ratios of herring caught in close proximity to the spring spawn using various gear types. In recent years, the overall sex ratio of Pacific herring in PWS has been skewed towards males (>60%), but only if samples from cast nets are included, which generally catch spawning fish. In contrast, purse seine samples, generally collected days to weeks prior to the spawn, had relatively equal sex ratios. Age also affected the sex ratio, with a higher proportion of older fish being females. Using an age-structured simulation model, we illustrate that overestimating the number of males in the population can lead to biases in estimated model parameters (such as vulnerability at age) and as a result, biases in the inferred age composition of the population, and other derived quantities. After accounting for differences in sampling gears to improve estimated sex ratios, we recommend that future work focus attention on separating spatial and temporal differences in sex ratios of this otherwise much-studied population.

Tuberculosis in Cape Town: An age-structured transmission model

BackgroundTuberculosis (TB) is the leading cause of death in South Africa. The burden of disease varies by age, with peaks in TB notification rates in the HIV-negative population at ages 0−5, 20−24, and 45−49 years. There is little variation between age groups in the rates in the HIV-positive population. The drivers of this age pattern remain unknown. MethodsWe developed an age-structured simulation model of Mycobacterium tuberculosis (Mtb) transmission in Cape Town, South Africa. We considered five states of TB progression: susceptible, infected (latent TB), active TB, treated TB, and treatment default. Latently infected individuals could be re-infected; a previous Mtb infection slowed progression to active disease. We further considered three states of HIV progression: HIV negative, HIV positive, on antiretroviral therapy. To parameterize the model, we analysed treatment outcomes from the Cape Town electronic TB register, social mixing patterns from a Cape Town community and used literature estimates for other parameters. To investigate the main drivers behind the age patterns, we conducted sensitivity analyses on all parameters related to the age structure. ResultsThe model replicated the age patterns in HIV-negative TB notification rates of Cape Town in 2009. Simulated TB notification rate in HIV-negative patients was 1000/100,000 person-years (pyrs) in children aged <5 years and decreased to 51/100,000 in children 5−15 years. The peak in early adulthood occurred at 25−29 years (463/100,000 pyrs). After a subsequent decline, simulated TB notification rates gradually increased from the age of 30 years. Sensitivity analyses showed that the dip after the early adult peak was due to the protective effect of latent TB and that retreatment TB was mainly responsible for the rise in TB notification rates from the age of 30 years. ConclusionThe protective effect of a first latent infection on subsequent infections and the faster progression in previously treated patients are the key determinants of the age-structure of TB notification rates in Cape Town.

Effects of Climate Change on Pest-Parasitoid Dynamics: Development of a Simulation Model and First Results

The influence of predicted climatic change on agricultural pest and beneficial insect species is of high importance for growers since increasing temperatures may have a direct impact on the developmental rates of insect populations. These parameters are species-specific and result in variable reactions to climate change, potentially disrupting the synchrony of pest-parasitoid dynamics. This study investigated the effect of increasing temperatures caused by climate change on the population dynamics of the mealy cabbage aphid Brevicoryne brassicae, a worldwide occurring pest species in cruciferous crops, and the endoparasitoid Diaeretiella rapae. For three vegetable growing regions in lower Saxony, the population development of both species was simulated for (1) the near future (2041–2050), (2) the far future (2090–2099) and (3) the reference time period (1991–2000), using an age structured simulation model including simulated temperature data. An earlier first occurrence of D. rapae in spring compared to B. brassicae was shown, however with no disruption of the synchrony between the two populations. Despite the earlier occurrence and increased population size of D. rapae in future periods, B. brassicae maximum population size also increased. Furthermore, an earlier occurrence of alate aphids during the season resulted from the model, indicating a potential need to adapt pest management.

Stocking for rehabilitation of burbot in the Kootenai River, Idaho, USA and British Columbia, Canada

Summary The burbot Lota lota is widespread globally, but the population in the Kootenai River, Idaho and British Columbia, Canada is at risk of extirpation because of habitat changes caused by operation of Libby Dam in Montana, 100 km upstream of the border with Idaho. We developed an age-structured simulation model to estimate the number of age-0 burbot (fall fingerlings) to stock annually to rebuild the population in the Kootenai River. We found with the estimated annual survival of about 38% that 110 000–900 000 age-0 burbot per year will need to be stocked to rebuild the burbot population in the Kootenai River in 25 years, depending on the rehabilitation goal, either 5500 age-4 burbot and older as an interim goal or 17 000 age-4 and older burbot as an ultimate goal (longer than 250 mm). If survival is higher at 61% then the stocking numbers could range from 12 000 to 35 000 age-0 fingerlings per year. After stocked burbot in the population reach age 4, discharge from Libby Dam must be regulated to provide suitable temperatures and flows during the burbot pre-spawning and spawning periods, to enable the population to reproduce and return to self-sustaining status. Our findings will serve as an example for similar efforts to restore depleted burbot populations elsewhere in the world.

Predicting Effects of Exploitation Rate on Weight-at-Age, Population Dynamics, and Bioaccumulation of PCDD/Fs and PCBs in Herring (Clupea harengus L.) in the Northern Baltic Sea

The Baltic Sea ecosystem and fish stocks contain high concentrations of environmental chemicals such as polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans (PCDD/Fs), and polychlorinated biphenyls (PCBs). This study forecasts how changes in fishing or natural mortality would probably influence concentrations of PCDD/F and PCB in the Bothnian Sea (Northern Baltic) herring (Clupea harengus L.). An age-structured simulation model was developed to forecast herring stock dynamics, catches, and weight-at-age under different assumptions about exploitation and natural mortality. The simulated herring weight-at-age estimates were employed in a bioenergetics model capable of simultaneous estimation of bioaccumulation of 17 PCDD/F and 37 PCB congeners. Although the natural variability in recruitment greatly influences the stock dynamics, considerable changes in weight-at-age would ensue changes in exploitation rate or in natural mortality rate. If exploitation rates increase, growth rates would be higher and herring in the weight categories of commercial fisheries would be younger and contain less PCDD/F and PCB. Hence, the average toxicant concentrations in catches would also decline. However, it is likely that only fairly small changes would occur in toxicant concentrations-at-age. On the other hand, a drastic decrease in herring fishing would substantially increase PCDD/F and PCB concentrations in herring. The study indicated that, in spite of the clear influences of fishing on the toxicant concentrations, fishing alone cannot resolve the problems associated with a high concentration of toxicants in herring; further decreases in loading are still required.

Optimum fishing strategies for Isostichopusfuscus (Echinodermata: Holothuroidea) in the Gulf Of California, Mexico.

The Isostichopus fuscus fishery in Mexico was heavily exploited until 1994, when it was closed due to overfishing. However, no information existed on the status of the populations. The fishery was evaluated through an age structured simulation model, and according to our analysis of the stock, the fishery can be feasible and sustainable as long as fishing mortality and age of first catch are optimized. In order to evaluate exploitation strategies, several scenarios were simulated considering different combinations of fishing intensities and ages of first catch. Input data for the model included population parameters, commercial catch and costs and benefits of the fishing operations. Yield production was strongly influenced by the fishing pressure and by the age of first capture. When the first one increased, significant decreases in yield and profits occurred. The best exploitation strategy was these parameters: fishing mortality level F = 0.15, age at first capture t(c) = 4 years, and yielding of approximately 430 tons. However, since the species reproduces for the first time at 5 years, extracting younger specimens would collapse the population. The critical value of fishing mortality was detected at Fc = 0.25. If exceeded, the population tends to exhaustion and the fishery is no longer profitable. In conclusion, I. fuscus fishery is highly vulnerable to overfishing and age of catch. It must be taken into account that the management policies should be considered as pilot and used on a regional basis. Continuous monitoring of the stock, control of the number of fishing licenses and extracting only specimens 5 yeasr-old and older (around 20 cm and >400 g), will allow the populations to recover from fishing activities. Rev. Biol. Trop.

Simulated Impacts of Tournament-Associated Mortality on Largemouth Bass Fisheries

Abstract We used creel survey data combined with a simulation model to assess how tournament-associated mortality could increase exploitation of largemouth bass Micropterus salmoides and influence largemouth bass fisheries. We obtained estimates of total largemouth bass harvest (HARV) and total tournament catch (TC, i.e., the number of fish brought to judging stations) at nine lakes from Arkansas, Florida, and Texas. The ratio of TC to HARV exceeded 1.0 at five of the nine lakes studied and ranged from 0.35 to 5.18. We simulated potential tournament-associated mortality rates ranging from 0% to 70% applied to TC fish. Because exploitation was not known, we modeled harvest estimates to represent four potential exploitation rates (5, 15, 25, and 35%). The age-structured simulation model predicted that at three of nine lakes where TC/HARV ratios exceeded 3.0, tournament-associated mortality rates of 20–30% could cause 5–12% declines in the abundance of largemouth bass larger than 300 mm total length and resulted in declines in population size structure. At lakes with TC/HARV ratios of less than 1.0 (N = 4 lakes), the model predicted that tournament-associated mortality would have a negligible impact (i.e., &amp;lt;5%) on the abundance of adult fish and population size structure, regardless of the tournament-associated mortality rate. Tournament-associated mortality may not significantly influence most largemouth bass fisheries. However, in lakes where tournament catch was substantially higher than harvest, tournament-associated mortality could encompass a large portion of fishing-associated mortality and would influence largemouth bass fisheries if harvest estimates corresponded to exploitation rates of 15% or more. Exploitation measures based solely on harvest may not reveal significant portions of fishing-associated mortality for fisheries where tournament catch can exceed harvest.

Assessment of the Pacific red snapper (Lutjanus peru) fishery in the southwestern Gulf of California

The Pacific red snapper (Lutjanus peru) fishery in the southwestern Gulf of California was analyzed with an age-structured simulation model. In addition to natural mortality (M) and fishing mortality (F), the model incorporates juvenile by-catch mortality (f) caused by the shrimp fishery in the zone. Four simulated scenarios were tested in which different levels of mortality were combined. Contrary to what is established in the National Fishing Charter, simulation outputs showed that the Pacific red snapper fishery cannot be developed if both F and f are kept unregulated as presently occurs. According to the model, the fishery could only be developed with an effective regulation of these mortality sources, which implies control measures for both the artisanal fleet and the shrimp fleet.

Effective Population Size and Genetic Conservation Criteria for Bull Trout

Abstract Effective population size (Ne ) is an important concept in the management of threatened species like bull trout Salvelinus confluentus. General guidelines suggest that effective population sizes of 50 or 500 are essential to minimize inbreeding effects or maintain adaptive genetic variation, respectively. Although Ne strongly depends on census population size, it also depends on demographic and life history characteristics that complicate any estimates. This is an especially difficult problem for species like bull trout, which have overlapping generations; biologists may monitor annual population number but lack more detailed information on demographic population structure or life history. We used a generalized, age-structured simulation model to relate Ne to adult numbers under a range of life histories and other conditions characteristic of bull trout populations. Effective population size varied strongly with the effects of the demographic and environmental variation included in our simulation...

Evaluation of the green abalone haliotis fulgens fishery in bahía asunción, baja california sur, mexico

The fishery of green abalone in Bahía Asunción, Baja California Sur (Mexico), was analyzed with an age-structured simulation model using data on catch, effort, abundance estimates, natural mortality and the population growth parameters (k, L∞, to, a and b of the length-weight relationship, age at first capture and longevity). The parent-recruit relationship can be established from the correspondence between the adult stock and the one-year-old juveniles and was analyzed as a random variable with normal distribution; it shows anomalies with a sinusoid pattern. Estimates of potential yield show that current yields are below the biologic maximum sustainable yield and economic maximum sustainable yield levels.

Modification of the random-search type II functional response equation for incorporation into simulation models

Because of the assumptions implicit in the Royama-Rogers' Type II Random Search Parasitoid Equation (RSPE), the estimates of parameters are valid only within an area unit equal to the experimental area used to estimate them. This assumption was tested using different values of N t (host density) and P t (parasitoid density), while maintaining the host: parasitoid ratio constant at 10:1. If the RSPE is valid at any area unit, then the value of F( N t, P t) (probability of being parasitized) should be constant at all values of N t and P t provided that the N t: P t ratio remains constant. Instead, the value of F( N t, P t) showed an asymptotic rise to a plateau. This result supports the assumption that the RSPE validity is limited by the area unit in which its parameters are estimated. Such a limitation precludes the incorporation of this Type II equation into an age-structured simulation model. A modification to the RSPE which lacks these space-dependence limitations is proposed. The modification consisted of the division of the coefficient a' by parasitoid density ( t). This modification transforms the instantaneous rate of discovery into a per capita basis.

Choosing fisheries harvest policies: when does uncertainty matter?

Fisheries harvest policies are formulated under uncertainty because estimates of stock abundance and biological parameters are imprecise. However, allowable harvests are often based solely on point estimates of these quantities, essentially ignoring uncertainty. Some fishery scientists have advocated adjusting harvest levels downward to account for uncertainty, but few formal methods have been developed to determine how large these "uncertainty adjustments" should be. We describe an age-structured simulation model that explicitly incorporated uncertainty in parameters of the stock–recruitment relationship, errors in abundance estimates, and year-to-year variability in recruitment and calculated which uncertainty adjustment was optimal in terms of expected discounted yield. The optimal adjustment varied considerably, depending on the stock and harvest policy simulated. The increase in expected value from incorporating the adjustment into the harvest policy was usually small, except when we modeled a biological "threshold", where overharvests could lead to an irreversible stock collapse. Therefore, while our analysis suggests that basing harvest decisions solely on the best point estimates may often be an approximately optimal strategy, it also indicates that large adjustments may sometimes be appropriate. Consequently, fishery managers should avoid making arbitrary adjustments for uncertainty, and instead derive the optimal adjustment for each situation.

Sensitivity of Optimum Harvest Strategy Estimates to Alternative Definitions of Risk

A stochastic age-structured bioeconomic simulation model was developed as a tool for evaluating economic returns to a fishery from alternative harvest policies. The model, which was applied to the Gulf of Alaska walleye pollock (Theragra chalcogramma) fishery, combines the dual goals of protection of the base stock and efficient use of the public resource into an explicit objective function. This paper presents the results of several experiments in which the simulation model is used to examine the sensitivity of the optimum harvest strategy estimates to alternative definitions of risk and assumptions regarding recruitment. Alternative definitions of risk consider assumptions about stock productivity, threshold biomass, economic factors, and hybrid formulations. The bioeconomic extension of the population dynamics model is used to quantify differences in the estimates of optimum fishing mortality obtained from the different risk definitions. Model results demonstrate that estimates of optimal fishing mortality and economic return to the fishery are sensitive to the specific definition of risk used to manage the fishery. The recruitment assumption turned out to be more important to optimum harvest strategy estimates than did risk definitions.

Development and Evaluation of a Biological Model to Assess Regional-Scale Effects of Acidification on Atlantic Salmon (Salmo salar)

We developed an age-structured simulation model incorporating pH-dependent mortality to assess impacts of acidification on Atlantic salmon (Salmo salar) populations at the reach and river system level. Applied to the LaHave River, Nova Scotia, acidic reaches (mean annual pH 4.6–5.1) were predicted to have 0–15% of the annual smoit production and 0–31% of the maiden spawner production compared with circumneutral reaches (pH ≥ 5.6) and increased juvenile growth due to lower parr densities. The benefit of increased growth (earlier age of smoltification and increased early marine survival) was not sufficient to outweigh impacts of higher freshwater juvenile mortality. Simulated removal of acidic conditions resulted in a 41% increase in recruits, but only after several decades following complete chemical recovery. Circumneutral reaches were predicted to be 4–12 times more efficient at producing smolts and 3–7 times more efficient at producing adults from hatchery fingerlings compared with acidic reaches. To maintain current target egg deposition rates of 240 eggs/100 m2, circumneutral reaches could withstand grilse exploitation rates of up to 65%, while acidic reaches, even without harvesting mortality, could not maintain this level. Fisheries management strategies need to account for variability in freshwater production both within and between river systems.

A per-recruit simulation model for evaluating spatial closures in an Australian penaeid fishery

Spatial closures are commonly used by Australian fisheries managers to alter fishing patterns. To evaluate different fishing closures, however, fishery scientists have to understand and model the spatiotemporal interactions between fish stocks and fishing fleets. We develop a deterministic, stationary, per-recuit, age-structured simulation model to assess different spatial closure strategies, and use date from the Torres Strait tiger prawn fishery, Penaeus esculentus, as a working example. Our results show that selection of an optimum spatial closure largely depends on the relative importance given to changes of the different utility functions evaluated (yield, value, egg production). We show that, on average, with a spatial closure yield-per-recruit would decrease, but also show that value-per-recruit may increase 10% with the appropriate closure. Our results suggest that egg-per-recruit would always increase in the presence of a closure. By incorporating parameter uncertainty within the simulation model we predict the uncertainty associated with alternative closure strategies, and thus provide valuable information for the decision-making process.

An age-structured simulation model to investigate species replacement between pilchard and anchovy populations in the southern Benguela

Clupeoids form the basis of important commercial fisheries off Namibia and South Africa's Western Cape. Studies on the abundance of pilchard (sardine) and anchovy populations subject to heavy exploitation have revealed the possible succession of sardine by anchovy as the dominant species. In investigating the evidence for species replacement, a simple, age-structured computer simulation model was developed, which assumes that the system is initially in a steady state. The model's sensitivity to starting biomass, natural mortality, harvesting, the level at which density-dependence is initiated and environmental perturbation is considered. Important factors determining the results are the present estimates of natural mortality and the level at which density-dependence is initiated. A lower natural mortality in pilchard results in dominance by anchovy. High threshold values of density-dependence produce dynamic oscillation in the model populations. Harvesting affects the natural balance between populations i...