The Experts below are selected from a list of 126690 Experts worldwide ranked by ideXlab platform
André E. Punt - One of the best experts on this subject based on the ideXlab platform.
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exploring the effect of sampling protogyny and larval advection on stock estimates subject to no take closures in a spatially complex coral reef line fishery on the great barrier reef australia
Canadian Journal of Fisheries and Aquatic Sciences, 2017Co-Authors: Richard L Little, André E. Punt, Geoffrey N Tuck, Bruce D MapstoneAbstract:Simulation is used to evaluate the ability of a two-region, age-structured assessment Model to provide accurate and precise estimates of stock status (i.e., the ratio of female spawning biomass to unfished female spawning biomass) for coral trout (Plectropomus leopardus) on the Great Barrier Reef (GBR), Australia. The Model used to generate the simulated data used by the assessment Model is a spatially complex age- and sex-structured Population Dynamics Model that captures the protogynous nature of coral trout. Stock status is underestimated (negatively biased), with the extent of negative bias related to mis-specification of the breeding strategy of the target fish stock, the impact of the amount of larval connectivity among reefs, the number of reefs closed to fishing, as well as exploitation rates. The estimates of stock status were less negatively biased when fishery-independent index and age- and length-composition data were available from closed areas. The results will inform the development of mana...
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the utility of genetics in marine fisheries management a simulation study based on pacific cod off alaska
Canadian Journal of Fisheries and Aquatic Sciences, 2015Co-Authors: Ingrid B Spies, André E. PuntAbstract:Information on genetic Population structure has been documented in many marine fish species, but it is not always incorporated into management plans. This study examines how conservation status and yield change when management units are established using genetic data versus treating the entire area as a single management unit. Simulations use a spatially structured, individual-based Model that combines multilocus microsatellite genotypes and a traditional fish Population Dynamics Model that establishes abundance-at-age by cohort. Results are considered in terms of marine fish species in general, and parameters in the Model are based on Pacific cod (Gadus macrocephalus) in the Bering Sea and Aleutian Islands region of Alaska. Population Dynamics are projected under several management strategies, some of which establish management units based on the results of genetic testing and some that do not. Simulations incorporate annual stock assessments and fishing for 100 years. Results show that managed fishing c...
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in pursuit of maximum economic yield in an itq managed lobster fishery
Fisheries Research, 2015Co-Authors: C Gardner, André E. Punt, Klaas Hartmann, Sarah JenningsAbstract:A bioeconomic analysis of the Tasmanian rock lobster Jasus edwardsii fishery was conducted using a length- and sex-structured Population Dynamics Model. This Model was also spatially- and temporally-structured to account for differences in costs of fishing and prices as well as differences in abundance and productivity among regions within the fishery. The current total allowable commercial catch (TACC) was found to be higher than the level that would maximise economic yield, and this left the industry vulnerable to temporal changes in productivity. Alternative pathways to lower TACCs were explored, but these had less effect on economic yield than the final TACC. The TACC did not move towards MEY through normal decision-making based on biological stock assessments despite the fishery operating under individual transferable quota (ITQ) management for over a decade. This is because industry and government have struggled to accept that economic yield and asset values could increase with lower catches. Bioeconomic analysis assisted in debate on decreasing the TACC, suggesting formal economic analysis is required for effective ITQ management.
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calculating optimal effort and catch trajectories for multiple species Modelled using a mix of size structured delay difference and biomass Dynamics Models
Fisheries Research, 2011Co-Authors: André E. Punt, Roy Deng, Sean Pascoe, Catherine M Dichmont, Shijie Zhou, Eva E Plaganyi, Trevor Hutton, W N Venables, R A KenyonAbstract:Abstract A framework is described whereby effort levels and their associated catches consistent with maximizing the net present value (NPV) of fishery profits over time can be calculated when each harvested species is Modelled using a different Population Dynamics Model. Results are presented based on three species (Penaeus semisulcatus, P. esculentus, and Metapenaeus endeavouri) in Australia's Northern Prawn Fishery and three Population Dynamics Models (size-structured, delay-difference, and biomass Dynamics). The results indicate that there is a considerable between-Model variation in key Model outputs such as the catch predicted for 2010 and the estimated future long-term catches corresponding to maximum economic yield. This variation is comparable with that due to uncertainty about economic parameters when all species are Modelled using a size-structured Population Dynamics Model, highlighting the importance of both good Population Dynamics Models and accurate economic parameter inputs. The results also highlight some of the implications (in terms of estimating effort and catch levels which maximize NPV) of not having sufficient data when using Population Dynamics Models to explicitly represent some of the species caught in a multi-species fishery.
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application of a weekly delay difference Model to commercial catch and effort data for tiger prawns in australia s northern prawn fishery
Fisheries Research, 2003Co-Authors: Catherine M Dichmont, André E. Punt, Aijun Deng, Q Dell, W N VenablesAbstract:Abstract The two species of tiger prawn (Penaeus semisulcatus and P. esculentus) harvested in Australia’s Northern Prawn Fishery are assessed by fitting a Deriso–Schnute delay-difference Model to catch and effort data. The Population Dynamics Model has a weekly time-step and allows for week-specificity in recruitment, spawning, availability and fishing mortality. The stock–recruitment relationship is fitted assuming temporally correlated environmental variability and by downweighting recruitments that are poorly determined by the catch and effort data. Uncertainty is quantified through sensitivity tests, variance estimation and future projections. The projections account for the technical interaction between the two species in that effort directed at one species leads to some mortality on the other species. Recruitment and spawning stock size are robustly estimated to have declined substantially but the status of the resource relative to MSY-based reference points is uncertain. The three factors to which the results are most sensitive are the value assumed for the catchability coefficient, the rate of change over time in fishing efficiency, and the future within-year effort distribution. Seasonal closures are shown to lead to increased yields at similar levels of risk to the resource, particularly for P. semisulcatus.
Yandong Xiao - One of the best experts on this subject based on the ideXlab platform.
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Horizontal gene transfer can help maintain the equilibrium of microbial communities.
Journal of Theoretical Biology, 2018Co-Authors: Yuhang Fan, Yandong Xiao, Babak Momeni, Yang-yu LiuAbstract:Abstract Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. Yet, the evolutionary advantage of horizontal gene transfer has not been well understood and is constantly being debated. Here we propose a simple Population Dynamics Model based on frequency-dependent genotype interactions to evaluate the influence of horizontal gene transfer on microbial communities. In particular, we examine the structural stability of coexistence (i.e., the capability of the system to maintain species coexistence in response to small changes in parameters), as well as the robustness (defined as the maximal degree of perturbation the system can sustain around a stable coexistence steady state) of microbial communities. We find that both structural stability of coexistence and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stabilize the ecosystem, helping it recover from disturbance and maintain the species coexistence.
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mapping the ecological networks of microbial communities
Nature Communications, 2017Co-Authors: Marco Tulio Angulo, Yandong Xiao, Jonathan Friedman, Matthew K Waldor, Scott T. WeissAbstract:Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular Population Dynamics Model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular Population Dynamics Model. Additionally, when the Population Dynamics is assumed to follow the classic Generalized Lotka–Volterra Model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable Modeling of complex, real-world microbial communities, such as the human gut microbiota.
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Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities
bioRxiv, 2017Co-Authors: Yuhang Fan, Yandong Xiao, Babak Momeni, Yang-yu LiuAbstract:Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. The evolutionary advantage of horizontal gene transfer has not been well-understood and is constantly being debated. Here we propose a simple Population Dynamics Model based on the frequency-dependent interactions between different genotypes to evaluate the influence of horizontal gene transfer on microbial communities. We find that both structural stability and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stablize the ecosystem, helping it recover from disturbance and maintain the species coexistence.
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mapping the ecological networks of microbial communities from steady state data
bioRxiv, 2017Co-Authors: Yandong Xiao, Marco Tulio Angulo, Jonathan Friedman, Matthew K Waldor, Scott T. Weiss, Yang-yu LiuAbstract:Microbes form complex and dynamic ecosystems that play key roles in the health of the animals and plants with which they are associated. The inter-species interactions are often represented by a directed, signed and weighted ecological network, where nodes represent microbial species and edges represent ecological interactions. Inferring the underlying ecological networks of microbial communities is a necessary step towards understanding their assembly rules and predicting their dynamical response to external stimuli. However, current methods for inferring such networks require assuming a particular Population Dynamics Model, which is typically not known a priori. Moreover, those methods require fitting longitudinal abundance data, which is not readily available, and often does not contain the variation that is necessary for reliable inference. To overcome these limitations, here we develop a new method to map the ecological networks of microbial communities using steady-state data. Our method can qualitatively infer the inter-species interaction types or signs (positive, negative or neutral) without assuming any particular Population Dynamics Model. Additionally, when the Population Dynamics is assumed to follow the classic Generalized Lotka-Volterra Model, our method can quantitatively infer the inter-species interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to experimental data from a synthetic soil microbial community. Our method offers a novel framework to infer microbial interactions and reconstruct ecological networks, and represents a key step towards reliable Modeling of complex, real-world microbial communities, such as human gut microbiota.
Yang-yu Liu - One of the best experts on this subject based on the ideXlab platform.
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Horizontal gene transfer can help maintain the equilibrium of microbial communities.
Journal of Theoretical Biology, 2018Co-Authors: Yuhang Fan, Yandong Xiao, Babak Momeni, Yang-yu LiuAbstract:Abstract Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. Yet, the evolutionary advantage of horizontal gene transfer has not been well understood and is constantly being debated. Here we propose a simple Population Dynamics Model based on frequency-dependent genotype interactions to evaluate the influence of horizontal gene transfer on microbial communities. In particular, we examine the structural stability of coexistence (i.e., the capability of the system to maintain species coexistence in response to small changes in parameters), as well as the robustness (defined as the maximal degree of perturbation the system can sustain around a stable coexistence steady state) of microbial communities. We find that both structural stability of coexistence and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stabilize the ecosystem, helping it recover from disturbance and maintain the species coexistence.
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Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities
bioRxiv, 2017Co-Authors: Yuhang Fan, Yandong Xiao, Babak Momeni, Yang-yu LiuAbstract:Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. The evolutionary advantage of horizontal gene transfer has not been well-understood and is constantly being debated. Here we propose a simple Population Dynamics Model based on the frequency-dependent interactions between different genotypes to evaluate the influence of horizontal gene transfer on microbial communities. We find that both structural stability and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stablize the ecosystem, helping it recover from disturbance and maintain the species coexistence.
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mapping the ecological networks of microbial communities from steady state data
bioRxiv, 2017Co-Authors: Yandong Xiao, Marco Tulio Angulo, Jonathan Friedman, Matthew K Waldor, Scott T. Weiss, Yang-yu LiuAbstract:Microbes form complex and dynamic ecosystems that play key roles in the health of the animals and plants with which they are associated. The inter-species interactions are often represented by a directed, signed and weighted ecological network, where nodes represent microbial species and edges represent ecological interactions. Inferring the underlying ecological networks of microbial communities is a necessary step towards understanding their assembly rules and predicting their dynamical response to external stimuli. However, current methods for inferring such networks require assuming a particular Population Dynamics Model, which is typically not known a priori. Moreover, those methods require fitting longitudinal abundance data, which is not readily available, and often does not contain the variation that is necessary for reliable inference. To overcome these limitations, here we develop a new method to map the ecological networks of microbial communities using steady-state data. Our method can qualitatively infer the inter-species interaction types or signs (positive, negative or neutral) without assuming any particular Population Dynamics Model. Additionally, when the Population Dynamics is assumed to follow the classic Generalized Lotka-Volterra Model, our method can quantitatively infer the inter-species interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to experimental data from a synthetic soil microbial community. Our method offers a novel framework to infer microbial interactions and reconstruct ecological networks, and represents a key step towards reliable Modeling of complex, real-world microbial communities, such as human gut microbiota.
Eva E Plaganyi - One of the best experts on this subject based on the ideXlab platform.
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quantifying the projected impact of the south african sardine fishery on the robben island penguin colony
Ices Journal of Marine Science, 2015Co-Authors: William M. L. Robinson, Douglas S. Butterworth, Eva E PlaganyiAbstract:Quantitative methods are needed to evaluate the ecological effects of fishing forage species upon which predators depend. African penguin Spheniscus demersus numbers at the Robben Island colony rose during the 1990s co-incidental with a marked increase in sardine Sardinops sagax and anchovy Engraulis encrasicolus abundances, but decreased appreciably during the 2000s as sardine suffered a series of poor recruitments. A Population Dynamics Model is developed which relates penguin adult annual mortality to local sardine biomass, and is fit to penguin moult counts and re-sightings of tagged penguins. The predator–prey interaction is best explained by a sardine–penguin mortality relationship with average penguin survival decreasing only when the local sardine biomass is less than approximately one-quarter of the maximum observed. Results suggest that the rapid growth of the colony during the 1990s was driven primarily by immigration. Penguin projections are generated by linking to future sardine abundances predicted under the operational management procedure used to set catch limits for these sardine and anchovy fisheries, and compared with equivalent scenarios without fishing. Results indicate that fishing is likely to have a relatively small impact on penguins, especially when compared with uncertainties that arise from the variable spatial distribution of the sardine Population.
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calculating optimal effort and catch trajectories for multiple species Modelled using a mix of size structured delay difference and biomass Dynamics Models
Fisheries Research, 2011Co-Authors: André E. Punt, Roy Deng, Sean Pascoe, Catherine M Dichmont, Shijie Zhou, Eva E Plaganyi, Trevor Hutton, W N Venables, R A KenyonAbstract:Abstract A framework is described whereby effort levels and their associated catches consistent with maximizing the net present value (NPV) of fishery profits over time can be calculated when each harvested species is Modelled using a different Population Dynamics Model. Results are presented based on three species (Penaeus semisulcatus, P. esculentus, and Metapenaeus endeavouri) in Australia's Northern Prawn Fishery and three Population Dynamics Models (size-structured, delay-difference, and biomass Dynamics). The results indicate that there is a considerable between-Model variation in key Model outputs such as the catch predicted for 2010 and the estimated future long-term catches corresponding to maximum economic yield. This variation is comparable with that due to uncertainty about economic parameters when all species are Modelled using a size-structured Population Dynamics Model, highlighting the importance of both good Population Dynamics Models and accurate economic parameter inputs. The results also highlight some of the implications (in terms of estimating effort and catch levels which maximize NPV) of not having sufficient data when using Population Dynamics Models to explicitly represent some of the species caught in a multi-species fishery.
Yuhang Fan - One of the best experts on this subject based on the ideXlab platform.
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Horizontal gene transfer can help maintain the equilibrium of microbial communities.
Journal of Theoretical Biology, 2018Co-Authors: Yuhang Fan, Yandong Xiao, Babak Momeni, Yang-yu LiuAbstract:Abstract Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. Yet, the evolutionary advantage of horizontal gene transfer has not been well understood and is constantly being debated. Here we propose a simple Population Dynamics Model based on frequency-dependent genotype interactions to evaluate the influence of horizontal gene transfer on microbial communities. In particular, we examine the structural stability of coexistence (i.e., the capability of the system to maintain species coexistence in response to small changes in parameters), as well as the robustness (defined as the maximal degree of perturbation the system can sustain around a stable coexistence steady state) of microbial communities. We find that both structural stability of coexistence and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stabilize the ecosystem, helping it recover from disturbance and maintain the species coexistence.
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Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities
bioRxiv, 2017Co-Authors: Yuhang Fan, Yandong Xiao, Babak Momeni, Yang-yu LiuAbstract:Horizontal gene transfer and species coexistence are two focal points in the study of microbial communities. The evolutionary advantage of horizontal gene transfer has not been well-understood and is constantly being debated. Here we propose a simple Population Dynamics Model based on the frequency-dependent interactions between different genotypes to evaluate the influence of horizontal gene transfer on microbial communities. We find that both structural stability and robustness of the microbial community are strongly affected by the gene transfer rate and direction. An optimal gene flux can stablize the ecosystem, helping it recover from disturbance and maintain the species coexistence.