Harvesting at the Ecosystem Level

2020 ◽  
pp. 229-250
Author(s):  
Michael J. Fogarty ◽  
Jeremy S. Collie
Keyword(s):  
Chlorophyll Concentration ◽  
Network Models ◽  
Potential Effect ◽  
Management Options ◽  
Management Actions ◽  
Threatened And Endangered Species ◽  
Mass Balance Models ◽  
Ecosystem Level ◽  
Habitat Damage ◽  
And Function

Energy entering at the base of the food web places inherent constraints on total harvest from an ecosystem. Empirical relationships have been established between fishery yield and factors such as chlorophyll concentration, primary production, and other lower trophic level variables to guide management actions. Extension of network models to include harvesting has a long lineage and these models are now being employed worldwide to help guide management decisions. These static mass-balance models have been augmented with a fully dynamic modeling component to explore management options. Biomass spectrum models for exploited ecosystems have also been developed. In addition to direct effects on target species, fisheries can affect the structure and function of ecosystems through habitat damage and incidental catch of non-target organisms, including threatened and endangered species. Increasingly, the effects of climate change are being addressed in ecosystem models through their potential effect on production at all levels of the ecosystem.

Ecosystems processes

2018 ◽  
Author(s):  
Karen J. Esler ◽  
Anna L. Jacobsen ◽  
R. Brandon Pratt
Keyword(s):  
Ecosystem Function ◽  
Mineral Nutrients ◽  
Structure And Function ◽  
Water Dynamics ◽  
Ecosystem Level ◽  
Key Drivers ◽  
And Function ◽  
Mediterranean Type Ecosystems

Ecosystems are assemblages of organisms interacting with one another and their environment (Chapter 1). Key to the functioning of ecosystems is the flow of energy, carbon, mineral nutrients, and water in these systems. The numerous processes involved are chiefly driven by climate, soil, and fire (Chapter 2). In cases where the key drivers are the same in different areas, then ecosystems should converge in their structure and function, which has been a motivation for comparing across mediterranean-type climate (MTC) regions. Convergence of MTC regions has been evaluated, but such comparisons at the ecosystem level are challenging because ecosystems are complex and dynamic entities. Here we review carbon, nutrient, and water dynamics of mediterranean-type ecosystems in the context of ecosystem function. As nutrients in soils are low in some MTC regions, we review how this has led to unique adaptations to meet this challenge.

scholarly journals Epidemic Growth Rates and Host Movement Patterns Shape Management Performance for Pathogen Spillover at The Wildlife-livestock Interface

2019 ◽  
Author(s):  
Kezia R. Manlove ◽  
Laura M. Sampson ◽  
Benny Borremans ◽  
E. Frances Cassirer ◽  
Ryan S. Miller ◽  
...  
Keyword(s):  
Growth Rates ◽  
Life Histories ◽  
Animal Health ◽  
Movement Patterns ◽  
Health Food ◽  
Management Options ◽  
Management Performance ◽  
Fast Growing ◽  
Management Actions ◽  
Host Movement

ABSTRACTManaging pathogen spillover at the wildlife-livestock interface is a key step toward improving global animal health, food security, and wildlife conservation. However, predicting the effectiveness of management actions across host-pathogen systems with different life histories is an on-going challenge since data on intervention effectiveness are expensive to collect and results are system-specific. We developed a simulation model to explore how the efficacies of different management strategies vary according to host movement patterns and epidemic growth rates. The model suggested that fast-growing, fast-moving epidemics like avian influenza were best-managed with actions like biosecurity or containment, which limited and localized overall spillover risk. For fast-growing, slower-moving diseases like foot-and-mouth disease, depopulation or prophylactic vaccination were competitive management options. Many actions performed competitively when epidemics grew slowly and host movements were limited, and how management efficacy related to epidemic growth rate or host movement propensity depended on what objective was used to evaluate management performance. This framework may be a useful step in advancing how we classify and prioritise responses to novel pathogen spillover threats, and evaluate current management actions for pathogens emerging at the wildlife-livestock interface.

scholarly journals Overview on the distribution of gorgonian species in Tunisian marine coastal waters (central Mediterranean)

2018 ◽  
Vol 82 (1) ◽  
pp. 55 ◽  
Author(s):  
Raouia Ghanem ◽  
Emna Soufi Kechaou ◽  
Jamila Ben Souissi ◽  
Joaquim Garrabou
Keyword(s):  
Coastal Waters ◽  
Local Ecological Knowledge ◽  
Conservation Status ◽  
Ecological Knowledge ◽  
Central Mediterranean ◽  
Management Actions ◽  
Conservation Actions ◽  
Gorgonian Species ◽  
Species Richness And Abundance ◽  
And Function

Gorgonian species play an important ecological role in the structure and function of marine communities. Human activities are negatively affecting the conservation status of gorgonian populations in the Mediterranean. Acquiring knowledge of gorgonian distribution is therefore a key step required to promote efficient management and conservation actions. However, information on the distribution of gorgonian species is lacking in many Mediterranean areas. This study aimed to provide an overview of the geographic and bathymetric distributions of gorgonians in the coastal waters of the Tunisian coast (1136 km). The sampling design encompassed three sectors, 27 localities and 87 sites. Information was collected from scuba diving (26 sites) and local ecological knowledge surveys of fishermen and divers (132 interviews), as well as from a literature review. Overall, the occurrence of eight gorgonians was confirmed at 54 out of the 87 sites surveyed in Tunisian coastal waters (7-120 m depth). The species that were found were Eunicella singularis, Eunicella cavolini, Paramuricea clavata, Paramuricea macrospina, Leptogorgia sarmentosa, Eunicella verrucosa, Corallium rubrum and Ellisella paraplexauroides. The highest gorgonian species richness and abundance was recorded in northern, followed by eastern Tunisian waters. In the southern areas only one species was recorded. This pattern was related to the rocky substrate that characterizes the northern and eastern coasts of Tunisia. This study is the first to report the occurrence of E. singularis, E. cavolini, E. verrucosa and Leptogorgia sarmentosa in northern and eastern Tunisian waters. The results are discussed in the hope of guiding future conservation and management actions for gorgonian assemblages in Tunisia.

Identifying the weakest link: simulating adaptive management of the reintroduction of a threatened fish

2002 ◽  
Vol 59 (11) ◽  
pp. 1709-1716 ◽  
Author(s):  
Andrew R Bearlin ◽  
E S.G Schreiber ◽  
Simon J Nicol ◽  
A M Starfield ◽  
Charles R Todd
Keyword(s):  
Adaptive Management ◽  
Weak Link ◽  
Learning By Doing ◽  
Barriers To Learning ◽  
Management Options ◽  
Endangered Fish ◽  
Management Intervention ◽  
Management Actions ◽  
Goals And Objectives ◽  
Management Cycle

As part of an ongoing program of management for a critically endangered fish, we explored adaptive management as a method to overcome pervasive uncertainty regarding the reintroduction of trout cod (Maccullochella macquariensis Cuvier). We simulated the entire adaptive management cycle to explore the suitability of the approach for guiding threatened species management and to identify problems and barriers to "learning by doing". During the planning phase, a number of compromises were identified between specification of goals and objectives, the available management options, and current monitoring capacity. Undertaking a simulation of the implementation of alternate adaptive approaches to this reintroduction provided a number of insights into adaptive management in general. First, identifying the weak link in the process of inference emphasized the need to consider whether goals and objectives are achievable and meaningful and whether they complement monitoring and (or) any other limitations of the system. Second, in natural resource management, it is crucial to negotiate objectives in the light of what one can measure. Third, although there are lessons to be learned from each stage of the adaptive management cycle, there is value in simulating the entire adaptive management cycle, including management actions, monitoring, and the states of the system that lead to management intervention.

Abstract WP196: Selective Serotonin Reuptake Inhibitors (SSRI) for Depression and Functional Recovery After Stroke: A Meta-Analysis

Stroke ◽  
2020 ◽  
Vol 51 (Suppl_1) ◽  
Author(s):  
Thirumalaivasan Dhasakeerthi ◽  
Muhammad Ishfaq ◽  
Balaji Krishnaiah ◽  
Andrei Alexandrov ◽  
Georgios Tsivgoulis
Keyword(s):  
Functional Recovery ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Meta Analysis ◽  
Potential Effect ◽  
Control Group ◽  
Random Effects Models ◽  
Post Stroke Depression ◽  
Meta Analyses ◽  
And Function ◽  
Ssri Treatment

Background: Post-stroke depression is common and it impedes rehabilitation and function recovery after stroke, and numerous trials evaluated SSRI’s for depression prophylaxis. The objective of this study is to assess the use of SSRI for prevention of poststroke depression and the potential effect on functional recovery after stroke. Methods: We searched electronic databases up to July 2019 for randomized controlled trials of SSRI’s for patients with stroke versus placebo. We calculated pooled odds ratios and 95% CIs by using random-effects models. The primary end points were depression and good functional outcome (modified Rankin Scale score of 0-2) at 90 days post-randomization. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Results: Twelve randomized control trials assessing 4,887 patients have been included in the meta-analysis. SSRI treatment after stroke decreased the odds of depression compared to control group (OR = 0.48, 95% CI - 0.30 to 0.78, p=0.003). There was no heterogeneity between the trials (Cochran’s Q statistic 4.623, df 5; P = .337, I 2 =5.626%). The proportion of subjects who achieved mRS 0-2 at 90 days was similar between SSRI and control groups (OR= 3.471, 95% CI - 0.59 to 20.38, p=0.168). Conclusion: SSRI treatment for the stroke patients reduces the incidence of depression but it does not increase the odds of good functional recovery.

scholarly journals Epidemic growth rates and host movement patterns shape management performance for pathogen spillover at the wildlife–livestock interface

2019 ◽  
Vol 374 (1782) ◽  
pp. 20180343 ◽  
Author(s):  
Kezia R. Manlove ◽  
Laura M. Sampson ◽  
Benny Borremans ◽  
E. Frances Cassirer ◽  
Ryan S. Miller ◽  
...  
Keyword(s):  
Growth Rates ◽  
Life Histories ◽  
Animal Health ◽  
Movement Patterns ◽  
Health Food ◽  
Management Options ◽  
Management Performance ◽  
Fast Growing ◽  
Management Actions ◽  
Host Movement

Managing pathogen spillover at the wildlife–livestock interface is a key step towards improving global animal health, food security and wildlife conservation. However, predicting the effectiveness of management actions across host–pathogen systems with different life histories is an on-going challenge since data on intervention effectiveness are expensive to collect and results are system-specific. We developed a simulation model to explore how the efficacies of different management strategies vary according to host movement patterns and epidemic growth rates. The model suggested that fast-growing, fast-moving epidemics like avian influenza were best-managed with actions like biosecurity or containment, which limited and localized overall spillover risk. For fast-growing, slower-moving diseases like foot-and-mouth disease, depopulation or prophylactic vaccination were competitive management options. Many actions performed competitively when epidemics grew slowly and host movements were limited, and how management efficacy related to epidemic growth rate or host movement propensity depended on what objective was used to evaluate management performance. This framework offers one means of classifying and prioritizing responses to novel pathogen spillover threats, and evaluating current management actions for pathogens emerging at the wildlife–livestock interface. This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.

scholarly journals A framework for ecosystem impacts assessment using an indicator approach

2005 ◽  
Vol 62 (3) ◽  
pp. 592-597 ◽  
Author(s):  
P.A. Livingston ◽  
K. Aydin ◽  
J. Boldt ◽  
J. Ianelli ◽  
J. Jurado-Molina
Keyword(s):  
Fishery Management ◽  
Ecosystem Impacts ◽  
Implementation Challenges ◽  
Management Actions ◽  
Indicator Approach ◽  
Research Organizations ◽  
Ecosystem Indicators ◽  
Ecosystem Level ◽  
Associated Species ◽  
The Impact

Abstract Assessment of the historical, present, and future states of marine ecosystems and the effects that humans and climate have on the state of an ecosystem are crucial to the scientific advice required to implement an ecosystem-based fishery management system. Management of federal groundfish fisheries in Alaska considers not just the target fishery, but also the possible impact those fisheries might have on other species and the ecosystem. Management actions have ranged from providing protection of endangered species in the region to preventing new fisheries from starting on key foodweb components such as forage fish. A scientific framework for providing ecosystem-based advice that puts the ecosystem first has been evolving over the past few years. This framework provides a way of assessing ecosystem factors that influence target species, the impact the target fishery may have on associated species, and ecosystem-level impacts of fishing. An indicator approach that describes ecosystem status, and trends and measures of human and climate influence has been developed to provide advice to fishery managers. This approach is now being expanded to utilize a variety of models to predict possible future trends in various ecosystem indicators. Future implementation challenges include the refinement of these predictive models, and the inclusion of climate into the models. Identification of sensitive and meaningful ecosystem indicators is also required before a more formalized decision-making process, one that includes ecosystem considerations, can be developed. Most important, the culture of fishery management and research organizations needs to change to embrace the ecosystem-based protections already mandated by various laws.

scholarly journals Intra-Protein Coevolution Is Increasingly Functional with Greater Proximity to Fertilization

2020 ◽  
Vol 160 (6) ◽  
pp. 295-308
Author(s):  
Marcel Kwiatkowski ◽  
Abdul R. Asif ◽  
Julia Schumacher ◽  
Bertram Brenig ◽  
Hans Zischler ◽  
...  
Keyword(s):  
Amino Acid ◽  
Potential Effect ◽  
Acid Sites ◽  
Cellular Level ◽  
Node Degree ◽  
Entire Body ◽  
Reproductive Proteins ◽  
Sperm Proteins ◽  
Postcopulatory Selection ◽  
And Function

Intramolecular coevolution of amino acid sites has repeatedly been studied to improve predictions on protein structure and function. Thereby, the focus was on bacterial proteins with available crystallographic data. However, intramolecular coevolution has not yet been compared between protein sets along a gradient of functional proximity to fertilization. This is especially true for the potential effect of external selective forces on intraprotein coevolution. In this study, we investigated both aspects in equally sized sets of mammalian proteins representing spermatozoa, testis, entire body, and liver. For coevolutionary analyses, we derived the proportion of covarying sites per protein from amino acid alignments of 10 mammalian orthologues each. In confirmation of the validity of our coevolution proxy, we found positive associations with the nonsynonymous or amino acid substitution rate in all protein sets. However, our coevolution proxy negatively correlated with the number of protein interactants (node degree) in male reproductive protein sets alone. In addition, a negative association of our coevolution proxy with protein hydrophobicity was significant in sperm proteins only. Accordingly, the restrictive effect of protein interactants was most pronounced in male reproductive proteins, and the tendency of sperm proteins to form internal structures decreased the more coevolutionary sites they had. Both aspects illustrate that the share of outward and thus functional coevolution increases with greater proximity to fertilization. We found this conclusion confirmed by additional comparisons within sperm proteins. Thus, sperm proteins with high hydrophobicity had the lowest proportions of covarying sites and, according to gene annotations, localized more frequently to internal cellular structures. They should therefore be less exposed to postcopulatory forms of sexual selection. Their counterparts with low hydrophobicity had larger proportions of covarying sites and more often resided at the cell membrane or were secreted. At the cellular level, they are thus closer to externally induced forces of postcopulatory selection which are known for their potential to increase substitution rates. In addition, we show that the intermediary status of the testicular protein set in correlation analyses is probably due to a special combination of reproductive and somatic involvements.

Wavelet transformed Gaussian network model

2014 ◽  
Vol 13 (06) ◽  
pp. 1450053 ◽  
Author(s):  
Meng Zhan ◽  
Suhong Li ◽  
Fan Li
Keyword(s):  
Protein Dynamics ◽  
Network Model ◽  
Protein Structures ◽  
Network Models ◽  
Experimental Results ◽  
Gaussian Network Model ◽  
The Mean ◽  
Dynamics And Function ◽  
And Function ◽  
Gaussian Network

Accurate prediction of the Debye–Waller temperature factor of proteins is of significant importance in the study of protein dynamics and function. This work explores the utility of wavelets for improving the performance of Gaussian network model (GNM). We propose two wavelet transformed Gaussian network models (wtGNM), namely a scale-one wtGNM and a scale-two wtGNM. Based on a set of 113 protein structures, it shows that the mean correlation with experimental results for the scale-one wtGNM is 0.714 and that for the scale-two wtGNM is 0.738. In contrast, the mean correlation for the original GNM is 0.594. Therefore, the wtGNM is a potential algorithm for improving the GNM prediction of protein B-factors.

scholarly journals Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories

2018 ◽  
Author(s):  
Sandro Bottaro ◽  
Giovanni Bussi ◽  
Giovanni Pinamonti ◽  
Sabine Reißer ◽  
Wouter Boomsma ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Molecular Simulations ◽  
Network Models ◽  
Molecular Conformations ◽  
Rna Molecules ◽  
Command Line Tool ◽  
Perform Cluster Analysis ◽  
And Function

AbstractRNA molecules are highly dynamic systems characterized by a complex interplay between sequence, structure, dynamics, and function. Molecular simulations can potentially provide powerful insights into the nature of these relationships. The analysis of structures and molecular trajectories of nucleic acids can be non-trivial because it requires processing very high-dimensional data that are not easy to visualize and interpret.Here we introduce Barnaba, a Python library aimed at facilitating the analysis of nucleic acids structures and molecular simulations. The software consists of a variety of analysis tools that allow the user to i) calculate distances between three-dimensional structures using different metrics, ii) back-calculate experimental data from three-dimensional structures, iii) perform cluster analysis and dimensionality reductions, iv) search three-dimensional motifs in PDB structures and trajectories and v) construct elastic network models (ENM) for nucleic acids and nucleic acids-protein complexes.In addition, Barnaba makes it possible to calculate torsion angles, pucker conformations and to detect base-pairing/base-stacking interactions. Barnaba produces graphics that conveniently visualize both extended secondary structure and dynamics for a set of molecular conformations. The software is available as a command-line tool as well as a library, and supports a variety of 1le formats such as PDB, dcd and xtc 1les. Source code, documentation and examples are freely available at https://github.com/srnas/barnaba under GNU GPLv3 license.

Sign in / Sign up

Export Citation Format

Share Document