Ecopath

Ecopath with Ecosim (EwE) is a free and open source ecosystem modelling software suite, initially started at NOAA by Jeffrey Polovina, but has since primarily been developed at the formerly UBC Fisheries Centre of the University of British Columbia. In 2007, it was named as one of the ten biggest scientific breakthroughs in NOAA's 200-year history. The NOAA citation states that Ecopath "revolutionized scientists' ability worldwide to understand complex marine ecosystems".[1] Behind this lie more than two decades of development work in association with Villy Christensen, Carl Walters, Daniel Pauly, and other fisheries scientists,[2] followed with the provision of user support, training and co-development collaborations. In 2013, development efforts were centralized under Ecopath International Initiative, Spain. Per January 2019 there are an estimated 8000+ users across academia, non-government organizations, industry and governments in 150+ countries.

Ecopath with Ecosim
EwE6Logo Transparent
Developer(s)Ecopath Research and Development Consortium
Initial release1992
Stable release
6.5 / 7 July 2016
Preview release
6.6 Beta / 21 November 2018
Repositoryhttp://sources.ecopath.org/trac/Ecopath
Written inVisual Basic.NET, C#
Operating systemWindows XP, Vista, 7, 8*, 10 (EwE desktop version), Unix and Linux (EwE core via Mono)
Platform.NET Framework 4
Available inEnglish
TypeEcosystem modeling
LicenseGPL v2
Websitehttp://www.ecopath.org

Components

EwE has three main components:

  • Ecopath – a static, mass-balanced snapshot of the system[3]
  • Ecosim – a time dynamic simulation module for policy exploration[4]
  • Ecospace – a spatial and temporal dynamic module designed for exploring the combined impacts of fishing, the placement of protected areas[5], and changing environmental conditions.

Capabilities

The Ecopath software package can be used to:

Development Ecopath version 6.0[15] received support from the Lenfest Ocean Program and the Pew Charitable trusts. In 2011 the Ecopath Research and Development Consortium was founded to share the responsibility of maintaining and further developing the approach with institutions around the world. EwE exclusively relyies on user involvement for continued software development and releases of new versions.

The desktop version of Ecopath with Ecosim runs only on Windows and requires Microsoft Access database drivers version 2007 or newer. The computational core of Ecopath with Ecosim can be executed on other operating systems such as Unix or Linux using the Mono common language runtime. Spin-off versions in R, Matlab and Fortran are developed independently of the main desktop version of EwE, and are not supported by the Ecopath Research and Development Consortium. [16]

References

  1. ^ NOAA, 2007. ECOPATH Modeling: Precursor to an Ecosystem Approach to Fisheries Management [WWW Document]. URL http://celebrating200years.noaa.gov/breakthroughs/ecopath/welcome.html (accessed 8.26.12).
  2. ^ Smikle, S.G., V. Christensen and K.A. Aiken (2010). "A review of caribbean ecosystems and fishery resources using ECOPATH models". Revue Etudes Caribéennes, n°15, https://etudescaribeennes.revues.org/4529
  3. ^ Christensen, V. and Pauly, D., 1992. Ecopath II - a software for balancing steady-state ecosystem models and calculating network characteristics. Ecological Modelling, 61:169-185.
  4. ^ Walters, C., Christensen, V. and Pauly, D., 1997. Structuring dynamic models of exploited ecosystems from trophic mass-balance assessments. Rev Fish Biol Fish, 7:139-172
  5. ^ Walters, C., Pauly, D. and Christensen, V., 1999. Ecospace: Prediction of mesoscale spatial patterns in trophic relationships of exploited ecosystems, with emphasis on the impacts of marine protected areas. Ecosystems, 2:539-554.
  6. ^ Christensen, V. and Pauly, D. (Editors), 1993. Trophic Models of Aquatic Ecosystems. ICLARM Conference Proceedings 26, Manila, 390 p.
  7. ^ Walters, C.J., Christensen, V., Martell, S.J. and Kitchell, J.F., 2005. Possible ecosystem impacts of applying MSY policies from single-species assessment. ICES J Mar Sci, 62:558-568.
  8. ^ Christensen, V. and Walters, C.J., 2004. Trade-offs in ecosystem-scale optimization of fisheries management policies. Bull Mar Sci, 74:549-562
  9. ^ Walters, C.J. and Martell, S.J.D., 2004. Fisheries Ecology and Management. Princeton University Press, Princeton, 399 p.
  10. ^ Christensen, V. and Booth, S., 2006. Ecosystem modeling of dioxin distribution patterns in the marine environment. Chapter 6. In: J. Alder and D. Pauly (Editor), On the multiple uses of small pelagic fishes: from ecosystems to markets. UBC Fisheries Centre Research Reports 14(3). Fisheries Centre, University of British Columbia [ISSN 1198-6727], Vancouver
  11. ^ Walters, William J.; Christensen, Villy (2018). "Ecotracer: analyzing concentration of contaminants and radioisotopes in an aquatic spatial-dynamic food web model". Journal of Environmental Radioactivity. 181: 118–127. doi:10.1016/j.jenvrad.2017.11.008. ISSN 0265-931X.
  12. ^ Guénette, Sylvie; Heymans, Sheila JJ; Christensen, Villy; Trites, Andrew W (2006). "Ecosystem models show combined effects of fishing, predation, competition, and ocean productivity on Steller sea lions (Eumetopias jubatus) in Alaska". Canadian Journal of Fisheries and Aquatic Sciences. 63 (11): 2495–2517. doi:10.1139/f06-136. ISSN 0706-652X.
  13. ^ Christensen, Villy; Coll, Marta; Steenbeek, Jeroen; Buszowski, Joe; Chagaris, Dave; Walters, Carl J. (2014). "Representing Variable Habitat Quality in a Spatial Food Web Model". Ecosystems. 17 (8): 1397–1412. doi:10.1007/s10021-014-9803-3. ISSN 1432-9840.
  14. ^ Steenbeek, Jeroen; Coll, Marta; Gurney, Leigh; Mélin, Frédéric; Hoepffner, Nicolas; Buszowski, Joe; Christensen, Villy (2013). "Bridging the gap between ecosystem modeling tools and geographic information systems: Driving a food web model with external spatial–temporal data". Ecological Modelling. 263: 139–151. doi:10.1016/j.ecolmodel.2013.04.027. ISSN 0304-3800.
  15. ^ Christensen, V. and Lai, S., 2007. Ecopath with Ecosim 6: the sequel. The Sea Around Us Project Newsletter, 43:1-4 (September–October).
  16. ^ Steenbeek, Jeroen; Buszowski, Joe; Christensen, Villy; Akoglu, Ekin; Aydin, Kerim; Ellis, Nick; Felinto, Dalai; Guitton, Jerome; Lucey, Sean; Kearney, Kelly; Mackinson, Steven; Pan, Mike; Platts, Mark; Walters, Carl (January 2016). "Ecopath with Ecosim as a model-building toolbox: Source code capabilities, extensions, and variations". Ecological Modelling. 319: 178–189. doi:10.1016/j.ecolmodel.2015.06.031.

External links

Bacterivore

Bacterivores are free-living, generally heterotrophic organisms, exclusively microscopic, which obtain energy and nutrients primarily or entirely from the consumption of bacteria. Many species of amoeba are bacterivores, as well as other types of protozoans. Commonly, all species of bacteria will be prey, but spores of some species, such as Clostridium perfringens, will never be prey, because of their cellular attributes.

Carl Walters

Carl Walters (born 1944) is an American-born Canadian biologist known for his work involving fisheries stock assessments, the adaptive management concept, and ecosystem modeling. Walters has been a professor of Zoology and Fisheries at the University of British Columbia since 1969. He is one of the main developers of the ecological modelling software Ecopath. His most recent work focuses on how to adjust human behaviors in environments that are full of uncertainty. He is a recent recipient of the Volvo Environment Prize (2006).

Copiotroph

A copiotroph is an organism found in environments rich in nutrients, particularly carbon. They are the opposite to oligotrophs, which survive in much lower carbon concentrations.

Copiotrophic organisms tend to grow in high organic substrate conditions. For example, copiotrophic organisms grow in Sewage lagoons. They grow in organic substrate conditions up to 100x higher than oligotrophs.

Decomposer

Decomposers are organisms that break down dead or decaying organisms, and in doing so, they carry out the natural process of decomposition. Like herbivores and predators, decomposers are heterotrophic, meaning that they use organic substrates to get their energy, carbon and nutrients for growth and development. While the terms decomposer and detritivore are often interchangeably used, detritivores must ingest and digest dead matter via internal processes while decomposers can directly absorb nutrients through chemical and biological processes hence breaking down matter without ingesting it. Thus, invertebrates such as earthworms, woodlice, and sea cucumbers are technically detritivores, not decomposers, since they must ingest nutrients and are unable to absorb them externally.

Dominance (ecology)

Ecological dominance is the degree to which a taxon is more numerous than its competitors in an ecological community, or makes up more of the biomass.

Most ecological communities are defined by their dominant species.

In many examples of wet woodland in western Europe, the dominant tree is alder (Alnus glutinosa).

In temperate bogs, the dominant vegetation is usually species of Sphagnum moss.

Tidal swamps in the tropics are usually dominated by species of mangrove (Rhizophoraceae)

Some sea floor communities are dominated by brittle stars.

Exposed rocky shorelines are dominated by sessile organisms such as barnacles and limpets.

Ecosystem model

An ecosystem model is an abstract, usually mathematical, representation of an ecological system (ranging in scale from an individual population, to an ecological community, or even an entire biome), which is studied to better understand the real system.Using data gathered from the field, ecological relationships—such as the relation of sunlight and water availability to photosynthetic rate, or that between predator and prey populations—are derived, and these are combined to form ecosystem models. These model systems are then studied in order to make predictions about the dynamics of the real system. Often, the study of inaccuracies in the model (when compared to empirical observations) will lead to the generation of hypotheses about possible ecological relations that are not yet known or well understood. Models enable researchers to simulate large-scale experiments that would be too costly or unethical to perform on a real ecosystem. They also enable the simulation of ecological processes over very long periods of time (i.e. simulating a process that takes centuries in reality, can be done in a matter of minutes in a computer model).Ecosystem models have applications in a wide variety of disciplines, such as natural resource management, ecotoxicology and environmental health, agriculture, and wildlife conservation. Ecological modelling has even been applied to archaeology with varying degrees of success, for example, combining with archaeological models to explain the diversity and mobility of stone tools.

Feeding frenzy

In ecology, a feeding frenzy occurs when predators are overwhelmed by the amount of prey available. For example, a large school of fish can cause nearby sharks, such as the lemon shark, to enter into a feeding frenzy. This can cause the sharks to go wild, biting anything that moves, including each other or anything else within biting range. Another functional explanation for feeding frenzy is competition amongst predators. This term is most often used when referring to sharks or piranhas. It has also been used as a term within journalism.

Fish measurement

Fish measurement is the measuring of the length of individual fish and of various parts of their anatomy. These data are used in many areas of ichthyology, including taxonomy and fisheries biology.

Fisheries management

Fisheries management is the activity of protecting fishery resources so sustainable exploitation is possible, drawing on fisheries science, and including the precautionary principle. Modern fisheries management is often referred to as a governmental system of appropriate management rules based on defined objectives and a mix of management means to implement the rules, which are put in place by a system of monitoring control and surveillance. A popular approach is the ecosystem approach to fisheries management. According to the Food and Agriculture Organization of the United Nations (FAO), there are "no clear and generally accepted definitions of fisheries management". However, the working definition used by the FAO and much cited elsewhere is:

The integrated process of information gathering, analysis, planning, consultation, decision-making, allocation of resources and formulation and implementation, with enforcement as necessary, of regulations or rules which govern fisheries activities in order to ensure the continued productivity of the resources and the accomplishment of other fisheries objectives.

Fishing down the food web

Fishing down the food web is the process whereby fisheries in a given ecosystem, "having depleted the large predatory fish on top of the food web, turn to increasingly smaller species, finally ending up with previously spurned small fish and invertebrates".The process was first demonstrated by the fisheries scientist Daniel Pauly and others in an article published in the journal Science in 1998. Large predator fish with higher trophic levels have been depleted in wild fisheries. As a result, the fishing industry has been systematically "fishing down the food web", targeting fish species at progressively decreasing trophic levels.

The trophic level of a fish is the position it occupies on the food chain. The article establishes the importance of the mean trophic level of fisheries as a tool for measuring the health of ocean ecosystems. In 2000, the Convention on Biological Diversity selected the mean trophic level of fisheries catch, renamed the "Marine Trophic Index" (MTI), as one of eight indicators of ecosystem health. However, many of the world's most lucrative fisheries are crustacean and mollusk fisheries, which are at low trophic levels and thus result in lower MTI values.

Minimum landing size

The minimum landing size (MLS) is the smallest fish measurement at which it is legal to keep or sell a fish. What the MLS is depends on the species of fish. Sizes also vary around the world, as they are legal definitions which are defined by the local regulatory authority. Commercial trawl and seine fisheries can control the size of their catch by adjusting the mesh size of their nets.

European Union – The European Fishery MLS applies to all EU member states.

Mycotroph

A mycotroph is a plant that gets all or part of its carbon, water, or nutrient supply through symbiotic association with fungi. The term can refer to plants that engage in either of two distinct symbioses with fungi:

Many mycotrophs have a mutualistic association with fungi in any of several forms of mycorrhiza. The majority of plant species are mycotrophic in this sense. Examples include Burmanniaceae.

Some mycotrophs are parasitic upon fungi in an association known as myco-heterotrophy.

Organotroph

An organotroph is an organism that obtains hydrogen or electrons from organic substrates. This term is used in microbiology to classify and describe organisms based on how they obtain electrons for their respiration processes. Some organotrophs such as animals and many bacteria, are also heterotrophs. Organotrophs can be either anaerobic or aerobic.

Antonym: Lithotroph, Adjective: Organotrophic.

Planktivore

A planktivore is an aquatic organism that feeds on planktonic food, including zooplankton and phytoplankton.

Recruitment (biology)

In biology, especially marine biology, recruitment occurs when a juvenile organism joins a population, whether by birth or immigration, usually at a stage whereby the organisms are settled and able to be detected by an observer.There are two types of recruitment: closed and open.In the study of fisheries, recruitment is "the number of fish surviving to enter the fishery or to some life history stage such as settlement or maturity".

Relative abundance distribution

In the field of ecology, the relative abundance distribution (RAD) or species abundance distribution describes the relationship between the number of species observed in a field study as a function of their observed abundance. The graphs obtained in this manner are typically fitted to a Zipf–Mandelbrot law, the exponent of which serves as an index of biodiversity in the ecosystem under study.

SeaLifeBase

SeaLifeBase is a global online database of information about marine life. It aims to provide key information on the taxonomy, distribution and ecology of all marine species in the world apart from finfish. SeaLifeBase is in partnership with the WorldFish Center in Malaysia and the UBC Fisheries Centre at the University of British Columbia. Daniel Pauly is the principal investigator and it is coordinated by Maria Lourdes D. Palomares. As of October 2016, it included descriptions of 74,000 species, 47,700 common names, 12,400 pictures, and references to 31,700 works in the scientific literature. SeaLifeBase complements FishBase, which provides parallel information for finfish.

Villy Christensen

Villy Christensen is an ecosystem modeller with a background in fisheries science. He is known for his work as a project leader and core developer of Ecopath, an ecosystem modelling software system widely used in fisheries management. Ecopath was initially an initiative of the NOAA, but since primarily developed at the UBC Fisheries Centre of the University of British Columbia. In 2007, it was named as one of the ten biggest scientific breakthroughs in NOAA’s 200-year history. The citation states that Ecopath “revolutionized scientists’ ability worldwide to understand complex marine ecosystems".

General
Producers
Consumers
Decomposers
Microorganisms
Food webs
Example webs
Processes
Defense,
counter
Ecology: Modelling ecosystems: Other components
Population
ecology
Species
Species
interaction
Spatial
ecology
Niche
Other
networks
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