Ecosystem Modeling

Ecosystem Modeling

  • Rüdiger Grote added an answer:
    What are the emerging issues for urban environments and ecosystems i.e. potential threats and opportunities that are currently poorly recognized?

    We are having a workshop in Auckland in 2 weeks to consider urban pressures on the horizon.  The challenge is to think of new ideas, or issues poorly studied, rather than the usual problems or exacerbators of the usual problems. Your ideas would be welcome.

  • Harry ten Brink added an answer:
    Is the green house effect or global warming responsible for climate change?

    What are the main causes of climate change? How do they influence climate change, and in what ratio? 

    Harry ten Brink · Energy Research Centre of the Netherlands


    I have already privately mailed you that 2014 was the warmest year on record in the Netherlands, which means in the last 300 years and by a long-shot

    it was 1.4 C warmer than the average, that is over the period 1980-2010 (average 10.1 C)

  • Nathalie Niquil added an answer:
    What are your thoughts on using Large Fish Index as an ecosystem health indicator characterizing the food web ?
    Your answers will be usefull in the discussions on finding common indicators in Europe for monitoring food web health in marine ecosystems. LFI is for example monitored within OSPAR as the percentage of fish > 40 cm when performing a bottom trawl. The idea beyond is that food webs are shortened by overfishing. What do you think of it as an indicator not only of the fish community but also of the whole food web. Is this indicator sensitive to other pressures than fishing ? How could this indicator be modified for a better food web use ? Would it make sense to apply it to benthic species and especially invertebrates ?
    Nathalie Niquil · French National Centre for Scientific Research

    Thank you very much for these answers. They are all very compmlementary !

  • Harry Hurd added an answer:
    How do I add different degrees of nonstationarity into a monthly flow series?

    One great influence of climate change on water resources system is the growing degree of nonstationarity of hydrological time series. Nonstationarity is a very broad word, trend, growing variance, unexpected extreme values could all be considered as non-stationary.

    Then if we want to generate monthly flow series with different degree of nonstationarity, the questions are which part of nonstationarity show we concentrate on, how to define the degree of nonstationarity, and how to add different degree of nonstationarity into a stationary monthly flow series.

    Harry Hurd · University of North Carolina at Chapel Hill

    Dear Pan,

    I suggest you look up papers dealing with PARMA (periodic ARMA) and PAR as a special case.. These models have been studied fairly extensively for river flows. Check papers by Vecchia, Lund. Anderson, Meerschart, Tesfaye.

  • Maowei Liang added an answer:
    Can anyone suggest how to scalie a Static chamber to Eddy covariance about net ecosystem CO2 exchange?

    The main methods of net ecosystem CO2 exchange are static chamber and eddy covariance. I have done some experiments about static chamber and got some data about eddy covariance in the same place during the same period. So I want to combine the data of static chamber with the data of eddy covariance, and scale the static chamber to the eddy covariance by using some models. However, I have no idea how to scale or use the model.
    Would you like give me some advise?
    Any help appreciated.
    Thank you much indeed!

    Maowei Liang · Inner Mongolia University

    Hi Frank,

    Thank you very much,you're so nice.


  • Marcelo Negri Soares added an answer:
    Can anyone add a list of deadlier animals found in Mangrove ecosystems in eastern Indian mangrove forest?

    Mangrove ecosystem is one of the important richer biodiversity zone in the world. I am adding two- the Royal Bengal tiger and the cobra. Add more as per your knowledge.

    Marcelo Negri Soares · Universidade Nove de Julho

    The forest covers 10,000 km2 of which about 6,000 are in Bangladesh. It became inscribed as a UNESCO world heritage site in 1997, but while the Bangladeshi and Indian portions constitute the same continuous ecotope, these are separately listed in the UNESCO world heritage list as the Sundarbans and Sundarbans National Park, respectively. The Sundarbans is intersected by a complex network of tidal waterways, mudflats and small islands of salt-tolerant mangrove forests. The area is known for the eponymous Royal Bengal Tiger (Panthera tigris tigris), as well as numerous fauna including species of birds, spotted deer, crocodiles and snakes. It is estimated that there are now 500[citation needed] Bengal tigers and about 30,000 spotted deer in the area. Sundarbans was designated a Ramsar site on May 21, 1992. The fertile soils of the delta have been subject to intensive human use for centuries, and the ecoregion has been mostly converted to intensive agriculture, with few enclaves of forest remaining. The remaining forests, together with the Sundarbans mangroves, are important habitat for the endangered tiger. Additionally, the Sundarbans serves a crucial function as a protective flood barrier for the millions of inhabitants in and around Kolkata (Calcutta) against the result of cyclone activity. Sundarbans is home to many different species of birds, mammals, insects, reptiles and fish. It is estimated that there may be found more than 120 species of fish and over 260 species of birds and more than fifty species of reptiles and eight amphibians. Many tourists go there to see the Bengal tigers, saltwater crocodiles, leopards and snakes cobra.

  • Dan Laurentiu Stoica added an answer:
    Does anyone have experience in habitat quality modelling?
    I am designing a habitat quality index using amphibians to assess the health of forest biodiversity. I therefore need help with expertise and advice.
    Dan Laurentiu Stoica · Local Environmental Protection Agency in Iaşi

    I think you need to develop two important issues. Strucutral connectivity or fragmentation and functional connectivity or fragmentation. It might be there are proper habitats for amphibians in your forest yet you have no or little population and then you have to discover why. Then you have a suitable forest habitat with amphibians which means it is functional.

  • Imtiaz Dharssi added an answer:
    Are physically-based land surface models less skillful than simple statistical models using linear regression?

    See results from the international benchmarking project, PLUMBER (PALS Land Surface Model Benchmarking Evaluation Project).

    Imtiaz Dharssi · Bureau of Meteorology

    Many Thanks to those who answered this question. I would also have expected a physically based land surface model to easily outperform any simple statistical model. However, unfortunately, land surface models seem to have some fundamental problems so that they ALL under-perform. This has been discovered by the PALS Land sUrface Model Benchmarking Evaluation pRoject (PLUMBER). A peer-reviewed paper should be released soon but in the meantime more information can be found from this presentation:

  • Gábor L. Lövei added an answer:
    Do you have any suggestion pseudoreplication in system analysis?

    Hi everybody,

    Starting from 1st (maybe 2nd) of January I will perform a system analysis concerning ecosystem services provided by a transumant farmer in central Italy.

    So, in addition to other things (biodiversity, insects etc.), I will monitor CO2 effluxes from grazed fields (e.g. Alfa alfa...) compared with traditional ones (e.g. durum wheat, sunflowers...) in i) plain, ii) hills and iii) mountain areas following the transumant movements during one year.

    Concerning CO2 efflux I can use just pseudoreplication because it's impossible to use any different expetimental design. 

    So, any suggestions? (numers of sampling)... 

    Take a look at the picture, thanks!

    Gábor L. Lövei · Aarhus University & Fujian University of Agriculture & Forestry

    Yes, Matteo, precisely. If you need to, you may reduce the within-field replication. For example, if you have capacity to do 60 measurements in total, it is much better to do 4 repeat measurements/field, and increase the no. of fields measured (like you write: 5 each of pasture, wheat & sunflower) than 20 measurements per field, but only one field each of pasture, wheat and sunflower. This will make your life more difficult, but I am afraid there is no other way to get resutls in which you can be confident.

  • Panos V. Petrakis added an answer:
    Can someone inform me about the 7 aspects and 22 indexes reflecting ecosystem stability, first presented by H.T. Odum in 1970s?

    Pls. provide the relevant full text or aiticle link

    The answer is quite complex. Actually, I understand that only relevant articles on ecosystem strategies are sought and not papers on the properties of indices.

    For this I sent two papers (files) from my library. 

  • Brenden S Holland added an answer:
    Does molecular biology change the numbers that estimate biodiversity losses?

    I'm interested in knowing how the estimates of the numbers of species present in an ecosystem are made, and how the biodiversity losses are evaluated. In particular:

    * is it based on the macrofauna/macroflora only, or does it also include microbes?

    * does the advent of metagenomics/barcoding technologies change the estimates, as new species /OTUs are constantly being described?

    Brenden S Holland · University of Hawaiʻi at Mānoa

    Very interesting question: I think most conservation biologists might agree that molecular data  "change the numbers that estimate biodiversity", specifically this category of phylogenetic and systematic characters (i.e. DNA markers/genomics) allow robust, repeatable, quantitative phylogeographic and reconstruction.  So by "change" what I mean is potential to "refine", "improve" and "increase resolution" of biodiversity assessments.  However, along the lines of what is stated above, usually we can only assess what is remaining, unless comprehensive baseline studies have been conducted, and / or, ancient or museum samples are available for the pre- versus post-impact comparison.

  • YOGESH CHANDRA TRIPATHI added an answer:
    Why Porteresia sp can be called a pioneer species during an island formation?

    See Carbon sequestration book

  • Mohammed Layelmam added an answer:
    How can I estimate the moisture from the MODIS data ?

    I have a daily database of MODIS and I would use a models or functions to estimate moisture,

    Thank You

    Mohammed Layelmam · Institut Agronomique et Vétérinaire Hassan II

    Merci monsieur Babah, mon adresse Email est 

  • Amartya K Saha added an answer:
    Why did the IUCN decide this 6 meter limit for wetland? and not 5 meters or 7 meters ?

    For wetland IUCN adopted the following definition in 1971 (4; 2) :
    “. . . areas of marsh, fen, peatland or water, whether natural or arti-
    ficial, permanent or temporary, with water that is static or flowing,
    fresh, brackish, or salt including areas of marine water, the depth of
    which at low tide does not exceed 6 meters.”

    Amartya K Saha · Florida International University

    The wording indicates the max 6 m depth is for coastal marine ecosystems - including  mangrove/saltmarsh, and not for freshwater environments. While a large wetland may 6 m deep depressions, i think the average depth of a freshwater wetland would be far less, like 1-2 m at most. Else it becomes a pond or lake or river.

  • Jacob Yu added an answer:
    Are Dr. John Todd's "Living Machines" a viable way to treat wastewater on a large scale?

    They are supposedly a way to treat wastewater without using chemicals, but instead by creating an "ecosystem", whose constituent organisms filter the water. I gathered from this paper

    that "the ideal closed system as having three major components or subsystems. It consists of a sunlight-based,
    photosynthetically driven system that is connected to an animal consumer component, which in turn, is connected to a detritus/bacterial system.
    Our experience supports the Adey and Loveland (1991) requirement of a minimum of three distinct subecosystems. We have found it is best to house the subsystems in distinct cells separated in space but connected by flows." 

    He has a company:

    which installs these for a fee....Can anyone comment on if this is a viable method for the future? It seems almost "too good to be true" - an all natural way to deal with the waste products of society purely relying on "natural" processes..

    Jacob Yu · Boston University

    Fascinating answers, thank you all, will read further on the leads you all have given me thus far..

  • Maowei Liang added an answer:
    Is Net Ecosystem Production Equal to Net Ecosystem Exchange minus Ecosystem Respiration?

    The NEE CO2 (Net Ecosystem CO2 Exchange/umol.m-2.s-1) and ER(Ecosystem Respiration/umol.m-2.s-1) were measured in growing season from 2012 to 2013, respectively. Recently, I'm frustrated when I have to calculate the Net Ecosystem Production (NEP/gCm-2.yr-1).
    Is NEP equal to NEE minus ER in numerically?
    Can I directly calculate the Ecosystem Carbon Accumulation in growing season (gCm-2.yr-1) using the NEP(umolCO2.m-2.s-1)?
    What is the equation from umol CO2.m-2.s-1 turn to g C.m-2.yr-1?
    I‘m not assure about it.
    Any help appreciated.
    Thank you much indeed!

    Maowei Liang · Inner Mongolia University

    To Sara,

    It's very grateful for your help,you're very nice.

    Thank you very much.

  • Unachukwu G.O added an answer:
    Do any GCM modellers use the Craig-Gordon parameterization?

    Craig-Gordon (1965) is a common parameterization scheme used in ecosystem models but more commonly Merlivat and Jouzel (1979) is used for GCMs. Do any GCMs use C-G?

    Unachukwu G.O · University of Nigeria

    I do not have formal idea about this.

    Kind regards

  • John J Gibson added an answer:
    Have the models developed by Craig-Gordon (1965) and Merlivat-Jouzel (1979) been compared in an ecosystem model or GCM?

    Two basic parameterization schemes have been utilized for predicting the isotopic enrichment of surface waters during evaporation. I am looking for studies or models that compare both approaches. C-G typically uses turbulence-dependant weighted kinetic fractionation whereas M-J uses separate wind-speed-dependent algorithms for smooth and rough surfaces. 

    John J Gibson · University of Victoria

    I think the answer may be no

  • Younes Shahrokhzade added an answer:
    What software has worked well for modeling population densities in the past (like 2000 ya) using habitat/density information?

    I am working on a project modeling the possible densities of seabirds in my area in the pre-human past (1,500 ya).  I will be using habitat-population density relationships do model several possible scenarios.  Do any of you folks have software suggestions for this type of work?

    Younes Shahrokhzade · Tarbiat Modares University


    marxan one madel in the IDRISI that  determined decision support and reserve system with minimum cost

  • Jason S Link added an answer:
    How can and should discard indicators be incorporated into the ecosystem approach of fisheries management?

    Currently, discard rates are discussed as indicators for the EU Common fisheries Policy (CFP) and the Marine Strategy Framework Directive (MSFD). However, I am not sure, what is the intention of such indicators?  Do they want to improve mortality estimates? Or do they want to assess the way fishing is performed i.e. how wasteful a fisheries is?

    Jason S Link · National Oceanic and Atmospheric Administration

    Consider as mortality on populations noted, but also in an energetic context for the entire system.

  • Craig Dremann added an answer:
    Is anyone producing the mathematical models of non-riparian plant ecosystem functions?

    In non-riparian plant ecosystems, if you measure percentage plant cover, mathematical models and equations could be produced, to describe the spatial interactions between plant species. Is anyone doing anything like that?

    Craig Dremann · The Reveg Edge

    Thanks for your reply.  For example, I work in arid grasslands, and when I conduct vegetation transects, I am measuring the percentage basal cover of each plant species.  For example everything measured together is going to equal 100% cover for a given area, so what are the parameters of Species A when it is growing with Species B for example, and can those percentage cover relationships be expressed as a mathematical equation?

  • Tarmo Ketola added an answer:
    Serratia marcescens is a pathogen of cucurbits, sunflower, alfalfa. Is it an example of general trend of opportunistic pathogen to turn to plant?
    More and more opportunistic bacterial pathogens like Serratia, Pantoea, E. coli are isolated from plants and cause new plant diseases. Is there an increasing risk for people?
    Tarmo Ketola · University of Jyväskylä

    Thanks Alex for the information, maybe I try some of the plants and methods in near future.

  • Harley Schinagl added an answer:
    Can you recommend methods for species distribution modelling?

    Over the years I have been working, I have been compiling a presence only list (coordinates) of a rare tree species from my area. I have good reason to believe (from industry experts and the literature) that my list may be one of the most comprehensive that exists. As well as compiling this info for submission to flora databases, I wanted to put in some time to help develop the knowledge of the species, as well as learn some skills myself. I was hoping to undertake some form of species modelling to determine the species original extent (prior to european settlement which resulted in extensive clearing) and combining that with extant layers of native vegetation to get an idea on how many may still be present in remnant populations (I believe the number of trees left is far different to that commonly stated). I may even try and field truth the predictions. The species occupies a relatively narrow area of (approximately) 300x100 kilometers. 

    When I browse through the literature in this topic, I am overwhelmed. I am hoping to get some direction on the type of modelling I should do with some good guidance on how to go about it (seeing as I have limited experience in the field). Software suggestions (I am an independent researcher so free would be ideal), type of analysis to run, and guides on using the software would be ideal. I have a moderate skill set with ESRI products but again, because I am not affiliated with a university, i can not afford extensions. I know I am probably underestimating the difficulty of this task but I am willing to treat this as a learning exercise and put in the time.

    Harley Schinagl · Indigenous Design

    Thanks everyone for your contributions. As I first thought, this is a very large topic I am about to embark upon and I have a lot of reading to do. Even this thread offers a good amount of background. But please don't let that stop more people from contributing. 

  • Rüdiger Grote added an answer:
    Can anyone recommend process models for carbon allocation in grassland species?

    I am looking for a process models that I can use to simulate carbon allocation in herbaceous species (I want to compare it against experimental data). Any advice or suggestions?

  • Jan Hackenberg added an answer:
    Is there any free terrestrial LiDAR point data at fine scale about single tree?
    I am working on characterizing a tree, and the recent progress is shown in the attached link. To display it, you may need any browser (e.g. Chrome) that supports WebGL. The problem seems to be the low density of the point cloud.
    Jan Hackenberg · University of Freiburg

    Hi Zhouxin,

    you might want to visit my project homepage,

    I already made some point clouds available of single trees. There are scans of two cherry trees(dbh ~ 20cm), training data of single branches and some more data. I will coninue publishing this kind of data. All data is open data. Feel freee to also contact me.



  • Marthias Silwamba added an answer:
    Which objective function is better for non linear optimization algorithm in EXCEL?
    I used for a non-linear optimization problem the objective function O.F.=Σ(xs-xo)^2, where xs is the simulated value and xo is the observed. The algorithm runs adequately but I would like to know if this objective function is limited only for linear problems or whether it can also be used for non-linear problems.
    Marthias Silwamba · University of the Witwatersrand

    what objective function can I use apart from the linear objective function for me to find the optimum of non-linear model (say parabolic function)? Because the linear the optimum is always on constraints. help me please.

  • Deborah Van Gaans added an answer:
    How can I measure distance between populations across continents?
    I'm dealing with a diverse genus (>50 spp) that contains a great deal of cosmopolitan fungal species, and I have a set of DNA sequences of one to three genes. I would like to know if there is a way to quantify the distance between populations from different countries on different continents (and see if I can relate the geographic distance to genetic distance). It seems obvious that using Euclidian distances is biologically meaningless. How can I compare populations of a species that is distributed in, say, France, India, and South Africa (just to give an extreme example)? Is there a way to consider biomes? How can I account for them moving across the ocean?

    I think my question is rather complex, but I would love to hear all sort of opinions and suggestions.
    Deborah Van Gaans · University of Adelaide
    Hi Sandra,

    This might help:

    kind regards,

  • Rokhshad Hejazi added an answer:
    Can I use the cropwat model for measuring damage of rangelands?
    Which model would you recommended for this purpose?
    Rokhshad Hejazi · Islamic Azad University Tehran North Branch
    با عرض سلام دفتر اقتصاد محیط زیست سازمان حفاطت محیط زیست در تابستان 1390 یک نشست یک روزه در این مورد برگزار کرده که گزارش از کارهای تحقیقاتی انجام شده را ارایه کرده
    2/ خانم دکتر زهرا عابدی سرپرست یک گروه تحقیقاتی در این زمینه بوده اند
    3/ نام خانم مونا نظیری را جستجو فارسی کنید
    4 در SID نام SEEA را جستجو لفرمتیید مقلات زیادی را مییابید
    موفق باشید
  • Anurag Saha added an answer:
    Will sound maps be helpful in determining ecosystem services in urban cities?
    Currently, I'm doing my thesis on Mapping habitats and Ecosystem services in Dublin parks, Ireland. I was thinking about using the urban population and the level of sound they produce in determining a major aspect of ecosystem service in urban parks. What can be the possibilities of using such factor in determining the habitat biodiversity?
    Anurag Saha · University College Dublin
    Thank you all...for your responses!!
  • C. Haetinger added an answer:
    Could anyone provide linear algebra and analytic geometry applications for use in my classroom of several engineering students?
    Maybe in environmental modeling, ecology, robotics, and so on.
    C. Haetinger · Centro Universitário UNIVATES
    Dear prof. Ganesh: both applications are interesting. thanks again, C.

About Ecosystem Modeling

An ecosystem model is an abstract, usually mathematical, representation of an ecological system, which is studied to gain a deeper understanding of the real system. Ecosystem models are formed by combining known ecological relations with data gathered from field observations. 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. They also enable the simulation of ecological processes over very long periods of time. Ecosystem models have applications in a wide variety of disciplines, such as natural resource management, ecotoxicology and environmental health,agriculture, and wildlife conservation. (Wikipedia)

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