Ecosystem Modeling

Ecosystem Modeling

  • 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

  • Paul R. Yarnold 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).

    Paul R. Yarnold · Optimal Data Analysis LLC

    I absolutely concur--it is indisputable--that parametric statistical models can't predict precipitation or temperature well due to inherent limitations including paradoxical confounding.

    However, optimal (maximum-accuracy) statistical models remedy the problems of antiquated methods, and predict precipitation and temperature anomalies very well. The following open access article demonstrates these methods in this context:

  • 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.

  • Heino O. Fock 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 ?
    Heino O. Fock · Thünen Institute

    Hi Nathalie

    as a food web AND ecosystem health indicator, LFI would be more usefull if it would include also diversity, see

    Fock HO, Kloppmann M, Probst WN (2014) An early footprint of fisheries: changes for a demersal fish assemblage in the German Bight from 1902-1932 to 1991-2009. Journal of Sea Research 85:325-335

    All the best Heino

  • 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.
  • Is there any tool that can generate raster longitude and latitude in Arcgis?
    This research is wonderful, congratulations. My question is, is there any tool that can generate raster longitude and latitude in Arcgis?
    José Ignacio Álvarez Francoso · Universidad de Sevilla
    Hola Fernando,

    I'm afraid there is no tool to do that, but you can find several methods that resolve it.

    These esri's threads may help you:

    If you are not familiarized with python nor modelBuilder, you could try a simple approach:
    - Convert a raster of the study area to point.
    - Create two fields (floating or double) to store x and y.
    - Calculate geometry (longitude for x, latitude for y)
    - Convert to raster using x field (longitude raster)
    - Convert to raster using y field (latitude raster).

  • Frank Veroustraete added an answer:
    Does anyone know how to download the standalone version of the IPSL's land surface model "ORCHIDEE"?
    Is the model ORCHIDEE available for public use or is it available for a few selected research organizations only?
    Frank Veroustraete · University of Antwerp
    Hi Aniket,
    Go to the following URL:
    It is the contact site. To become a user, you will have to formulate a demand and the application you have in mind. I guess then a board at Jussieu will decide to allow you as a user or not.
    I figger that this will not be a problem, since your Institute is well known, Especially its director.
    Give it a try,
    Cheers and success,
  • Claire C. Treat added an answer:
    Is there any study which shows how the permeability of peat declines with time (as it grows older)?
    Or how permeability of peat decline with depth?
    Claire C. Treat · United States Geological Survey
    I would check the references cited by Steve Frolking:

    Frolking, S., N. T. Roulet, E. Tuittila, J. L. Bubier, A. Quillet, J. Talbot and P. J. H. Richard (2010). "A new model of Holocene peatland net primary production, decomposition, water balance, and peat accumulation." Earth Syst. Dynam. 1(1): 115-167.
  • Lidia Lopez added an answer:
    What are the key roles in an OSS Project?
    If we want to represent the OSS Project Ecosystem, we need to identify the roles that we cannot forget
    Lidia Lopez · Polytechnic University of Catalonia
    A college give a couple of "interesting" roles:

    - Lone Wolf. The role of Lone Wolf is based on the role of a ‘Niche Player’ Specific to this context it is defined as a developer who has developed gems that are of importance within the Ruby ecosystem, but has almost no connections with other developers

    - “Linchpin developers” participate in or span multiple FOSSD projects. In so doing, they create alliances between otherwise independent FOSSD projects. Contributors who span multiple FOSS project communities serve as “social gateways” that increase the ongoing project’s social mass , as well as affording opportunities for inter-project software composition and interoperation

    Anyone has mopre?
  • Lorenzo Menichetti added an answer:
    Do ALL the OSS Projects have a Benevolent Dictator for Life?
    Do ALL the OSS Projects have a Project Leader (1 or 2 individuals)?

    Is the Contributor License Agreement an agreement between the committer and the Project Leader?

    Is the OSS License an agreement between the user and the Porject Leader?
    Lorenzo Menichetti · Cranfield University
    I don't think so. The concept of benevolent dictator is only one possible model for software development, and it is relatively close to the "normal" paradigm for software development. The classical example in the Free Software community is Stallmann, and I guess Torvalds on the OSS side would be maybe something in the middle (as I believe nowadays he's influencing the development direction). But the development paradigm can open up to several degrees.
    The classical text you should read I think is E. Raymond: It is almost iconic as an essay, and it explains really well two possible development paradigms. It was quite a breakthrough at the time. And I've heard people saying that OSS is more on the Bazaar side while Free Software is more on the Cathedral side, but I don't think one can make such generalization.

    For the stakeholders with licenses, there are several possibilities. Regarding the GPL no, i think it is more an agreement between the end user and the community.
  • Adomako Boakye asked a question:
    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.
  • Frank Veroustraete added an answer:
    Is it better to use a solar cell with batteries or the normal electricity which is generated by gas for an Eco-house?
    We are building an Eco-house and we have solar cells but the problem is that the batteries are not eco-friendly. We plan to use the solar cells' energy during the day and the normal electricity at night. What do you think is better?
    Frank Veroustraete · University of Antwerp
    Hi Husam,

    That's exactly what I have done about three years ago. I installed on the rooftop of my house a total 3kWp PV panels. I have to add that addiotionally I produce hot water as well with a solar boiler panel. It saves me on the consumption of natural gas.
    With the 3 kWp grid connected PV installation, I can cover 60% of my total yearly electricity consumption, The investment in the PV panels,e.g. the panels, the DC to AC converter, and the installation costs, are earned back in 5 years. Since the lifetime of the PV panels is estimated to be 20 years, that, means that after 5 years I can reduce my electricity costs (grid-connected PV installation) with 60% for at leat the following 15 years.
    Hot water is produced from March till end of October. During winter I have to heat the water with a natural gas boiler.
    Heating my house itself is mainly from end of September to end of April with peak consumption of natural gas in december and january. The heating is done with a high efficiency ondensation boiler on natural gas as well.
    Since I live in a city the grid-connected PV solution is quite profitable. This may be different when living on the countryside, with no grid in the neighbourhood.
    So depending on whether you live at the countryside without a grid connection available, or with a grid connection available in the city or countryside, I would state that when the grid is availbale, use it. But don't produce more electric power than you need, if you don't get paid for the surplus which you would provide to the grid.
    Where I live I am not paid for any surplus which I produce and put on the grid. Hence, I dimensioned my PV installation thus, that I produce less electric power than what is consumed on a yearly basis. I am also charged two electricity tariffs. An expensive one during daytime and a cheap one during nighttime. Hence I wash the dishes, clothes etc ..., at nigh tariff. During the day in summer my kWh counter turns back, when there is enough sun and that's when I make the profit which i consume again during winter when there is not enough solar energy. Hence I use the grid as an electricity reservoir, which allows me to consume electric power, when my PV production is too low. I provide to the grid what I need in winter from the grid, when my production is high in summer. This configuration equilibrates at a 60 % consumption reduction and hence reduction in cost (because I reduce costs mainly on the expensive tariff (the day tariff).
    Hope these tips help Husam,

  • Neele Larondelle added an answer:
    Can you suggest some good papers with regard to modelling interactions among ecosystem services?
    E.g., methods to analyse interactions among variables in complex interacting systems.
    Neele Larondelle · Humboldt-Universität zu Berlin
    Check the publication by Haase, Schwarz, Strohbach, Kroll and Seppelt 2012: Synergies, Trade-offs, and Losses of Ecosystem Services in Urban Regions: an Integrated Multiscale Framework Applied to the Leipzig-
    Halle Region, Germany. published in Ecology and Society
    I found this to be very helpful!

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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