TY  - JOUR
A1  - Stillman, Richard A.
A1  - Railsback, Steven Floyd
A1  - Giske, Jarl
A1  - Berger, Uta
A1  - Grimm, Volker
T1  - Making Predictions in a Changing World: The Benefits of Individual-Based Ecology
JF  - Bioscience
N2  - Ecologists urgently need a better ability to predict how environmental change affects biodiversity. We examine individual-based ecology (IBE), a research paradigm that promises better a predictive ability by using individual-based models (IBMs) to represent ecological dynamics as arising from how individuals interact with their environment and with each other. A key advantage of IBMs is that the basis for predictions-fitness maximization by individual organisms-is more general and reliable than the empirical relationships that other models depend on. Case studies illustrate the usefulness and predictive success of long-term IBE programs. The pioneering programs had three phases: conceptualization, implementation, and diversification. Continued validation of models runs throughout these phases. The breakthroughs that make IBE more productive include standards for describing and validating IBMs, improved and standardized theory for individual traits and behavior, software tools, and generalized instead of system-specific IBMs. We provide guidelines for pursuing IBE and a vision for future IBE research.
KW  - ecology
KW  - fitness-maximization
KW  - individual-based
KW  - modeling
KW  - prediction
Y1  - 2015
U6  - https://doi.org/10.1093/biosci/biu192
SN  - 0006-3568
SN  - 1525-3244
VL  - 65
IS  - 2
SP  - 140
EP  - 150
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Kissling, W. D.
A1  - Dormann, Carsten F.
A1  - Groeneveld, Juergen
A1  - Hickler, Thomas
A1  - Kühn, Ingolf
A1  - McInerny, Greg J.
A1  - Montoya, Jose M.
A1  - Römermann, Christine
A1  - Schiffers, Katja
A1  - Schurr, Frank Martin
A1  - Singer, Alexander
A1  - Svenning, Jens-Christian
A1  - Zimmermann, Niklaus E.
A1  - O'Hara, Robert B.
T1  - Towards novel approaches to modelling biotic interactions in multispecies assemblages at large spatial extents
JF  - Journal of biogeography
N2  - Aim Biotic interactions within guilds or across trophic levels have widely been ignored in species distribution models (SDMs). This synthesis outlines the development of species interaction distribution models (SIDMs), which aim to incorporate multispecies interactions at large spatial extents using interaction matrices. Location Local to global. Methods We review recent approaches for extending classical SDMs to incorporate biotic interactions, and identify some methodological and conceptual limitations. To illustrate possible directions for conceptual advancement we explore three principal ways of modelling multispecies interactions using interaction matrices: simple qualitative linkages between species, quantitative interaction coefficients reflecting interaction strengths, and interactions mediated by interaction currencies. We explain methodological advancements for static interaction data and multispecies time series, and outline methods to reduce complexity when modelling multispecies interactions. Results Classical SDMs ignore biotic interactions and recent SDM extensions only include the unidirectional influence of one or a few species. However, novel methods using error matrices in multivariate regression models allow interactions between multiple species to be modelled explicitly with spatial co-occurrence data. If time series are available, multivariate versions of population dynamic models can be applied that account for the effects and relative importance of species interactions and environmental drivers. These methods need to be extended by incorporating the non-stationarity in interaction coefficients across space and time, and are challenged by the limited empirical knowledge on spatio-temporal variation in the existence and strength of species interactions. Model complexity may be reduced by: (1) using prior ecological knowledge to set a subset of interaction coefficients to zero, (2) modelling guilds and functional groups rather than individual species, and (3) modelling interaction currencies and species effect and response traits. Main conclusions There is great potential for developing novel approaches that incorporate multispecies interactions into the projection of species distributions and community structure at large spatial extents. Progress can be made by: (1) developing statistical models with interaction matrices for multispecies co-occurrence datasets across large-scale environmental gradients, (2) testing the potential and limitations of methods for complexity reduction, and (3) sampling and monitoring comprehensive spatio-temporal data on biotic interactions in multispecies communities.
KW  - Community ecology
KW  - ecological networks
KW  - global change
KW  - guild assembly
KW  - multidimensional complexity
KW  - niche theory
KW  - prediction
KW  - species distribution model
KW  - species interactions
KW  - trait-based community modules
Y1  - 2012
U6  - https://doi.org/10.1111/j.1365-2699.2011.02663.x
SN  - 0305-0270
VL  - 39
IS  - 12
SP  - 2163
EP  - 2178
PB  - Wiley-Blackwell
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Ryngajllo, Malgorzata
A1  - Childs, Liam H.
A1  - Lohse, Marc
A1  - Giorgi, Federico M.
A1  - Lude, Anja
A1  - Selbig, Joachim
A1  - Usadel, Björn
T1  - SLocX  predicting subcellular localization of Arabidopsis proteins leveraging gene expression data
JF  - Frontiers in plant science
N2  - Despite the growing volume of experimentally validated knowledge about the subcellular localization of plant proteins, a well performing in silico prediction tool is still a necessity. Existing tools, which employ information derived from protein sequence alone, offer limited accuracy and/or rely on full sequence availability. We explored whether gene expression profiling data can be harnessed to enhance prediction performance. To achieve this, we trained several support vector machines to predict the subcellular localization of Arabidopsis thaliana proteins using sequence derived information, expression behavior, or a combination of these data and compared their predictive performance through a cross-validation test. We show that gene expression carries information about the subcellular localization not available in sequence information, yielding dramatic benefits for plastid localization prediction, and some notable improvements for other compartments such as the mito-chondrion, the Golgi, and the plasma membrane. Based on these results, we constructed a novel subcellular localization prediction engine, SLocX, combining gene expression profiling data with protein sequence-based information. We then validated the results of this engine using an independent test set of annotated proteins and a transient expression of GFP fusion proteins. Here, we present the prediction framework and a website of predicted localizations for Arabidopsis. The relatively good accuracy of our prediction engine, even in cases where only partial protein sequence is available (e.g., in sequences lacking the N-terminal region), offers a promising opportunity for similar application to non-sequenced or poorly annotated plant species. Although the prediction scope of our method is currently limited by the availability of expression information on the ATH1 array, we believe that the advances in measuring gene expression technology will make our method applicable for all Arabidopsis proteins.
KW  - subcellular localization
KW  - support vector machine
KW  - prediction
KW  - gene expression
Y1  - 2011
U6  - https://doi.org/10.3389/fpls.2011.00043
SN  - 1664-462X
VL  - 2
PB  - Frontiers Research Foundation
CY  - Lausanne
ER  - 
TY  - GEN
A1  - Mooij, Wolf M.
A1  - Trolle, Dennis
A1  - Jeppesen, Erik
A1  - Arhonditsis, George B.
A1  - Belolipetsky, Pavel V.
A1  - Chitamwebwa, Deonatus B. R.
A1  - Degermendzhy, Andrey G.
A1  - DeAngelis, Donald L.
A1  - Domis, Lisette Nicole de Senerpont
A1  - Downing, Andrea S.
A1  - Elliott, J. Alex
A1  - Fragoso Jr., Carlos Ruberto
A1  - Gaedke, Ursula
A1  - Genova, Svetlana N.
A1  - Gulati, Ramesh D.
A1  - Håkanson, Lars
A1  - Hamilton, David P.
A1  - Hipsey, Matthew R.
A1  - ‘t Hoen, Jochem
A1  - Hülsmann, Stephan
A1  - Los, F. Hans
A1  - Makler-Pick, Vardit
A1  - Petzoldt, Thomas
A1  - Prokopkin, Igor G.
A1  - Rinke, Karsten
A1  - Schep, Sebastiaan A.
A1  - Tominaga, Koji
A1  - Van Dam, Anne A.
A1  - Van Nes, Egbert H.
A1  - Wells, Scott A.
A1  - Janse, Jan H.
T1  - Challenges and opportunities for integrating lake ecosystem modelling approaches
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1326 
KW  - aquatic
KW  - food web dynamics
KW  - plankton
KW  - nutrients
KW  - spatial
KW  - lake
KW  - freshwater
KW  - marine
KW  - community
KW  - population
KW  - hydrology
KW  - eutrophication
KW  - global change
KW  - climate warming
KW  - fisheries
KW  - biodiversity
KW  - management
KW  - mitigation
KW  - adaptive processes
KW  - non-linear dynamics
KW  - analysis
KW  - bifurcation
KW  - understanding
KW  - prediction
KW  - model limitations
KW  - model integration
Y1  - 2010
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429839
SN  - 1866-8372
IS  - 1326
ER  - 
TY  - JOUR
A1  - Mooij, Wolf M.
A1  - Trolle, Dennis
A1  - Jeppesen, Erik
A1  - Arhonditsis, George B.
A1  - Belolipetsky, Pavel V.
A1  - Chitamwebwa, Deonatus B. R.
A1  - Degermendzhy, Andrey G.
A1  - DeAngelis, Donald L.
A1  - Domis, Lisette Nicole de Senerpont
A1  - Downing, Andrea S.
A1  - Elliott, J. Alex
A1  - Fragoso Jr, Carlos Ruberto
A1  - Gaedke, Ursula
A1  - Genova, Svetlana N.
A1  - Gulati, Ramesh D.
A1  - Håkanson, Lars
A1  - Hamilton, David P.
A1  - Hipsey, Matthew R.
A1  - ‘t Hoen, Jochem
A1  - Hülsmann, Stephan
A1  - Los, F. Hans
A1  - Makler-Pick, Vardit
A1  - Petzoldt, Thomas
A1  - Prokopkin, Igor G.
A1  - Rinke, Karsten
A1  - Schep, Sebastiaan A.
A1  - Tominaga, Koji
A1  - Van Dam, Anne A.
A1  - Van Nes, Egbert H.
A1  - Wells, Scott A.
A1  - Janse, Jan H.
T1  - Challenges and opportunities for integrating lake ecosystem modelling approaches
JF  - Aquatic ecology
N2  - A large number and wide variety of lake ecosystem models have been developed and published during the past four decades. We identify two challenges for making further progress in this field. One such challenge is to avoid developing more models largely following the concept of others ('reinventing the wheel'). The other challenge is to avoid focusing on only one type of model, while ignoring new and diverse approaches that have become available ('having tunnel vision'). In this paper, we aim at improving the awareness of existing models and knowledge of concurrent approaches in lake ecosystem modelling, without covering all possible model tools and avenues. First, we present a broad variety of modelling approaches. To illustrate these approaches, we give brief descriptions of rather arbitrarily selected sets of specific models. We deal with static models (steady state and regression models), complex dynamic models (CAEDYM, CE-QUAL-W2, Delft 3D-ECO, LakeMab, LakeWeb, MyLake, PCLake, PROTECH, SALMO), structurally dynamic models and minimal dynamic models. We also discuss a group of approaches that could all be classified as individual based: super-individual models (Piscator, Charisma), physiologically structured models, stage-structured models and traitbased models. We briefly mention genetic algorithms, neural networks, Kalman filters and fuzzy logic. Thereafter, we zoom in, as an in-depth example, on the multi-decadal development and application of the lake ecosystem model PCLake and related models (PCLake Metamodel, Lake Shira Model, IPH-TRIM3D-PCLake). In the discussion, we argue that while the historical development of each approach and model is understandable given its 'leading principle', there are many opportunities for combining approaches. We take the point of view that a single 'right' approach does not exist and should not be strived for. Instead, multiple modelling approaches, applied concurrently to a given problem, can help develop an integrative view on the functioning of lake ecosystems. We end with a set of specific recommendations that may be of help in the further development of lake ecosystem models.
KW  - aquatic
KW  - food web dynamics
KW  - plankton
KW  - nutrients
KW  - spatial
KW  - lake
KW  - freshwater
KW  - marine
KW  - community
KW  - population
KW  - hydrology
KW  - eutrophication
KW  - global change
KW  - climate warming
KW  - fisheries
KW  - biodiversity
KW  - management
KW  - mitigation
KW  - adaptive processes
KW  - non-linear dynamics
KW  - analysis
KW  - bifurcation
KW  - understanding
KW  - prediction
KW  - model limitations
KW  - model integration
Y1  - 2010
U6  - https://doi.org/10.1007/s10452-010-9339-3
SN  - 1573-5125
SN  - 1386-2588
VL  - 44
SP  - 633
EP  - 667
PB  - Springer Science + Business Media B.V.
CY  - Dordrecht
ER  -