@misc{CabralValenteHartig2017,
  author    = {Cabral, Juliano Sarmento and Valente, Luis and Hartig, Florian},
  title     = {Mechanistic simulation models in macroecology and biogeography},
  series = {Ecography : pattern and diversity in ecology},
  volume    = {40},
  journal   = {Ecography : pattern and diversity in ecology},
  number    = {2},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0906-7590},
  doi       = {10.1111/ecog.02480},
  pages     = {267 -- 280},
  year      = {2017},
  abstract  = {Macroecology and biogeography are concerned with understanding biodiversity patterns across space and time. In the past, the two disciplines have addressed this question mainly with correlative approaches, despite frequent calls for more mechanistic explanations. Recent advances in computational power, theoretical understanding, and statistical tools are, however, currently facilitating the development of more system-oriented, mechanistic models. We review these models, identify different model types and theoretical frameworks, compare their processes and properties, and summarize emergent findings. We show that ecological (physiology, demographics, dispersal, biotic interactions) and evolutionary processes, as well as environmental and human-induced drivers, are increasingly modelled mechanistically; and that new insights into biodiversity dynamics emerge from these models. Yet, substantial challenges still lie ahead for this young research field. Among these, we identify scaling, calibration, validation, and balancing complexity as pressing issues. Moreover, particular process combinations are still understudied, and so far models tend to be developed for specific applications. Future work should aim at developing more flexible and modular models that not only allow different ecological theories to be expressed and contrasted, but which are also built for tight integration with all macroecological data sources. Moving the field towards such a 'systems macroecology' will test and improve our understanding of the causal pathways through which eco-evolutionary processes create diversity patterns across spatial and temporal scales.},
  language  = {en}
}
@misc{DormannSchymanskiCabraletal.2012,
  author    = {Dormann, Carsten F. and Schymanski, Stanislaus J. and Cabral, Juliano Sarmento and Chuine, Isabelle and Graham, Catherine and Hartig, Florian and Kearney, Michael and Morin, Xavier and R{\"o}mermann, Christine and Schr{\"o}der-Esselbach, Boris and Singer, Alexander},
  title     = {Correlation and process in species distribution models: bridging a dichotomy},
  series = {Journal of biogeography},
  volume    = {39},
  journal   = {Journal of biogeography},
  number    = {12},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0305-0270},
  doi       = {10.1111/j.1365-2699.2011.02659.x},
  pages     = {2119 -- 2131},
  year      = {2012},
  abstract  = {Within the field of species distribution modelling an apparent dichotomy exists between process-based and correlative approaches, where the processes are explicit in the former and implicit in the latter. However, these intuitive distinctions can become blurred when comparing species distribution modelling approaches in more detail. In this review article, we contrast the extremes of the correlativeprocess spectrum of species distribution models with respect to core assumptions, model building and selection strategies, validation, uncertainties, common errors and the questions they are most suited to answer. The extremes of such approaches differ clearly in many aspects, such as model building approaches, parameter estimation strategies and transferability. However, they also share strengths and weaknesses. We show that claims of one approach being intrinsically superior to the other are misguided and that they ignore the processcorrelation continuum as well as the domains of questions that each approach is addressing. Nonetheless, the application of process-based approaches to species distribution modelling lags far behind more correlative (process-implicit) methods and more research is required to explore their potential benefits. Critical issues for the employment of species distribution modelling approaches are given, together with a guideline for appropriate usage. We close with challenges for future development of process-explicit species distribution models and how they may complement current approaches to study species distributions.},
  language  = {en}
}
@misc{SchurrPagelSarmentoetal.2012,
  author    = {Schurr, Frank Martin and Pagel, J{\"o}rn and Sarmento, Juliano Sarmento and Groeneveld, Juergen and Bykova, Olga and O'Hara, Robert B. and Hartig, Florian and Kissling, W. Daniel and Linder, H. Peter and Midgley, Guy F. and Schr{\"o}der-Esselbach, Boris and Singer, Alexander and Zimmermann, Niklaus E.},
  title     = {How to understand species' niches and range dynamics: a demographic research agenda for biogeography},
  series = {Journal of biogeography},
  volume    = {39},
  journal   = {Journal of biogeography},
  number    = {12},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {0305-0270},
  doi       = {10.1111/j.1365-2699.2012.02737.x},
  pages     = {2146 -- 2162},
  year      = {2012},
  abstract  = {Range dynamics causes mismatches between a species geographical distribution and the set of suitable environments in which population growth is positive (the Hutchinsonian niche). This is because sourcesink population dynamics cause species to occupy unsuitable environments, and because environmental change creates non-equilibrium situations in which species may be absent from suitable environments (due to migration limitation) or present in unsuitable environments that were previously suitable (due to time-delayed extinction). Because correlative species distribution models do not account for these processes, they are likely to produce biased niche estimates and biased forecasts of future range dynamics. Recently developed dynamic range models (DRMs) overcome this problem: they statistically estimate both range dynamics and the underlying environmental response of demographic rates from species distribution data. This process-based statistical approach qualitatively advances biogeographical analyses. Yet, the application of DRMs to a broad range of species and study systems requires substantial research efforts in statistical modelling, empirical data collection and ecological theory. Here we review current and potential contributions of these fields to a demographic understanding of niches and range dynamics. Our review serves to formulate a demographic research agenda that entails: (1) advances in incorporating process-based models of demographic responses and range dynamics into a statistical framework, (2) systematic collection of data on temporal changes in distribution and abundance and on the response of demographic rates to environmental variation, and (3) improved theoretical understanding of the scaling of demographic rates and the dynamics of spatially coupled populations. This demographic research agenda is challenging but necessary for improved comprehension and quantification of niches and range dynamics. It also forms the basis for understanding how niches and range dynamics are shaped by evolutionary dynamics and biotic interactions. Ultimately, the demographic research agenda should lead to deeper integration of biogeography with empirical and theoretical ecology.},
  language  = {en}
}
@article{MarionMcInernyPageletal.2012,
  author    = {Marion, Glenn and McInerny, Greg J. and Pagel, J{\"o}rn and Catterall, Stephen and Cook, Alex R. and Hartig, Florian and O\&rsquo, and Hara, Robert B.},
  title     = {Parameter and uncertainty estimation for process-oriented population and distribution models: data, statistics and the niche},
  series = {JOURNAL OF BIOGEOGRAPHY},
  volume    = {39},
  journal   = {JOURNAL OF BIOGEOGRAPHY},
  number    = {12},
  publisher = {WILEY-BLACKWELL},
  address   = {HOBOKEN},
  issn      = {0305-0270},
  doi       = {10.1111/j.1365-2699.2012.02772.x},
  pages     = {2225 -- 2239},
  year      = {2012},
  abstract  = {The spatial distribution of a species is determined by dynamic processes such as reproduction, mortality and dispersal. Conventional static species distribution models (SDMs) do not incorporate these processes explicitly. This limits their applicability, particularly for non-equilibrium situations such as invasions or climate change. In this paper we show how dynamic SDMs can be formulated and fitted to data within a Bayesian framework. Our focus is on discrete state-space Markov process models which provide a flexible framework to account for stochasticity in key demographic processes, including dispersal, growth and competition. We show how to construct likelihood functions for such models (both discrete and continuous time versions) and how these can be combined with suitable observation models to conduct Bayesian parameter inference using computational techniques such as Markov chain Monte Carlo. We illustrate the current state-of-the-art with three contrasting examples using both simulated and empirical data. The use of simulated data allows the robustness of the methods to be tested with respect to deficiencies in both data and model. These examples show how mechanistic understanding of the processes that determine distribution and abundance can be combined with different sources of information at a range of spatial and temporal scales. Application of such techniques will enable more reliable inference and projections, e.g. under future climate change scenarios than is possible with purely correlative approaches. Conversely, confronting such process-oriented niche models with abundance and distribution data will test current understanding and may ultimately feedback to improve underlying ecological theory.},
  language  = {en}
}