@phdthesis{LozadaGobilard2019,
  author    = {Lozada Gobilard, Sissi Donna},
  title     = {From genes to communities: Assessing plant diversity and connectivity in kettle holes as metaecosystems in agricultural landscapes},
  doi       = {10.25932/publishup-43768},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437684},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xiii, 147},
  year      = {2019},
  abstract  = {Species assembly from a regional pool into local metacommunities and how they colonize and coexist over time and space is essential to understand how communities response to their environment including abiotic and biotic factors. In highly disturbed landscapes, connectivity of isolated habitat patches is essential to maintain biodiversity and the entire ecosystem functioning. In northeast Germany, a high density of the small water bodies called kettle holes, are good systems to study metacommunities due to their condition as "aquatic islands" suitable for hygrophilous species that are surrounded by in unsuitable matrix of crop fields. The main objective of this thesis was to infer the main ecological processes shaping plant communities and their response to the environment, from biodiversity patterns and key life-history traits involved in connectivity using ecological and genetic approaches; and to provide first insights of the role of kettle holes harboring wild-bee species as important mobile linkers connecting plant communities in this insular system. t a community level, I compared plant diversity patterns and trait composition in ephemeral vs. permanent kettle holes). My results showed that types of kettle holes act as environmental filers shaping plant diversity, community-composition and trait-distribution, suggesting species sorting and niche processes in both types of kettle holes. At a population level, I further analyzed the role of dispersal and reproductive strategies of four selected species occurring in permanent kettle holes. Using microsatellites, I found that breeding system (degree of clonality), is the main factor shaping genetic diversity and genetic divergence. Although, higher gene flow and lower genetic differentiation among populations in wind vs. insect pollinated species was also found, suggesting that dispersal mechanisms played a role related to gene flow and connectivity. For most flowering plants, pollinators play an important role connecting communities. Therefore, as a first insight of the potential mobile linkers of these plant communities, I investigated the diversity wild-bees occurring in these kettle holes. My main results showed that local habitat quality (flower resources) had a positive effect on bee diversity, while habitat heterogeneity (number of natural landscape elements surrounding kettle holes 100-300m), was negatively correlated. This thesis covers from genetic flow at individual and population level to plant community assembly. My results showed how patterns of biodiversity, dispersal and reproduction strategies in plant population and communities can be used to infer ecological processes. In addition, I showed the importance of life-history traits and the relationship between species and their abiotic and biotic interactions. Furthermore, I included a different level of mobile linkers (pollinators) for a better understanding of another level of the system. This integration is essential to understand how communities respond to their surrounding environment and how disturbances such as agriculture, land-use and climate change might affect them. I highlight the need to integrate many scientific areas covering from genes to ecosystems at different spatiotemporal scales for a better understanding, management and conservation of our ecosystems.},
  language  = {en}
}
@article{MalchowBocediPalmeretal.2021,
  author    = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris},
  title     = {RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes},
  series = {Ecography},
  volume    = {44},
  journal   = {Ecography},
  number    = {10},
  publisher = {John Wiley \& Sons, Inc.},
  address   = {New Jersey},
  issn      = {1600-0587},
  pages     = {10},
  year      = {2021},
  abstract  = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.},
  language  = {en}
}
@misc{MalchowBocediPalmeretal.2021,
  author    = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris},
  title     = {RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {10},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-52397},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523979},
  pages     = {12},
  year      = {2021},
  abstract  = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.},
  language  = {en}
}
@article{MalchowBocediPalmeretal.2021,
  author    = {Malchow, Anne-Kathleen and Bocedi, Greta and Palmer, Stephen C. F. and Travis, Justin M. J. and Zurell, Damaris},
  title     = {RangeShiftR},
  series = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos},
  volume    = {44},
  journal   = {Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos},
  number    = {10},
  publisher = {Wiley-Blackwell},
  address   = {Oxford [u.a.]},
  issn      = {1600-0587},
  doi       = {10.1111/ecog.05689},
  pages     = {1443 -- 1452},
  year      = {2021},
  abstract  = {Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.},
  language  = {en}
}