TY - GEN A1 - Heinken, Thilo A1 - Winkler, Eckart T1 - Non-random dispersal by ants : long-term field data versus model predictions of population spread of a forest herb N2 - Myrmecochory, i.e. dispersal of seeds by ants towards and around their nests, plays an important role in temperate forests. Yet hardly any study has examined plant population spread over several years and the underlying joint contribution of a hierarchy of dispersal modes and plant demography. We used a seed-sowing approach with three replicates to examine colonization patterns of Melampyrum pratense, an annual myrmecochorous herb, in a mixed Scots pine forest in northeastern Germany. Using a spatially explicit individualbased (SEIB) model population patterns over 4 years were explained by short-distance transport of seeds by small ant species with high nest densities, resulting in random spread. However, plant distributions in the field after another 4 years were clearly deviating from model predictions. Mean annual spread rate increased from 0.9 m to 5.1 m per year, with a clear inhomogeneous component. Obviously, after a lag-phase of several years, non-random seed dispersal by large red wood ants (Formica rufa) was determining the species’ spread, thus resulting in stratified dispersal due to interactions with different-sized ant species. Hypotheses on stratified dispersal, on dispersal lag, and on non-random dispersal were verified using an extended SEIB model, by comparison of model outputs with field patterns (individual numbers, population areas, and maximum distances). Dispersal towards red wood ant nests together with seed loss during transport and redistribution around nests were essential features of the model extension. The observed lag-phase in the initiation of non-random, medium-distance transport was probably due to a change of ant behaviour towards a new food source of increasing importance, being a meaningful example for a lag-phase in local plant species invasion. The results demonstrate that field studies should check model predictions wherever possible. Future research will show whether or not the M. pratense–ant system is representative for migration patterns of similar animal dispersal systems after having crossed range edges by long-distance dispersal events. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 151 KW - Melampyrum pratense KW - population dynamics KW - seed dispersal KW - non-random dispersal KW - plant-animal interaction Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-46482 ER - TY - JOUR A1 - Itonaga, Naomi A1 - Köppen, Ulrich A1 - Plath, Martin A1 - Wallschläger, Hans-Dieter T1 - Declines in breeding site fidelity in an increasing population of White Storks Ciconia ciconia JF - IBIS N2 - Following a steep decline, White Stork Ciconia ciconia populations in Germany are currently increasing, allowing us to examine potential density-dependent effects on breeding dispersal. Our data suggest that the proportion of breeding dispersers has increased over time, indicating a density-dependent component in nest-site fidelity that may be linked to increased competition. KW - age-dependent dispersal KW - density-dependent dispersal KW - population dynamics Y1 - 2011 SN - 0019-1019 VL - 153 IS - 3 SP - 636 EP - 639 PB - Wiley-Blackwell CY - Malden ER - TY - THES A1 - Patra, Pintu T1 - Population dynamics of bacterial persistence T1 - Populationsdynamik von Bakterielle Persistenz N2 - The life of microorganisms is characterized by two main tasks, rapid growth under conditions permitting growth and survival under stressful conditions. The environments, in which microorganisms dwell, vary in space and time. The microorganisms innovate diverse strategies to readily adapt to the regularly fluctuating environments. Phenotypic heterogeneity is one such strategy, where an isogenic population splits into subpopulations that respond differently under identical environments. Bacterial persistence is a prime example of such phenotypic heterogeneity, whereby a population survives under an antibiotic attack, by keeping a fraction of population in a drug tolerant state, the persister state. Specifically, persister cells grow more slowly than normal cells under growth conditions, but survive longer under stress conditions such as the antibiotic administrations. Bacterial persistence is identified experimentally by examining the population survival upon an antibiotic treatment and the population resuscitation in a growth medium. The underlying population dynamics is explained with a two state model for reversible phenotype switching in a cell within the population. We study this existing model with a new theoretical approach and present analytical expressions for the time scale observed in population growth and resuscitation, that can be easily used to extract underlying model parameters of bacterial persistence. In addition, we recapitulate previously known results on the evolution of such structured population under periodically fluctuating environment using our simple approximation method. Using our analysis, we determine model parameters for Staphylococcus aureus population under several antibiotics and interpret the outcome of cross-drug treatment. Next, we consider the expansion of a population exhibiting phenotype switching in a spatially structured environment consisting of two growth permitting patches separated by an antibiotic patch. The dynamic interplay of growth, death and migration of cells in different patches leads to distinct regimes in population propagation speed as a function of migration rate. We map out the region in parameter space of phenotype switching and migration rate to observe the condition under which persistence is beneficial. Furthermore, we present an extended model that allows mutation from the two phenotypic states to a resistant state. We find that the presence of persister cells may enhance the probability of resistant mutation in a population. Using this model, we explain the experimental results showing the emergence of antibiotic resistance in a Staphylococcus aureus population upon tobramycin treatment. In summary, we identify several roles of bacterial persistence, such as help in spatial expansion, development of multidrug tolerance and emergence of antibiotic resistance. Our study provides a theoretical perspective on the dynamics of bacterial persistence in different environmental conditions. These results can be utilized to design further experiments, and to develop novel strategies to eradicate persistent infections. N2 - Das Leben von Mikroorganismen kann in zwei charakteristische Phasen unterteilt werde, schnelles Wachstum unter Wachstumsbedingungen und Überleben unter schwierigen Bedingungen. Die Bedingungen, in denen sich die Mikroorganismen aufhalten, verändern sich in Raum und Zeit. Um sich schnell an die ständig wechselnden Bedingungen anzupassen entwickeln die Mikroorganismen diverse Strategien. Phänotypische Heterogenität ist eine solche Strategie, bei der sich eine isogene Popolation in Untergruppen aufteilt, die unter identischen Bedingungen verschieden reagieren. Bakterielle Persistenz ist ein Paradebeispiel einer solchen phänotypischen Heterogenität. Hierbei überlebt eine Popolation die Behandlung mit einem Antibiotikum, indem sie einen Teil der Bevölkerung in einem, dem Antibiotikum gegenüber tolerant Zustand lässt, der sogenannte "persister Zustand". Persister-Zellen wachsen unter Wachstumsbedingungen langsamer als normale Zellen, jedoch überleben sie länger in Stress-Bedingungen, wie bei Antibiotikaapplikation. Bakterielle Persistenz wird experimentell erkannt indem man überprüft ob die Population eine Behandlung mit Antibiotika überlebt und sich in einem Wachstumsmedium reaktiviert. Die zugrunde liegende Popolationsdynamik kann mit einem Zwei-Zustands-Modell für reversibles Wechseln des Phänotyps einer Zelle in der Bevölkerung erklärt werden. Wir untersuchen das bestehende Modell mit einem neuen theoretischen Ansatz und präsentieren analytische Ausdrücke für die Zeitskalen die für das Bevölkerungswachstums und die Reaktivierung beobachtet werden. Diese können dann einfach benutzt werden um die Parameter des zugrunde liegenden bakteriellen Persistenz-Modells zu bestimmen. Darüber hinaus rekapitulieren wir bisher bekannten Ergebnisse über die Entwicklung solch strukturierter Bevölkerungen unter periodisch schwankenden Bedingungen mithilfe unseres einfachen Näherungsverfahrens. Mit unserer Analysemethode bestimmen wir Modellparameter für eine Staphylococcus aureus-Popolation unter dem Einfluss mehrerer Antibiotika und interpretieren die Ergebnisse der Behandlung mit zwei Antibiotika in Folge. Als nächstes betrachten wir die Ausbreitung einer Popolation mit Phänotypen-Wechsel in einer räumlich strukturierten Umgebung. Diese besteht aus zwei Bereichen, in denen Wachstum möglich ist und einem Bereich mit Antibiotikum der die beiden trennt. Das dynamische Zusammenspiel von Wachstum, Tod und Migration von Zellen in den verschiedenen Bereichen führt zu unterschiedlichen Regimen der Populationsausbreitungsgeschwindigkeit als Funktion der Migrationsrate. Wir bestimmen die Region im Parameterraum der Phänotyp Schalt-und Migrationsraten, in der die Bedingungen Persistenz begünstigen. Darüber hinaus präsentieren wir ein erweitertes Modell, das Mutation aus den beiden phänotypischen Zuständen zu einem resistenten Zustand erlaubt. Wir stellen fest, dass die Anwesenheit persistenter Zellen die Wahrscheinlichkeit von resistenten Mutationen in einer Population erhöht. Mit diesem Modell, erklären wir die experimentell beobachtete Entstehung von Antibiotika- Resistenz in einer Staphylococcus aureus Popolation infolge einer Tobramycin Behandlung. Wir finden also verschiedene Funktionen bakterieller Persistenz. Sie unterstützt die räumliche Ausbreitung der Bakterien, die Entwicklung von Toleranz gegenüber mehreren Medikamenten und Entwicklung von Resistenz gegenüber Antibiotika. Unsere Beschreibung liefert eine theoretische Betrachtungsweise der Dynamik bakterieller Persistenz bei verschiedenen Bedingungen. Die Resultate könnten als Grundlage neuer Experimente und der Entwicklung neuer Strategien zur Ausmerzung persistenter Infekte dienen. KW - Populationsdynamik KW - Antibiotikaresistenz KW - Antibiotika-Toleranz KW - Phänotypische Heterogenität KW - population dynamics KW - drug tolerance KW - antibiotic resistance KW - phenotypic heterogeneity Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-69253 ER - TY - JOUR A1 - Sibly, Richard M. A1 - Grimm, Volker A1 - Martin, Benjamin T. A1 - Johnston, Alice S. A. A1 - Kulakowska, Katarzyna A1 - Topping, Christopher J. A1 - Calow, Peter A1 - Nabe-Nielsen, Jacob A1 - Thorbek, Pernille A1 - DeAngelis, Donald L. T1 - Representing the acquisition and use of energy by individuals in agent-based models of animal populations JF - Methods in ecology and evolution : an official journal of the British Ecological Society N2 - Agent-based models (ABMs) are widely used to predict how populations respond to changing environments. As the availability of food varies in space and time, individuals should have their own energy budgets, but there is no consensus as to how these should be modelled. Here, we use knowledge of physiological ecology to identify major issues confronting the modeller and to make recommendations about how energy budgets for use in ABMs should be constructed. Our proposal is that modelled animals forage as necessary to supply their energy needs for maintenance, growth and reproduction. If there is sufficient energy intake, an animal allocates the energy obtained in the order: maintenance, growth, reproduction, energy storage, until its energy stores reach an optimal level. If there is a shortfall, the priorities for maintenance and growth/reproduction remain the same until reserves fall to a critical threshold below which all are allocated to maintenance. Rates of ingestion and allocation depend on body mass and temperature. We make suggestions for how each of these processes should be modelled mathematically. Mortality rates vary with body mass and temperature according to known relationships, and these can be used to obtain estimates of background mortality rate. If parameter values cannot be obtained directly, then values may provisionally be obtained by parameter borrowing, pattern-oriented modelling, artificial evolution or from allometric equations. The development of ABMs incorporating individual energy budgets is essential for realistic modelling of populations affected by food availability. Such ABMs are already being used to guide conservation planning of nature reserves and shell fisheries, to assess environmental impacts of building proposals including wind farms and highways and to assess the effects on nontarget organisms of chemicals for the control of agricultural pests. KW - bioenergetics KW - energy budget KW - individual-based models KW - population dynamics Y1 - 2013 U6 - https://doi.org/10.1111/2041-210x.12002 SN - 2041-210X VL - 4 IS - 2 SP - 151 EP - 161 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Massie, Thomas Michael A1 - Ryabov, Alexei A1 - Blasius, Bernd A1 - Weithoff, Guntram A1 - Gaedke, Ursula T1 - Complex transient dynamics of stage-structured populations in response to environmental changes JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - Stage structures of populations can have a profound influence on their dynamics. However, not much is known about the transient dynamics that follow a disturbance in such systems. Here we combined chemostat experiments with dynamical modeling to study the response of the phytoplankton species Chlorella vulgaris to press perturbations. From an initially stable steady state, we altered either the concentration or dilution rate of a growth-limiting resource. This disturbance induced a complex transient response-characterized by the possible onset of oscillations-before population numbers relaxed to a new steady state. Thus, cell numbers could initially change in the opposite direction of the long-term change. We present quantitative indexes to characterize the transients and to show that the dynamic response is dependent on the degree of synchronization among life stages, which itself depends on the state of the population before perturbation. That is, we show how identical future steady states can be approached via different transients depending on the initial population structure. Our experimental results are supported by a size-structured model that accounts for interplay between cell-cycle and population-level processes and that includes resource-dependent variability in cell size. Our results should be relevant to other populations with a stage structure including organisms of higher order. KW - chemostat experiments KW - Chlorella vulgaris KW - environmental changes KW - population dynamics KW - stage structure KW - transient dynamics Y1 - 2013 U6 - https://doi.org/10.1086/670590 SN - 0003-0147 SN - 1537-5323 VL - 182 IS - 1 SP - 103 EP - 119 PB - Univ. of Chicago Press CY - Chicago ER - TY - THES A1 - Martin, Benjamin T1 - Linking individual-based models and dynamic energy budget theory : lessons for ecology and ecotoxicology T1 - Individuenbasierte Modelle mit dynamischen Energiehaushalten bereichern die Ökologie und Ökotoxikologie N2 - In the context of ecological risk assessment of chemicals, individual-based population models hold great potential to increase the ecological realism of current regulatory risk assessment procedures. However, developing and parameterizing such models is time-consuming and often ad hoc. Using standardized, tested submodels of individual organisms would make individual-based modelling more efficient and coherent. In this thesis, I explored whether Dynamic Energy Budget (DEB) theory is suitable for being used as a standard submodel in individual-based models, both for ecological risk assessment and theoretical population ecology. First, I developed a generic implementation of DEB theory in an individual-based modeling (IBM) context: DEB-IBM. Using the DEB-IBM framework I tested the ability of the DEB theory to predict population-level dynamics from the properties of individuals. We used Daphnia magna as a model species, where data at the individual level was available to parameterize the model, and population-level predictions were compared against independent data from controlled population experiments. We found that DEB theory successfully predicted population growth rates and peak densities of experimental Daphnia populations in multiple experimental settings, but failed to capture the decline phase, when the available food per Daphnia was low. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small- and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detecting gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology. In addition to theoretical explorations, we tested the potential of DEB theory combined with IBMs to extrapolate effects of chemical stress from the individual to population level. For this we used information at the individual level on the effect of 3,4-dichloroanailine on Daphnia. The individual data suggested direct effects on reproduction but no significant effects on growth. Assuming such direct effects on reproduction, the model was able to accurately predict the population response to increasing concentrations of 3,4-dichloroaniline. We conclude that DEB theory combined with IBMs holds great potential for standardized ecological risk assessment based on ecological models. N2 - Für die ökologische Risikobewertung von Chemikalien sind individuenbasierte Populationsmodelle ein vielversprechendes Werkzeug um heutige Bewertungen ökologisch realistischer zu gestalten. Allerdings ist die Entwicklung und Parametrisierung derartiger Modelle zeitaufwendig und oft wenig systematisch. Standardisierte, geprüfte Untermodelle, die Einzelorganismen beschreiben, würden die individuenbasierte Modellierung effizienter und kohärenter machen. In meiner Dissertation habe ich daher untersucht, inwieweit sich die Dynamic Energy Budget-Theorie (DEB) als Standardmodell innerhalb individuenbasierter Populationsmodelle eignet, und zwar sowohl für die ökologische Risikobewertung als auch für die theoretische Populationsökologie. Zunächst habe ich eine generische Implementierung der DEB-Theorie im Rahmen individuenbasierter Modellen (IBM) erstellt: DEB-IBM. Dieses Werkzeug nutzend habe ich dann untersucht, ob es mit Hilfe der DEB-Theorie gelingt, ausgehend von den Eigenschaften und Aktivitäten einzelner Individuen, Populationsdynamik vorherzusagen. Wir nutzten dabei Daphnia magna als Modellart, für die Daten auf der Individuenebene verfügbar waren, um das Modell zu parametrisieren, sowie Populationsdaten, mit denen Modellvorhersagen verglichen werden konnten. DEB-Theorie war in der Lage, beobachtete Populationswachstumsraten sowie die maximalen Abundanzen korrekt vorherzusagen, und zwar für verschiedene Umweltbedingungen. Für Phasen des Rückgangs der Population allerdings, wenn die für die Daphnien verfügbare Nahrungsmenge gering war, kam es zu Abweichungen. Es waren deshalb zusätzliche Annahmen über nahrungsabhängige Sterblichkeit von juvenilen Daphnien erforderlich, um die gesamte Populationsdynamik korrekt vorherzusagen. Das resultierende Modell konnte dann, ohne weitere Kalibrierungen, den für Daphnien charakteristischen Wechsel zwischen Populationszyklen mit großen und kleinen Amplituden richtig vorhersagen. Wir folgern daraus, daß Ebenen übergreifende Tests dabei helfen, Lücken in aktuellen Theorien über Einzelorganismen aufzudecken Dies trägt zur Theorieentwicklung bei und liefert Grundlagen für individuenbasierte Modellierung und Ökologie. Über diese Grundlagenfragen hinaus haben wir überprüft, ob DEB-Theorie in Kombination mit IBMs es ermöglicht, den Effekt von chemischem Streß auf Individuen auf die Populationsebene zu extrapolieren. Wir nutzten Daten über die Auswirkungen von 3,4 Dichloroanalin auf einzelne Daphnien, die zeigten daß im Wesentlichen die Reproduktion, nicht aber das Wachstum beeinträchtigt ist. Mit entsprechenden Annahmen konnte unser Modell den Effekt auf Populationsebene, für den unabhängige Daten vorlagen, korrekt vorhersagen. DEB-Theorie in Kombination mit individuenbasierter Modellierung birgt somit großes Potential für einen standardisierten modellbasierten Ansatz in der ökologischen Risikobewertung von Chemikalien. KW - Ökologie KW - Ökotoxikologie KW - Populationsdynamik KW - Ecology KW - Ecotoxicology KW - population dynamics Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-67001 ER - TY - JOUR A1 - Martin, Benjamin T. A1 - Jager, Tjalling A1 - Nisbet, Roger M. A1 - Preuss, Thomas G. A1 - Grimm, Volker T1 - Predicting population dynamics from the properties of individuals - a cross-level test of dynamic energy budget theory JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - Individual-based models (IBMs) are increasingly used to link the dynamics of individuals to higher levels of biological organization. Still, many IBMs are data hungry, species specific, and time-consuming to develop and analyze. Many of these issues would be resolved by using general theories of individual dynamics as the basis for IBMs. While such theories have frequently been examined at the individual level, few cross-level tests exist that also try to predict population dynamics. Here we performed a cross-level test of dynamic energy budget (DEB) theory by parameterizing an individual-based model using individual-level data of the water flea, Daphnia magna, and comparing the emerging population dynamics to independent data from population experiments. We found that DEB theory successfully predicted population growth rates and peak densities but failed to capture the decline phase. Further assumptions on food-dependent mortality of juveniles were needed to capture the population dynamics after the initial population peak. The resulting model then predicted, without further calibration, characteristic switches between small-and large-amplitude cycles, which have been observed for Daphnia. We conclude that cross-level tests help detect gaps in current individual-level theories and ultimately will lead to theory development and the establishment of a generic basis for individual-based models and ecology. KW - population dynamics KW - dynamic energy budget theory KW - bioenergetics KW - individual-based model Y1 - 2013 U6 - https://doi.org/10.1086/669904 SN - 0003-0147 VL - 181 IS - 4 SP - 506 EP - 519 PB - Univ. of Chicago Press CY - Chicago ER - TY - JOUR A1 - Bauer, Barbara A1 - Vos, Matthijs A1 - Klauschies, Toni A1 - Gaedke, Ursula T1 - Diversity, functional similarity, and top-down control drive synchronization and the reliability of ecosystem function JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences N2 - The concept that diversity promotes reliability of ecosystem function depends on the pattern that community-level biomass shows lower temporal variability than species-level biomasses. However, this pattern is not universal, as it relies on compensatory or independent species dynamics. When in contrast within--trophic level synchronization occurs, variability of community biomass will approach population-level variability. Current knowledge fails to integrate how species richness, functional distance between species, and the relative importance of predation and competition combine to drive synchronization at different trophic levels. Here we clarify these mechanisms. Intense competition promotes compensatory dynamics in prey, but predators may at the same time increasingly synchronize, under increasing species richness and functional similarity. In contrast, predators and prey both show perfect synchronization under strong top-down control, which is promoted by a combination of low functional distance and high net growth potential of predators. Under such conditions, community-level biomass variability peaks, with major negative consequences for reliability of ecosystem function. KW - biodiversity KW - ecosystem services KW - population dynamics KW - predator-prey system KW - species richness KW - synchrony Y1 - 2014 U6 - https://doi.org/10.1086/674906 SN - 0003-0147 SN - 1537-5323 VL - 183 IS - 3 SP - 394 EP - 409 PB - Univ. of Chicago Press CY - Chicago ER - TY - JOUR A1 - Martin, Benjamin A1 - Jager, Tjalling A1 - Nisbet, Roger M. A1 - Preuss, Thomas G. A1 - Grimm, Volker T1 - Limitations of extrapolating toxic effects on reproduction to the population level JF - Ecological applications : a publication of the Ecological Society of America N2 - For the ecological risk assessment of toxic chemicals, standardized tests on individuals are often used as proxies for population-level effects. Here, we address the utility of one commonly used metric, reproductive output, as a proxy for population-level effects. Because reproduction integrates the outcome of many interacting processes (e.g., feeding, growth, allocation of energy to reproduction), the observed toxic effects in a reproduction test could be due to stress on one of many processes. Although this makes reproduction a robust endpoint for detecting stress, it may mask important population-level consequences if the different physiological processes stress affects are associated with different feedback mechanisms at the population level. We therefore evaluated how an observed reduction in reproduction found in a standard reproduction test translates to effects at the population level if it is caused by hypothetical toxicants affecting different physiological processes (physiological modes of action; PMoA). For this we used two consumer-resource models: the Yodzis-Innes (YI) model, which is mathematically tractable, but requires strong assumptions of energetic equivalence among individuals as they progress through ontogeny, and an individual-based implementation of dynamic energy budget theory (DEB-IBM), which relaxes these assumptions at the expense of tractability. We identified two important feedback mechanisms controlling the link between individual- and population-level stress in the YI model. These mechanisms turned out to also be important for interpreting some of the individual-based model results; for two PMoAs, they determined the population response to stress in both models. In contrast, others stress types involved more complex feedbacks, because they asymmetrically stressed the production efficiency of reproduction and somatic growth. The feedbacks associated with different PMoAs drastically altered the link between individual- and population-level effects. For example, hypothetical stressors with different PMoAs that had equal effects on reproduction had effects ranging from a negligible decline in biomass to population extinction. Thus, reproduction tests alone are of little use for extrapolating toxicity to the population level, but we showed that the ecological relevance of standard tests could easily be improved if growth is measured along with reproduction. KW - Daphnia KW - dynamic energy budget KW - ecological risk assessment KW - ecotoxicology KW - ontogenetic symmetry KW - physiological mode of action KW - PMoA KW - population dynamics KW - reproduction test KW - Yodzis-Innes Y1 - 2014 U6 - https://doi.org/10.1890/14-0656.1 SN - 1051-0761 SN - 1939-5582 VL - 24 IS - 8 SP - 1972 EP - 1983 PB - Wiley CY - Washington ER - TY - JOUR A1 - Imholt, Christian A1 - Reil, Daniela A1 - Eccard, Jana A1 - Jacob, Daniela A1 - Hempelmann, Nils A1 - Jacob, Jens T1 - Quantifying the past and future impact of climate on outbreak patterns of bank voles (Myodes glareolus) JF - Pest management science N2 - BACKGROUND Central European outbreak populations of the bank vole (Myodes glareolus Schreber) are known to cause damage in forestry and to transmit the most common type of Hantavirus (Puumala virus, PUUV) to humans. A sound estimation of potential effects of future climate scenarios on population dynamics is a prerequisite for long-term management strategies. Historic abundance time series were used to identify the key weather conditions associated with bank vole abundance, and were extrapolated to future climate scenarios to derive potential long-term changes in bank vole abundance dynamics. RESULTS Classification and regression tree analysis revealed the most relevant weather parameters associated with high and low bank vole abundances. Summer temperatures 2 years prior to trapping had the highest impact on abundance fluctuation. Extrapolation of the identified parameters to future climate conditions revealed an increase in years with high vole abundance. CONCLUSION Key weather patterns associated with vole abundance reflect the importance of superabundant food supply through masting to the occurrence of bank vole outbreaks. Owing to changing climate, these outbreaks are predicted potentially to increase in frequency 3-4-fold by the end of this century. This may negatively affect damage patterns in forestry and the risk of human PUUV infection in the long term. (c) 2014 Society of Chemical Industry KW - climate change KW - population dynamics KW - bank vole KW - regression tree KW - outbreak Y1 - 2015 U6 - https://doi.org/10.1002/ps.3838 SN - 1526-498X SN - 1526-4998 VL - 71 IS - 2 SP - 166 EP - 172 PB - Wiley-Blackwell CY - Hoboken ER - TY - GEN A1 - Reil, Daniela A1 - Rosenfeld, Ulrike M. A1 - Imholt, Christian A1 - Schmidt, Sabrina A1 - Ulrich, Rainer G. A1 - Eccard, Jana A1 - Jacob, Jens T1 - Puumala hantavirus infections in bank vole populations BT - host and virus dynamics in Central Europe T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background In Europe, bank voles (Myodes glareolus) are widely distributed and can transmit Puumala virus (PUUV) to humans, which causes a mild to moderate form of haemorrhagic fever with renal syndrome, called nephropathia epidemica. Uncovering the link between host and virus dynamics can help to prevent human PUUV infections in the future. Bank voles were live trapped three times a year in 2010–2013 in three woodland plots in each of four regions in Germany. Bank vole population density was estimated and blood samples collected to detect PUUV specific antibodies. Results We demonstrated that fluctuation of PUUV seroprevalence is dependent not only on multi-annual but also on seasonal dynamics of rodent host abundance. Moreover, PUUV infection might affect host fitness, because seropositive individuals survived better from spring to summer than uninfected bank voles. Individual space use was independent of PUUV infections. Conclusions Our study provides robust estimations of relevant patterns and processes of the dynamics of PUUV and its rodent host in Central Europe, which are highly important for the future development of predictive models for human hantavirus infection risk. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 957 KW - Myodes glareolus KW - population dynamics KW - Puumala virus seroprevalence KW - space use KW - survival Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431232 SN - 1866-8372 IS - 957 ER - TY - JOUR A1 - Reil, Daniela A1 - Binder, Florian A1 - Freise, Jona A1 - Imholt, Christian A1 - Beyrers, Konrad A1 - Jacob, Jens A1 - Krüger, Detlev H. A1 - Hofmann, Jörg A1 - Dreesman, Johannes A1 - Ulrich, Rainer Günter T1 - Hantaviren in Deutschland BT - Aktuelle Erkenntnisse zu Erreger, Reservoir, Verbreitung und Prognosemodellen JF - Berliner und Münchener tierärztliche Wochenschrift N2 - Hantaviruses are small mammal-associated pathogens that are found in rodents but also in shrews, moles and bats. Aim of this manuscript is to give a current overview of the epidemiology and ecology of hantaviruses in Germany and to discuss respective models for the prediction of virus outbreaks. In Germany the majority of human disease cases are caused by the Puumala virus (PUUV), transmitted by the bank vole (Myodes glareolus). PUUV is associated with the Western evolutionary lineage of the bank vole and is not present in the eastern and northern parts of Germany. A second human pathogenic hantavirus is the Dobrava-Belgrade virus (DOBV), genotype Kurkino; its reservoir host, the striped field mouse (Apodemus agrarius), is mostly occurring in the eastern part of Germany. A PUUV-related hantavirus is the rarely pathogenic Tula virus (TULV), that is associated with the common vole (Microtus arvalis). In addition, Seewis virus, Asikkala virus, and Bruges virus are shrew- and mole-associated hantaviruses with still unknown pathogenicity in humans. Human disease cases are associated with the different hantaviruses according to their regional distribution. The viruses can cause mild to severe but also subclinical courses of the respective disease. The number of human PUUV disease cases in 2007, 2010, 2012, 2015 and 2017 correlates with the occurrence of high levels of seed production of beech trees ("beech mast") in the preceding year. Models based on weather parameters for the prediction of PUUV disease clusters as developed in recent years need further validation and optimisation. in addition to the abundance of infected reservoir rodents, the exposure behaviour of humans affects the risk of human infection. The application of robust forecast models can assist the public health service to develop and communicate spatially and temporally targeted information. Thus, further recommendations to mitigate infection risk for the public may be provided. N2 - Hantaviren sind Kleinsäuger-assoziierte Krankheitserreger, die vor allem in Nagetieren, aber auch in Spitzmäusen, Maulwürfen und Fledermäusen vorkommen. Ziel dieser Arbeit ist es, einen aktuellen Überblick zur Epidemiologie und Ökologie der Hantaviren in Deutschland zu geben und Modelle zur Vorhersage von Virusausbrüchen zu diskutieren. In Deutschland werden die meisten humanen Erkrankungsfälle beim Menschen durch das von der Rötelmaus (Myodes glareolus) übertragene Puumalavirus (PUUV) verursacht. PUUV ist mit der westlichen evolutionären Linie der Rötelmaus assoziiert und fehlt im östlichen und nördlichen Teil Deutschlands. Ein zweites humanpathogenes Hantavirus ist das Dobrava-Belgrad-Virus (DOBV), Genotyp Kurkino, dessen Reservoir die vor allem im östlichen Teil Deutschlands vorkommende Brandmaus (Apodemus agrarius) ist. Ein PUUV-verwandtes Hantavirus ist das selten humanpathogene Tulavirus (TULV), das mit der Feldmaus (Microtus arvalis) assoziiert ist. Darüber hinaus wurden mit dem Seewis-, Asikkala- und Brugesvirus Spitzmaus- und Maulwurf-assoziierte Hantaviren mit noch unklarer Humanpathogenität gefunden. Die humanen Erkrankungen sind jeweils mit den verschiedenen Hantaviren in deren regionaler Verteilung assoziiert und können mild bis schwer, aber auch subklinisch verlaufen. Das Auftreten von Häufungen humaner, durch PUUV verursachter Erkrankungen in den Jahren 2007, 2010, 2012, 2015 und 2017 korreliert mit dem Auftreten einer starken Fruktifikation der Buche („Buchenmast“) im jeweiligen Vorjahr. Auf der Basis von Wetterparametern sind Modelle zur Vorhersage von PUUV-Erkrankungshäufungen entwickelt worden, die zukünftig validiert und optimiert werden müssen. Neben dem Ausmaß des Virusvorkommens im Reservoir wird das Risiko humaner Infektionen durch das Expositionsverhalten des Menschen beeinflusst. Durch die Anwendung von Prognosemodellen soll der öffentliche Gesundheitsdienst in die Lage versetzt werden, räumlich und zeitlich gezielte und sachgerechte Präventionsempfehlungen für die Bevölkerung abzugeben. T2 - Hantaviruses in Germany: current knowledge on pathogens, reservoirs, distribution and forecast models KW - early warning system KW - hantavirus KW - hantavirus disease KW - rodents KW - population dynamics KW - Frühwarn-System KW - Hantavirus KW - Hantavirus-Erkrankung KW - Nagetiere KW - Populationsdynamik Y1 - 2018 U6 - https://doi.org/10.2376/0005-9366-18003 SN - 0005-9366 SN - 1439-0299 VL - 131 IS - 11-12 SP - 453 EP - 464 PB - Schlütersche Verlagsgesellschaft mbH & Co. KG. CY - Hannover ER - TY - GEN A1 - Raatz, Michael A1 - van Velzen, Ellen A1 - Gaedke, Ursula T1 - Co‐adaptation impacts the robustness of predator–prey dynamics against perturbations T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Global change threatens the maintenance of ecosystem functions that are shaped by the persistence and dynamics of populations. It has been shown that the persistence of species increases if they possess larger trait adaptability. Here, we investigate whether trait adaptability also affects the robustness of population dynamics of interacting species and thereby shapes the reliability of ecosystem functions that are driven by these dynamics. We model co‐adaptation in a predator–prey system as changes to predator offense and prey defense due to evolution or phenotypic plasticity. We investigate how trait adaptation affects the robustness of population dynamics against press perturbations to environmental parameters and against pulse perturbations targeting species abundances and their trait values. Robustness of population dynamics is characterized by resilience, elasticity, and resistance. In addition to employing established measures for resilience and elasticity against pulse perturbations (extinction probability and return time), we propose the warping distance as a new measure for resistance against press perturbations, which compares the shapes and amplitudes of pre‐ and post‐perturbation population dynamics. As expected, we find that the robustness of population dynamics depends on the speed of adaptation, but in nontrivial ways. Elasticity increases with speed of adaptation as the system returns more rapidly to the pre‐perturbation state. Resilience, in turn, is enhanced by intermediate speeds of adaptation, as here trait adaptation dampens biomass oscillations. The resistance of population dynamics strongly depends on the target of the press perturbation, preventing a simple relationship with the adaptation speed. In general, we find that low robustness often coincides with high amplitudes of population dynamics. Hence, amplitudes may indicate the robustness against perturbations also in other natural systems with similar dynamics. Our findings show that besides counteracting extinctions, trait adaptation indeed strongly affects the robustness of population dynamics against press and pulse perturbations. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 809 KW - disturbance KW - evolutionary rescue KW - population dynamics KW - stability KW - trait adaptation Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-442489 SN - 1866-8372 IS - 809 ER - TY - JOUR A1 - Grimm-Seyfarth, Annegret A1 - Mihoub, Jean-Baptiste A1 - Gruber, Bernd A1 - Henle, Klaus T1 - Some like it hot BT - from individual to population responses of an arboreal arid-zone gecko to local and distant climate JF - Ecological monographs N2 - Accumulating evidence has demonstrated considerable impact of climate change on biodiversity, with terrestrial ectotherms being particularly vulnerable. While climate-induced range shifts are often addressed in the literature, little is known about the underlying ecological responses at individual and population levels. Using a 30-yr monitoring study of the long-living nocturnal gecko Gehyra variegata in arid Australia, we determined the relative contribution of climatic factors acting locally (temperature, rainfall) or distantly (La Nina induced flooding) on ecological processes ranging from traits at the individual level (body condition, body growth) to the demography at population level (survival, sexual maturity, population sizes). We also investigated whether thermoregulatory activity during both active (night) and resting (daytime) periods of the day can explain these responses. Gehyra variegata responded to local and distant climatic effects. Both high temperatures and high water availability enhanced individual and demographic parameters. Moreover, the impact of water availability was scale independent as local rainfall and La Nina induced flooding compensated each other. When water availability was low, however, extremely high temperatures delayed body growth and sexual maturity while survival of individuals and population sizes remained stable. This suggests a trade-off with traits at the individual level that may potentially buffer the consequences of adverse climatic conditions at the population level. Moreover, hot temperatures did not impact nocturnal nor diurnal behavior. Instead, only cool temperatures induced diurnal thermoregulatory behavior with individuals moving to exposed hollow branches and even outside tree hollows for sun-basking during the day. Since diurnal behavioral thermoregulation likely induced costs on fitness, this could decrease performance at both individual and population level under cool temperatures. Our findings show that water availability rather than high temperature is the limiting factor in our focal population of G.variegata. In contrast to previous studies, we stress that drier rather than warmer conditions are expected to be detrimental for nocturnal desert reptiles. Identifying the actual limiting climatic factors at different scales and their functional interactions at different ecological levels is critical to be able to predict reliably future population dynamics and support conservation planning in arid ecosystems. KW - behavioral adaptation KW - body condition KW - body growth rate KW - climate change KW - El Nino Southern Oscillation (ENSO) KW - Gehyra variegata KW - population dynamics KW - population size KW - survival KW - thermoregulation Y1 - 2018 U6 - https://doi.org/10.1002/ecm.1301 SN - 0012-9615 SN - 1557-7015 VL - 88 IS - 3 SP - 336 EP - 352 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Rosenbaum, Benjamin A1 - Raatz, Michael A1 - Weithoff, Guntram A1 - Fussmann, Gregor F. A1 - Gaedke, Ursula T1 - Estimating parameters from multiple time series of population dynamics using bayesian inference JF - Frontiers in ecology and evolution N2 - Empirical time series of interacting entities, e.g., species abundances, are highly useful to study ecological mechanisms. Mathematical models are valuable tools to further elucidate those mechanisms and underlying processes. However, obtaining an agreement between model predictions and experimental observations remains a demanding task. As models always abstract from reality one parameter often summarizes several properties. Parameter measurements are performed in additional experiments independent of the ones delivering the time series. Transferring these parameter values to different settings may result in incorrect parametrizations. On top of that, the properties of organisms and thus the respective parameter values may vary considerably. These issues limit the use of a priori model parametrizations. In this study, we present a method suited for a direct estimation of model parameters and their variability from experimental time series data. We combine numerical simulations of a continuous-time dynamical population model with Bayesian inference, using a hierarchical framework that allows for variability of individual parameters. The method is applied to a comprehensive set of time series from a laboratory predator-prey system that features both steady states and cyclic population dynamics. Our model predictions are able to reproduce both steady states and cyclic dynamics of the data. Additionally to the direct estimates of the parameter values, the Bayesian approach also provides their uncertainties. We found that fitting cyclic population dynamics, which contain more information on the process rates than steady states, yields more precise parameter estimates. We detected significant variability among parameters of different time series and identified the variation in the maximum growth rate of the prey as a source for the transition from steady states to cyclic dynamics. By lending more flexibility to the model, our approach facilitates parametrizations and shows more easily which patterns in time series can be explained also by simple models. Applying Bayesian inference and dynamical population models in conjunction may help to quantify the profound variability in organismal properties in nature. KW - Bayesian inference KW - chemostat experiments KW - ordinary differential equation KW - parameter estimation KW - population dynamics KW - predator prey KW - time series analysis KW - trait variability Y1 - 2019 U6 - https://doi.org/10.3389/fevo.2018.00234 SN - 2296-701X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Pennekamp, Frank A1 - Iles, Alison C. A1 - Garland, Joshua A1 - Brennan, Georgina A1 - Brose, Ulrich A1 - Gaedke, Ursula A1 - Jacob, Ute A1 - Kratina, Pavel A1 - Matthews, Blake A1 - Munch, Stephan A1 - Novak, Mark A1 - Palamara, Gian Marco A1 - Rall, Bjorn C. A1 - Rosenbaum, Benjamin A1 - Tabi, Andrea A1 - Ward, Colette A1 - Williams, Richard A1 - Ye, Hao A1 - Petchey, Owen L. T1 - The intrinsic predictability of ecological time series and its potential to guide forecasting JF - Ecological monographs : a publication of the Ecological Society of America. KW - empirical dynamic modelling KW - forecasting KW - information theory KW - permutation entropy KW - population dynamics KW - time series analysis Y1 - 2019 U6 - https://doi.org/10.1002/ecm.1359 SN - 0012-9615 SN - 1557-7015 VL - 89 IS - 2 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Raatz, Michael A1 - van Velzen, Ellen A1 - Gaedke, Ursula T1 - Co‐adaptation impacts the robustness of predator–prey dynamics against perturbations JF - Ecology and Evolution N2 - Global change threatens the maintenance of ecosystem functions that are shaped by the persistence and dynamics of populations. It has been shown that the persistence of species increases if they possess larger trait adaptability. Here, we investigate whether trait adaptability also affects the robustness of population dynamics of interacting species and thereby shapes the reliability of ecosystem functions that are driven by these dynamics. We model co‐adaptation in a predator–prey system as changes to predator offense and prey defense due to evolution or phenotypic plasticity. We investigate how trait adaptation affects the robustness of population dynamics against press perturbations to environmental parameters and against pulse perturbations targeting species abundances and their trait values. Robustness of population dynamics is characterized by resilience, elasticity, and resistance. In addition to employing established measures for resilience and elasticity against pulse perturbations (extinction probability and return time), we propose the warping distance as a new measure for resistance against press perturbations, which compares the shapes and amplitudes of pre‐ and post‐perturbation population dynamics. As expected, we find that the robustness of population dynamics depends on the speed of adaptation, but in nontrivial ways. Elasticity increases with speed of adaptation as the system returns more rapidly to the pre‐perturbation state. Resilience, in turn, is enhanced by intermediate speeds of adaptation, as here trait adaptation dampens biomass oscillations. The resistance of population dynamics strongly depends on the target of the press perturbation, preventing a simple relationship with the adaptation speed. In general, we find that low robustness often coincides with high amplitudes of population dynamics. Hence, amplitudes may indicate the robustness against perturbations also in other natural systems with similar dynamics. Our findings show that besides counteracting extinctions, trait adaptation indeed strongly affects the robustness of population dynamics against press and pulse perturbations. KW - disturbance KW - evolutionary rescue KW - population dynamics KW - stability KW - trait adaptation Y1 - 2019 U6 - https://doi.org/10.1002/ece3.5006 SN - 2045-7758 VL - 9 IS - 7 SP - 3823 EP - 3836 PB - John Wiley & Sons CY - Hoboken, NJ ER - TY - THES A1 - Schäfer, Merlin T1 - Understanding and predicting global change impacts on migratory birds T1 - Verständnis und Vorhersage von Auswirkungen des globalen Wandels auf Zugvögel N2 - This is a publication-based dissertation comprising three original research stud-ies (one published, one submitted and one ready for submission; status March 2019). The dissertation introduces a generic computer model as a tool to investigate the behaviour and population dynamics of animals in cyclic environments. The model is further employed for analysing how migratory birds respond to various scenarios of altered food supply under global change. Here, ecological and evolutionary time-scales are considered, as well as the biological constraints and trade-offs the individual faces, which ultimately shape response dynamics at the population level. Further, the effect of fine-scale temporal patterns in re-source supply are studied, which is challenging to achieve experimentally. My findings predict population declines, altered behavioural timing and negative carry-over effects arising in migratory birds under global change. They thus stress the need for intensified research on how ecological mechanisms are affected by global change and for effective conservation measures for migratory birds. The open-source modelling software created for this dissertation can now be used for other taxa and related research questions. Overall, this thesis improves our mechanistic understanding of the impacts of global change on migratory birds as one prerequisite to comprehend ongoing global biodiversity loss. The research results are discussed in a broader ecological and scientific context in a concluding synthesis chapter. N2 - Dies ist eine publikationsbasierte Dissertation, welche aus drei wissenschaftlichen Originalstudien (eine publiziert, eine eingereicht und eine einreichbar; Stand März 2019) besteht. Die Dissertation stellt ein generisches Computermodell bereit, um das Verhalten und die Populationsdynamik von Tieren zu untersuchen, welche saisonale Umweltbedingungen erfahren. Mit diesem Computermodell untersuche ich in der vorliegenden Thesis, wie Zugvögel auf verschiedene Szenarien veränderter Nahrungsverfügbarkeit reagieren, welche im Rahmen des globalen Wandels wahrscheinlich sind. Dabei werden ökologische und evolutionäre Zeitskalen berücksichtigt. Außerdem werden biologisch bedingte Einschränkungen und Zielkonflikte einbezogen, welche das einzelne Individuum erfährt, die aber letztendlich auch das Geschehen auf Populationsebene bestimmen. Weiterhin studiere ich mit dem erstellten Computermodell am Beispiel des Weißstorchs, wie sich feinskalige Zeitmuster in der Nahrungsverfügbarkeit auf Zugvögel auswirken. Solche Studien würden eine enorme experimentelle Herausforderung darstellen. Die im Rahmen dieser Dissertation entstandene frei verfügbare Modellierungs-Software kann nun für andere Taxa und verwandte Forschungsfragen eingesetzt werden. Nach meinen Ergebnissen ist im Zuge des globalen Wandels mit verstärkten Populationsabnahmen bei Zugvögeln zu rechnen, sowie mit Änderungen im zeitlichen Verhaltensablauf und nichtlinearen negativen Carry-over-Effekten. Dies verdeutlicht, wie wichtig es ist, die vom globalen Wandel betroffenen ökologischen Mechanismen näher zu erforschen sowie effektive Schutzmaßnahmen für Zugvögel zu entwickeln. Allgemein erhöht die Dissertation unser mechanistisches Verständnis davon, wie sich der globale Wandel auf bedrohte Zugvogelarten auswirkt und damit die globale Biodiversität beeinflusst. Die Forschungsergebnisse werden in einem abschließenden Synthese-Kapitel zusammenführend diskutiert. KW - global change KW - migratory birds KW - life-history theory KW - movement ecology KW - bird migration KW - optimal annual routine model KW - stochastic dynamic programming KW - full annual cycle KW - population dynamics KW - carry-over effects KW - white stork KW - behavioural ecology KW - adaptation KW - mechanistic model KW - energetics KW - behavioural timing KW - reproduction KW - globaler Wandel KW - Zugvögel KW - Lebenszyklustheorie KW - Bewegungsökologie KW - Vogelzug KW - "Optimal annual routine"-Modell KW - stochastisch-dynamische Optimierung KW - vollständiger Jahreszyklus KW - Populationsdynamik KW - Carry-over-Effekte KW - Weißstorch KW - Verhaltensökologie KW - Anpassung KW - mechanistisches Modell KW - Energetik KW - Verhaltens-Timing KW - Reproduktion Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-439256 ER - TY - JOUR A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes JF - Ecography N2 - 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. KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 SN - 1600-0587 VL - 44 IS - 10 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - GEN A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR: an R package for individual-based simulation of spatial eco-evolutionary dynamics and speciesu0027 responses to environmental changes T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1178 KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-523979 SN - 1866-8372 IS - 10 ER - TY - JOUR A1 - Malchow, Anne-Kathleen A1 - Bocedi, Greta A1 - Palmer, Stephen C. F. A1 - Travis, Justin M. J. A1 - Zurell, Damaris T1 - RangeShiftR BT - an R package for individual-based simulation of spatial changes JF - Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos N2 - 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. KW - connectivity KW - conservation KW - dispersal KW - evolution KW - population dynamics KW - range dynamics Y1 - 2021 U6 - https://doi.org/10.1111/ecog.05689 SN - 1600-0587 VL - 44 IS - 10 SP - 1443 EP - 1452 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - THES A1 - Malchow, Anne-Kathleen T1 - Developing an integrated platform for predicting niche and range dynamics BT - inverse calibration of spatially-explicit eco-evolutionary models N2 - Species are adapted to the environment they live in. Today, most environments are subjected to rapid global changes induced by human activity, most prominently land cover and climate changes. Such transformations can cause adjustments or disruptions in various eco-evolutionary processes. The repercussions of this can appear at the population level as shifted ranges and altered abundance patterns. This is where global change effects on species are usually detected first. To understand how eco-evolutionary processes act and interact to generate patterns of range and abundance and how these processes themselves are influenced by environmental conditions, spatially-explicit models provide effective tools. They estimate a species’ niche as the set of environmental conditions in which it can persist. However, the currently most commonly used models rely on static correlative associations that are established between a set of spatial predictors and observed species distributions. For this, they assume stationary conditions and are therefore unsuitable in contexts of global change. Better equipped are process-based models that explicitly implement algorithmic representations of eco-evolutionary mechanisms and evaluate their joint dynamics. These models have long been regarded as difficult to parameterise, but an increased data availability and improved methods for data integration lessen this challenge. Hence, the goal of this thesis is to further develop process-based models, integrate them into a complete modelling workflow, and provide the tools and guidance for their successful application. With my thesis, I presented an integrated platform for spatially-explicit eco-evolutionary modelling and provided a workflow for their inverse calibration to observational data. In the first chapter, I introduced RangeShiftR, a software tool that implements an individual-based modelling platform for the statistical programming language R. Its open-source licensing, extensive help pages and available tutorials make it accessible to a wide audience. In the second chapter, I demonstrated a comprehensive workflow for the specification, calibration and validation of RangeShiftR by the example of the red kite in Switzerland. The integration of heterogeneous data sources, such as literature and monitoring data, allowed to successfully calibrate the model. It was then used to make validated, spatio-temporal predictions of future red kite abundance. The presented workflow can be adopted to any study species if data is available. In the third chapter, I extended RangeShiftR to directly link demographic processes to climatic predictors. This allowed me to explore the climate-change responses of eight Swiss breeding birds in more detail. Specifically, the model could identify the most influential climatic predictors, delineate areas of projected demographic suitability, and attribute current population trends to contemporary climate change. My work shows that the application of complex, process-based models in conservation-relevant contexts is feasible, utilising available tools and data. Such models can be successfully calibrated and outperform other currently used modelling approaches in terms of predictive accuracy. Their projections can be used to predict future abundances or to assess alternative conservation scenarios. They further improve our mechanistic understanding of niche and range dynamics under climate change. However, only fully mechanistic models, that include all relevant processes, allow to precisely disentangle the effects of single processes on observed abundances. In this respect, the RangeShiftR model still has potential for further extensions that implement missing influential processes, such as species interactions. Dynamic, process-based models are needed to adequately model a dynamic reality. My work contributes towards the advancement, integration and dissemination of such models. This will facilitate numeric, model-based approaches for species assessments, generate ecological insights and strengthen the reliability of predictions on large spatial scales under changing conditions. N2 - Arten sind an ihren jeweiligen Lebensraum angepasst, doch viele Lebensräume sind heute einem globalen Wandel unterworfen. Dieser äußert sich vor allem in Veränderungen von Landnutzung und Klima, welche durch menschliche Aktivitäten verursacht werden und ganze Ökosysteme in ihrem Gefüge stören können. Störungen der grundlegenden öko-evolutionären Prozesse können auf der Populationsebene in Form von veränderten Verbreitungsgebieten und Häufigkeitsmustern sichtbar werden. Hier werden die Auswirkungen des globalen Wandels auf eine Art oftmals zuerst beobachtet. Um zu untersuchen, wie die Wirkung und Wechselwirkung der verschiedenen öko-evolutionären Prozesse die beobachteten Verbreitungs- und Häufigkeitsmuster erzeugen, und wie diese Prozesse wiederum von Umweltbedingungen beeinflusst werden, stellen räumlich explizite Modelle wirksame Instrumente dar. Sie beschreiben die ökologische Nische einer Art, also die Gesamtheit aller Umweltbedingungen, unter denen die Art fortbestehen kann. Die derzeit am häufigsten verwendeten Modelle stützen sich auf statische, korrelative Zusammenhänge, die zwischen bestimmten räumlichen Prädiktoren und den beobachteten Artverteilungen hergestellt werden. Allerdings werden dabei stationäre Bedingungen angenommen, was sie im Kontext des globalen Wandels ungeeignet macht. Deutlich besser geeignet sind prozessbasierte Modelle, welche explizite, algorithmische Repräsentationen von ökologischen Prozessen beinhalten und deren gemeinsame Dynamik berechnen. Solche Modelle galten lange Zeit als schwierig zu parametrisieren, doch die zunehmende Verfügbarkeit von Beobachtungsdaten sowie die verbesserten Methoden zur Datenintegration machen ihre Verwendung zunehmend praktikabel. Das Ziel der vorliegenden Arbeit ist es, diese prozessbasierten Modelle weiterzuentwickeln, sie in umfassende Modellierungsabläufe einzubinden, sowie Software und Anleitungen für ihre erfolgreiche Anwendung verfügbar zu machen. In meiner Dissertation präsentiere ich eine integrierte Plattform für räumlich-explizite, öko-evolutionäre Modellierung und entwickle einen Arbeitsablauf für dessen inverse Kalibrierung an Beobachtungsdaten. Im ersten Kapitel stelle ich RangeShiftR vor: eine Software, die eine individuenbasierte Modellierungsplattform für die statistische Programmiersprache R implementiert. Durch die Open-Source-Lizenzierung, umfangreichen Hilfeseiten und online verfügbaren Tutorials ist RangeShiftR einem breiten Publikum zugänglich. Im zweiten Kapitel demonstriere ich einen vollständigen Modellierungsablauf am Beispiel des Rotmilans in der Schweiz, der die Spezifikation, Kalibrierung und Validierung von RangeShiftR umfasst.Durch die Integration heterogener Datenquellen, wie Literatur- und Monitoringdaten, konnte das Modell erfolgreich kalibriert werden. Damit konnten anschließend validierte, raum-zeitliche Vorhersagen über das Vorkommen des Rotmilans erstellt und die dafür relevanten Prozesse identifiziert werden. Der vorgestellte Arbeitsablauf kann auf andere Arten übertragen werden, sofern geeignete Daten verfügbar sind. Im dritten Kapitel habe ich RangeShiftR erweitert, sodass demografische Prozessraten direkt mit Klimavariablen verknüpft werden können. Dies ermöglichte es, die Reaktionen von acht Schweizer Brutvogelarten auf den Klimawandel genauer zu untersuchen. Insbesondere konnte das Modell die einflussreichsten klimatischen Faktoren identifizieren, demografisch geeignete Gebiete abgrenzen und aktuelle Populationstrends auf den bisherigen Klimawandel zurückführen. Meine Arbeit zeigt, dass die Anwendung komplexer, prozessbasierter Modelle in naturschutzrelevanten Kontexten mit verfügbaren Daten möglich ist. Solche Modelle können erfolgreich kalibriert werden und andere, derzeit verwendete Modellierungsansätze in Bezug auf ihre Vorhersagegenauigkeit übertreffen. Ihre Projektionen können zur Vorhersage zukünftiger Artvorkommen und zur Einschätzung alternativer Naturschutzmaßnahmen verwendet werden. Sie verbessern außerdem unser mechanistisches Verständnis von Nischen- und Verbreitungsdynamiken unter dem Einfluss des Klimawandels. Jedoch ermöglichen nur vollständig prozessbasierte Modelle, die alle relevanten Prozesse vereinen, eine korrekte Aufschlüsselung der Auswirkungen einzelner Prozesse auf die beobachteten Abundanzen. In dieser Hinsicht hat das RangeShiftR-Modell noch Potenzial für Weiterentwicklungen, um fehlende, einflussreiche Prozesse hinzuzufügen, wie zum Beispiel die Interaktionen zwischen Arten. Um eine dynamische Realität adäquat abbilden zu können, werden dynamische, prozessbasierte Modelle benötigt. Meine Arbeit leistet einen Beitrag zur Weiterentwicklung, Integration und Verbreitung solcher Modelle und stärkt somit die Anwendung numerischer, modellbasierter Methoden für die Bewertung des Zustands von Arten, die Untersuchung ökologischer Zusammenhänge und die Steigerung der Zuverlässigkeit von Vorhersagen auf großen räumlichen Skalen unter Umweltveränderungen. T2 - Entwicklung einer integrierten Modellierungs-Plattform zur Vorhersage von Nischen- und Verbreitungs-dynamiken: Inverse Kalibrierung räumlich-expliziter öko-evolutionärer Modelle KW - species distribution modelling KW - Bayesian inference KW - individual-based modelling KW - range shifts KW - ecological modelling KW - population dynamics KW - Bayes'sche Inferenz KW - ökologische Modellierung KW - individuen-basierte Modellierung KW - Populationsdynamik KW - Arealverschiebungen KW - Artverbreitungsmodelle Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-602737 ER -