Evoplex: A platform for agent-based modeling on networks

Agent-based modeling and network science have been used extensively to advance our understanding of emergent collective behavior in systems that are composed of a large number of simple interacting individuals or agents. With the increasing availability of high computational power in affordable personal computers, dedicated efforts to develop multi-threaded, scalable and easy-to-use software for agent-based simulations are needed more than ever. Evoplex meets this need by providing a fast, robust and extensible platform for developing agent-based models and multi-agent systems on networks. Each agent is represented as a node and interacts with its neighbors, as defined by the network structure. Evoplex is ideal for modeling complex systems, for example in evolutionary game theory and computational social science. In Evoplex, the models are not coupled to the execution parameters or the visualization tools, and there is a user-friendly graphical interface which makes it easy for all users, ranging from newcomers to experienced, to create, analyze, replicate and reproduce the experiments.Comment: 6 pages, 5 figures; accepted for publication in SoftwareX [software available at https://evoplex.org

Gene Dispersal In Tropical Trees: Ecological Processes And Genetic Consequences.

Tropical trees constitute an ecologically important functional group in terrestrial ecosystems because of the essential roles that they play in sustaining biodiversity and carbon storage. The persistence and evolutionary potentials of tropical trees are, however, increasingly threatened by human-induced rapid changes in abiotic and biotic environments. For long-lived forest trees, gene dispersal by seeds and pollen is critical for tracking shifting climatic niches and for maintaining genetic variation needed to adapt to changing environments. Understanding the potential responses of tropical trees to environmental changes depends in part upon quantifying the rates of seed and pollen dispersal. This dissertation aims to quantify the spatial extent and magnitude of seed and pollen dispersal and their respective genetic impacts in a comparative context, by focusing on four Neotropical tree species that have distinct dispersal and pollination syndromes and life-history strategies. By using parentage inference and inverse modeling, I found that long-distance gene dispersal by seeds is common in these vertebrate-dispersed tropical trees, in which models predicted 1–18% of dispersal events exceeding 1 km. This fraction of pollen dispersal >1 km could reach 10–20% in these species. Furthermore, simulations with gene dispersal distances realistically represented suggest that seed and pollen dispersal limitation can lead to genetic diversity loss in tropical tree populations. By examining the respective genetic impacts of seed vs. pollen dispersal, I found that seed dispersal is the primary force driving spatial genetic patterns in these species. It suggests that the functional loss of seed-dispersing vertebrates, as a result of anthropogenic disturbance in tropical forests, could alter not only tree population spatial structure and ecological dynamics, but also genetic structure and evolutionary dynamics.PHDEcology and Evolutionary BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113619/1/weina_1.pd

International Symposium on Evolutionary Breeding in Cereals

Evolutionary plant breeding has a long history, but has so far not become part of mainstream breeding research, nor has it been implemented in practice to any substantial degree. However, over the last decade, research in evolutionary plant breeding has markedly intensified. For example, there are currently major research projects on-going in this area, including the EU funded project SOLIBAM, the Wheat Breeding LINK project in the UK, and the Danish Biobreed project. Also, a new 3-year international research project called COBRA on this topic is due to start in March 2013. Funded by the CORE Organic 2 Eranet the project brings together over 40 partner organizations from 18 European countries. In addition, interest in evolutionary plant breeding is growing among farmers, breeders and policy makers. In fact, there are currently encouraging developments in the imminent revision of seed legislation in Europe that could lead to more room for evolutionary plant breeding approaches in the future. This renewed interest in evolutionary plant breeding is partly due to the recognition that mainstream plant breeding is limited in terms of its engagement with end users, i.e. farmers and growers. More urgently however, effects of climate change on agricultural production have become more noticeable and there is also a growing awareness of increasing resource constraints; together, these will create more stressful growing conditions for agricultural crops. With this background, it is now being recognized that crops need to be able to cope with more variable, contrasting, fluctuating, and generally more unpredictable growing conditions. To be able to deal with this large and increasing environmental variability, plant breeding needs to become more decentralized and diversified. Evolutionary plant breeding offers great potential in this respect. The contributions collated from this symposium explore this potential as well as the limitations of evolutionary plant breeding. While they only show a part of the on-going research activities in Europe, we hope that these proceedings provide inspiration both for further research and for implementation in practice

Local-scale patterns of genetic variability, outcrossing, and spatial structure in natural stands of Arabidopsis thaliana

As Arabidopsis thaliana is increasingly employed in evolutionary and ecological studies, it is essential to understand patterns of natural genetic variation and the forces that shape them. Previous work focusing mostly on global and regional scales has demonstrated the importance of historical events such as long-distance migration and colonization. Far less is known about the role of contemporary factors or environmental heterogeneity in generating diversity patterns at local scales. We sampled 1,005 individuals from 77 closely spaced stands in diverse settings around Tübingen, Germany. A set of 436 SNP markers was used to characterize genome-wide patterns of relatedness and recombination. Neighboring genotypes often shared mosaic blocks of alternating marker identity and divergence. We detected recent outcrossing as well as stretches of residual heterozygosity in largely homozygous recombinants. As has been observed for several other selfing species, there was considerable heterogeneity among sites in diversity and outcrossing, with rural stands exhibiting greater diversity and heterozygosity than urban stands. Fine-scale spatial structure was evident as well. Within stands, spatial structure correlated negatively with observed heterozygosity, suggesting that the high homozygosity of natural A. thaliana may be partially attributable to nearest-neighbor mating of related individuals. The large number of markers and extensive local sampling employed here afforded unusual power to characterize local genetic patterns. Contemporary processes such as ongoing outcrossing play an important role in determining distribution of genetic diversity at this scale. Local "outcrossing hotspots" appear to reshuffle genetic information at surprising rates, while other stands contribute comparatively little. Our findings have important implications for sampling and interpreting diversity among A. thaliana accessions.Financial support came from an NIH Ruth Kirschstein NRSA Postdoctoral Fellowship (KB), a Human Frontiers Science Program Postdoctoral Fellowship (RAL), grants DFG ERA-PG ARelatives and FP6 IP AGRON-OMICS (contract LSHG-CT-2006-037704), from a Gottfried Wilhelm Leibniz Award of the DFG, and the Max Planck Society (DW)

Monogenic modular forms in two and several real and complex variables

In this paper we deal with monogenic and $k$-monogenic Clifford-valued automorphic forms in two and several vector variables. We focus on the construction of several families of Eisenstein and Poincar\'{e} series within the setting of this function theory. The functions that we construct provide non-trivial examples for generalizations of the classical Hilbert modular forms within the framework of real and complex Clifford analysis

Evolution: Complexity, uncertainty and innovation

Complexity science provides a general mathematical basis for evolutionary thinking. It makes us face the inherent, irreducible nature of uncertainty and the limits to knowledge and prediction. Complex, evolutionary systems work on the basis of on-going, continuous internal processes of exploration, experimentation and innovation at their underlying levels. This is acted upon by the level above, leading to a selection process on the lower levels and a probing of the stability of the level above. This could either be an organizational level above, or the potential market place. Models aimed at predicting system behaviour therefore consist of assumptions of constraints on the micro-level – and because of inertia or conformity may be approximately true for some unspecified time. However, systems without strong mechanisms of repression and conformity will evolve, innovate and change, creating new emergent structures, capabilities and characteristics. Systems with no individual freedom at their lower levels will have predictable behaviour in the short term – but will not survive in the long term. Creative, innovative, evolving systems, on the other hand, will more probably survive over longer times, but will not have predictable characteristics or behaviour. These minimal mechanisms are all that are required to explain (though not predict) the co-evolutionary processes occurring in markets, organizations, and indeed in emergent, evolutionary communities of practice. Some examples will be presented briefly

Agent-Based Modeling of Human-Induced Spread of Invasive Species in Agricultural Landscapes: Insights from the Potato Moth in Ecuador

Agent-based models (ABM) are ideal tools to deal with the complexity of pest invasion throughout agricultural socio-ecological systems, yet very few studies have applied them in such context. In this work we developed an ABM that simulates interactions between farmers and an invasive insect pest in an agricultural landscape of the tropical Andes. Our specific aims were to use the model 1) to assess the importance of farmers\' mobility and pest control knowledge on pest expansion and 2) to use it as an educational tool to train farmer communities facing pest risks. Our model combined an ecological sub-model, simulating pest population dynamics driven by a cellular automaton including environmental factors of the landscape, with a social model in which we incorporated agents (farmers) potentially transporting and spreading the pest through displacements among villages. Results of model simulation revealed that both agents\' movements and knowledge had a significant, non-linear, impact on invasion spread, confirming previous works on disease expansion by epidemiologists. However, heterogeneity in knowledge among agents had a low effect on invasion dynamics except at high levels of knowledge. Evaluations of the training sessions using ABM suggest that farmers would be able to better manage their crop after our implementation. Moreover, by providing farmers with evidence that pests propagated through their community not as the result of isolated decisions but rather as the result of repeated interactions between multiple individuals over time, our ABM allowed introducing them with social and psychological issues which are usually neglected in integrated pest management programs.Socio-Ecological Systems, Farmers, Invasive Pest, Long Distance Dispersion, Teaching

Spatio-temporal analysis of vegetation dynamics of selected successional stages of dry acidic grasslands : experimental studies and model simulations

Austenfeld M. Spatio-temporal analysis of vegetation dynamics of selected successional stages of dry acidic grasslands : experimental studies and model simulations. Bielefeld (Germany): Bielefeld University; 2009.Eine allgemeine Entwicklungsumgebung wurde für die Analyse und Simulation von räumlich-zeitlichen Phänomenen in ökologischen Systemen entwickelt. Die gesamte Plattform basiert auf einer "Rich-Client-Platform" (RCP), die neue Konzepte der Modularisierung und allgemeinen Programmarchitektur mitbringt. Damit bietet sie die Grundlage für eine nachhaltige Weiterentwicklung und ist somit eine solide Basis für eine integrierte Entwicklungsumgebung für ökologische Modelle. Die Integration verschiedener statistischer Werkzeuge, Methoden der Bildverarbeitung und spezielle Visualisierungen qualifizieren diese Umgebung besonders für die Analyse der oben genannten räumlich-zeitlichen Prozesse. Aufgrund ihrer vergleichsweise geringen Komplexität wurden Sandlebensräume wiederholt für Studien von Vegetationsmustern und ihrer zugrunde liegenden biotischen Interaktionen genutzt. Für einen integrativen Überblick und weitere integrative Ansätze mit Hilfe von Simulationsmodellen wurde die oben genannte Plattform genutzt, um eine individuenbasierte Modellstruktur für die Analyse von Langzeiteffekten aufgrund von Umweltveränderungen auf die Stabilität von Sandlebensräumen zu entwickeln, die typischerweise von zwei Pionierarten, Corynephorus canescens und Polytrichum piliferum, dominiert werden. Das Modell wurde mit experimentellen Daten verifiziert, und die vom Modell erzeugten räumlich-zeitlichen Muster zeigten eine hohe Übereinstimmung mit natürlich gemessenen Mustern. Das Modell wurde dann genutzt, um Langzeiteffekte von Veränderungen der Temperatur, Nährstoffversorgung und Störungsraten in diesem System zu untersuchen. Die Ergebnisse zeigten eine generell hohe Stabilität des Systems unter veränderten Temperatur- und Nährstoffbedingungen, wobei temporal wiederkehrende, kleinräumige Störungen als Grundlage notwendig waren. Schließlich wurde noch eine Untersuchung über die Auswirkungen von Herbivorie und Konkurrenz auf Corynephorus canescens durchgeführt. In einem kontrollierten Freilandexperiment wurden die Auswirkungen von entfernter Biomasse von Blättern sowie die An- oder Abwesenheit eines intraspezifischen und interspezifischen Konkurrenten (Hieracium pilosella) auf die überirdische und unterirdische Allokation von Biomasse in der folgenden Regenerationsphase analysiert. Die Ergebnisse zeigten, dass Corynephorus canescens die Fähigkeit besitzt, leichte bis mittlere Blattverluste (die typische natürliche Herbivorie von Kaninchen und Paarhufern simulieren sollten) zu kompensieren, ohne dabei an Konkurrenzstärke zu verlieren. Unterirdisch konnten keine Auswirkungen der simulierten Herbivorie bzw. Konkurrenz festgestellt werden. Aufgrund dieser zu vernachlässigenden Effekte wurde Herbivorie nicht in dem Modell berücksichtigt.A generic modeling environment for the analysis and simulation of spatio-temporal phenomena in ecosystems was developed. This framework was built upon a Rich Client Platform (RCP) which uses new concepts of extensibility and software architecture for sustainable development and provides a solid basis for an Integrated Development Environment (IDE) for ecological models. The integration of various statistical tools, imaging routines and several specialized drawing panels makes this environment particularly suitable for the analysis of the above mentioned spatio-temporal ecological processes. Because of their comparatively low complexity, dry acidic grassland ecosystems have been repeatedly used for studying vegetation pattern formation and the underlying biotic interactions. In order to obtain an integrative view of the existing knowledge as well as to provide a possibility for further integrative analysis with the help of model simulations, the above described platform was used to develop an individual based Model structure for the investigation of long term effects of environmental changes on the stability of early successional stages of such dry acidic grasslands which are typically dominated by the two pioneer species Corynephorus canescens and Polytrichum piliferum. The model was validated with experimental data and the spatio-temporal patterns created by the model were in good accordance with the measured natural patterns. The model was then used to analyze the effect of changes in temperature, nutrient supply and disturbance rate on the long term behavior of this ecosystem. The results showed an overall high stability of this system under different temperature and nutrient scenarios as long as an intermediate disturbance frequency is assured. Finally, an experimental study on the effect of herbivory and competition on the Corynephorus canescens was conducted. In a controlled field experiment, the effects of the removal of various amounts of aboveground biomass on the above and belowground biomass allocation during the following regeneration phase was analyzed in the presence or absence of an intraspecific and interspecific competitor (Hieracium pilosella). The results show a rather high ability of C. canescens to compensate low to medium amounts of foliage loss (reflecting the typical natural herbivory induced by grasshoppers and rabbits) without significant changes in its competitive ability. Belowground, no biomass effects of foliage removal and/or competition could be detected. Because of these negligible effects, herbivory was not implemented in the above described model

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa