Twenty-five model food webs can be designed from five points (species) and five links (trophic in... more Twenty-five model food webs can be designed from five points (species) and five links (trophic interactions), if they contain a single top-predator (i.e. sink webs). According to a simple topological approach, we presented elsewhere a reliability theoretical analysis of this set of food web graphs. The question addressed here is how network flow reliability is related to the dynamical behavior and stability of these 'model communities'. We simulated the behavior of these webs and calculated their persistence, according to four models: (1) with symmetrical interaction coefficients between species; (2) with asymmetrical interaction coefficients and lower death rates for predators; and (3) with absolutely and (4) relatively perturbed, formerly persistent parameter sets of the asymmetrical model. We used both Lotka Á/Volterra (LV) and Holling II-type equations (with switching effect). Thus, we had eight persistence values for each web. Persistence (a dynamical property) and flow reliability (a structural property) were analyzed. We found that (1) reliable flow pattern is associated with high persistence in the Holling models, while the LV models predict no consistent correlations; (2) in asymmetrical situations, persistence is always much higher (in both LV and Holling models); and (3) the predictions of Holling models (versus LV models) are much less sensitive to local perturbations. Based on these results, we conclude that (1) reliable network flows can contribute to persistence only if switching is possible; (2) asymmetrical interactions increase persistence, independently of the switching effect but it indicates persistence in Holling II model; (3) switching makes the relationship much more predictable between structure and dynamics. Thus, the network design is less useful predictor of persistence without switching effect but well can ensure dynamical stability under the conditions of the Holling II model. We have presented how various dynamical models predict different behavior of modelled communities characterized by the same structure and complexity. Complementing dynamical with structural analysis may further increase our understanding of persistence in food webs. #
There is an increasing body of literature on the topological analysis of modules (motifs, buildin... more There is an increasing body of literature on the topological analysis of modules (motifs, building blocks) in different networks. Most of these results are of descriptive, comparative and statistical nature, while dynamical simulations of their behaviour are missing. We present a stochastic food web simulation and study the relative strength of different simple food web modules. We found that (1) the effects of prey groups on predators are significantly stronger than other effects, (2) indirect loops have strong effects only on mean population sizes, not on their variabilty, and (3) some short indirect interactions are not stronger than some longer ones. We believe that these findings may contribute to systems-based conservation practice in the future.
ABSTRACT A pályázat keretében végzett kutatásaink a következő elméleti témakörökben történtek: 1)... more ABSTRACT A pályázat keretében végzett kutatásaink a következő elméleti témakörökben történtek: 1) Párosodási típusok evolúciója térben explicit modellel 2) Korai evolúciós problémák vizsgálata 3) A diszperzió és a mutualizmus evolúciója 4) Metapopulációk erősen zajos környezetben 5) Az interferencia-kompetíció szerepe mikrobiális élet-közösségek diverzitásának fenntartásában 6) Táplálékhálózatok szerkezete és stabilitása. Ebben a hat témakörben összesen 38, a pályázat azonosító számának feltüntetésével megjelent publikáció született, melyek összesített impakt faktora 113.86. Mindegyik témában folytatjuk a kutatásokat. | We have accomplished research in the following theoretical topics with the support of the present grant: 1) The evolution of mating types in a spatially explicit model 2) Research on problems of early evolution 3) The evolution of dispersal and mutualism 4) The dynamics of metapopulations in very noisy environments 5) The role of interference competition in the maintenance of the diversity of microbial communities 6) The strucure and the stability of food webs We have published 38 papers on these six topics with the number of the grant mentioned in the Acknowledgements of the papers. The cumulative impact factor of these publications is 113.86. We are planning to continue research in all the six topics.
One source of complexity in ecological systems is the hierarchical organization of parallel biolo... more One source of complexity in ecological systems is the hierarchical organization of parallel biological processes. Our 'horizontal' knowledge describing different levels is quite massive, but the understanding of their vertical interactions is very poor. We present a toy model linking social networks, food webs and a landscape graph. Horizontal processes refer to population, community and metacommunity dynamics, while vertical processes connect the three organizational levels. The model is stochastic and individual-based. We parametrized it by using reasonable empirical values found in the literature. Sensitivity analysis shows how the parameters describing the dynamics of a particular species (e.g., probability of social tie formation with conspecific individuals, or migration rate) can affect metapopulation size and spatial heterogeneity of all food web species. Changing the values of various parameters at any of the three levels have commensurable effects on the population size of all species. In contrast to the general intuition, community dynamics do not dominate population biology; social and landscape processes can trigger greater effects than food web interactions. More rapidly changing social relationships lead to a decrease in social network cohesion, thus impairing the feeding efficiency of consumers. In food webs, trophic specialization provides an advantage when it contributes to avoid competition, being detrimental otherwise. Highest migration rates result in a more heterogeneous metapopulation distribution of the generalist consumer, indirectly supporting its specialist competitor. We discuss conceptual and methodological aspects of the model, demonstrating the importance of an integrative view. We also emphasize the relevance of vertical connections, suggesting how such a modelling framework could support conservation biology. Further studies should focus on methods to approximate external pressures with changes in model parameters, thus allowing to characterize possible impacts on ecological systems. 161 the individuals over large distances: in case of elephants, the spatial dynamics of the population is also related to the fine structure of the social network, at several levels . Barton et al. [7] have shown that social group coherence is related to predation pressure: the fragmentation of the social network of baboon groups can increase if the density of predators is lower.
In order to better understand several cellular processes, it is helpful to study how various comp... more In order to better understand several cellular processes, it is helpful to study how various components make up the system. This systems perspective is supported by several modelling tools including network analysis. Networks of protein-protein interactions (PPI networks) offer a way to depict, visualize and quantify the functioning and relative importance of particular proteins in cell function. The toolkit of network analysis ranges from the local indices describing individual proteins (as network nodes) to global indicators of system architecture, describing the total interaction system (as the whole network). We briefly introduce some of these network indices and present a case study where the connectedness and potential functional relationships between certain disease proteins are inferred. We argue that network analysis can be used, in general, to improve databases, to infer novel functions, to quantify positional importance and to support predictions in pathogenesis studies. ...
The Codes of Life: The Rules of Macroevolution, 2007
The origin of the genetic code is still not fully understood, despite considerable progress in th... more The origin of the genetic code is still not fully understood, despite considerable progress in the last decade. Far from being a frozen complete accident, the canonical genetic code is full of patterns that seem to open a window on its evolutionary history. In this chapter we rethink the hypothesis that the primary selective force in favour of the emergence of genetic coding was the added value by amino acids to the RNA world in the form of increased catalytic potential. We identify a novel pattern in the genetic code suggesting that the catalytic propensity of amino acids has considerably shaped its structure. This suggestion complements older ideas arguing in favour of a driving force to build the smallest stable oligopeptide structures, such as hairpins (β-turns stabilized by small β-sheets). We outline experiments to test some of the proposals.
Recent publications that have assessed the relationship between fishing and possible alterations ... more Recent publications that have assessed the relationship between fishing and possible alterations of direct and indirect trophic relationships within impacted ecosystems have detected strong ecological effects, such as trophic cascades and changes in ecosystem control equilibrium, either top-down or bottom-up (Barausse et al.
The study of gene and protein interaction networks has improved our understanding of the multiple... more The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify 'linker' proteins that bridge diverse cellular processes -integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key role in controlling the temporal changes in the localization of the polarity machinery. Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation. Detailed bibliographic inspection of other predicted 'linkers' also confirms the predictive power of the method. As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.
Ecological systems are complex assemblages of various species with interactions between them. The... more Ecological systems are complex assemblages of various species with interactions between them. The interactions can be even more important than the species themselves for understanding how the whole system is functioning and organized. For the representation of the topological space of interspecific relationships, graph theory is a suitable mathematical tool: the network perspective and the various techniques of network analysis are more and more elaborated and invading ecology. Beyond a static view on networks, fundamental questions can only be answered if dynamical analyses are also made, and now it is clear that structural and dynamical studies must not "compete" but strongly complement each other. Our aim is to give a menu of classical and more recently suggested network indices and to discuss what do we know about their relations to ecosystem dynamics. Since ecologists have very diverse problems, they need diverse techniques and a good insight in matching the adequate method to a particular problem. The main question is how to link certain graph properties to understanding and predicting the behaviour of an ecosystem. We wish to contribute to bridging the gap between extreme structural and extreme dynamical views.
Parasites are ubiquitous in ecological communities but it is only recently that they have been ro... more Parasites are ubiquitous in ecological communities but it is only recently that they have been routinely included in food web studies. Using recently published data and the tool of network analysis, we elucidate features associated with the pattern of parasitism in ecological communities. First we show here that parasitism is non-random in food webs. Second we demonstrate that parasite diversity, the number of parasite species harboured by a host species, is related to the network position of a host species. Specifically, a host species with high parasite diversity tends to have a wide diet range, occupy a network position close to many prey species, or occupy a network position that can better accumulate resources from species at lower trophic levels. Lastly our results also suggest that a host species with higher vulnerability to predators, being at a network position close to many predatory species, or being involved in many different food chains, tends to be important in parasite transmission.
Plant-derived natural products have important functions in ecological interactions. In some cases... more Plant-derived natural products have important functions in ecological interactions. In some cases these compounds are deployed to sites of pathogen challenge by vesicle-mediated trafficking. Polar vesicle trafficking of natural products, proteins and other, as yet uncharacterized, cargo is emerging as a common theme in investigations of diverse disease resistance mechanisms in plants. Root-derived natural products can have marked effects on interactions between plants and soilborne organisms, for example by serving as signals for initiation of symbioses with rhizobia and mycorrhizal fungi. They may also contribute to competitiveness of invasive plant species by inhibiting the growth of neighbouring plants (allelopathy). Very little is known about the mechanisms of release of natural products from aerial plant parts or from roots, although there are likely to be commonalities in these processes. There is increasing evidence to indicate that pathogens and symbionts can manipulate plant endomembrane systems to suppress host defence responses and facilitate accommodation within plant cells. The relationship between secretory processes and plant interactions forms the focus of this review, which brings together different aspects of the deployment of defence-related natural products by plants.
Recent investigations on the structure of complex networks have provided interesting results for ... more Recent investigations on the structure of complex networks have provided interesting results for ecologists. Being inspired by these studies, we analyse a well-defined set of small model food webs. The extinction probability caused by internal Lotka-Volterra dynamics is compared to the position of species. Simulations have revealed that some global properties of these food webs (e.g. the homogeneity of connectedness) and the positions of species therein (e.g. interaction pattern) make them prone to modelled biotic extinction caused by population dynamical effects. We found that: (a) homogeneity in the connectedness structure increases the probability of extinction events; (b) in addition to the number of interactions, their orientations also influence the future of species in a web. Since species in characteristic network positions are prone to extinction, results could also be interpreted as describing the properties of preferred states of food webs during community assembly. Our results may contribute to understanding the intimate relationship between pattern and process in ecology.
One of the main concerns of shrimp fisheries is the associated impact on ecosystem biodiversity, ... more One of the main concerns of shrimp fisheries is the associated impact on ecosystem biodiversity, particularly on fish assemblages that are poorly characterized yet likely very relevant to the health of the ecosystem. The continental shelf along the eastern coast of the mouth of the Gulf of California is a region of high biodiversity that harbors highly productive fisheries. This study aimed to analyze the changes in the soft bottom fish assemblages caught as bycatch in the shrimp fishery located in this region. Sampling was conducted with commercial trawls at 16 fixed stations during the 2006-2007 shrimp-fishing season. A total of 103 fish species from 80 genera and 47 families were collected. The ecological and taxonomic diversity as well as the composition and abundance of the fish community caught as bycatch in the shrimp trawl fishery were found to be significantly different in the autumn and winter. Ordination and similarity analyses also revealed differing patterns. Species abundance was strongly associated with sea bottom temperature, depth and latitude. The effects of these abiotic variables on the observed diversity patterns and the possible influences of the fishery are discussed.
We present a simple language tool, CoSBiLab LIME, for building ecosystem models for stochastic dy... more We present a simple language tool, CoSBiLab LIME, for building ecosystem models for stochastic dynamic simulation. The LIME language allows the user to give a biologically intuitive model description in a narrative style. After performing static analysis on the model structure, the software tool translates the model description into the BlenX programming language for stochastic dynamical simulation. These features facilitate the analysis of parallel, multiple ecological interactions in metacommunities. The software tool thus allows ecologists with no programming background to perform quite complicated, process-algebra-based simulations.
The development of approaches to estimate the vulnerability of biological communities and ecosyst... more The development of approaches to estimate the vulnerability of biological communities and ecosystems to extirpations and reductions of species is a central challenge of conservation biology. One key aim of this challenge is to develop quantitative approaches to estimate and rank interaction strengths and keystoneness of species and functional groups, i.e. to quantify the relative importance of species. Network analysis can be a powerful tool for this because certain structural aspects of ecological networks are good indicators of the mechanisms that maintain co-evolved, biotic interactions. A static view of ecological networks would lead us to focus research on highly-central species in food webs (topological key players in ecosystems). There are a variety of centrality indices, developed for several types of ecological networks (e.g. for weighted and un-weighted webs). However, truly understanding extinction and its community-wide effects requires the use of dynamic models. Deterministic dynamic models are feasible when population sizes are sufficiently large to minimize noise in the overall system. In models with small population sizes, stochasticity can be modelled explicitly. We present a stochastic simulation-based ecosystem model for identification of "dynamic key species" in situations where stochastic models are appropriate. To demonstrate this approach, we simulated ecosystem dynamics and performed sensitivity analysis using data from the Prince William Sound, Alaska ecosystem model. We then compare these results to those of purely topological analyses and deterministic dynamic (Ecosim) studies. We present the relationships between various topological and dynamic indices and discuss their biological relevance. The trophic group with the largest effect on others is nearshore demersals, the species mostly sensitive to others is halibut, and the group of both considerable effect on and sensitivity to others is juvenile herring. The most important trophic groups in our dynamical simulations appear to have intermediate trophic levels.
Twenty-five model food webs can be designed from five points (species) and five links (trophic in... more Twenty-five model food webs can be designed from five points (species) and five links (trophic interactions), if they contain a single top-predator (i.e. sink webs). According to a simple topological approach, we presented elsewhere a reliability theoretical analysis of this set of food web graphs. The question addressed here is how network flow reliability is related to the dynamical behavior and stability of these 'model communities'. We simulated the behavior of these webs and calculated their persistence, according to four models: (1) with symmetrical interaction coefficients between species; (2) with asymmetrical interaction coefficients and lower death rates for predators; and (3) with absolutely and (4) relatively perturbed, formerly persistent parameter sets of the asymmetrical model. We used both Lotka Á/Volterra (LV) and Holling II-type equations (with switching effect). Thus, we had eight persistence values for each web. Persistence (a dynamical property) and flow reliability (a structural property) were analyzed. We found that (1) reliable flow pattern is associated with high persistence in the Holling models, while the LV models predict no consistent correlations; (2) in asymmetrical situations, persistence is always much higher (in both LV and Holling models); and (3) the predictions of Holling models (versus LV models) are much less sensitive to local perturbations. Based on these results, we conclude that (1) reliable network flows can contribute to persistence only if switching is possible; (2) asymmetrical interactions increase persistence, independently of the switching effect but it indicates persistence in Holling II model; (3) switching makes the relationship much more predictable between structure and dynamics. Thus, the network design is less useful predictor of persistence without switching effect but well can ensure dynamical stability under the conditions of the Holling II model. We have presented how various dynamical models predict different behavior of modelled communities characterized by the same structure and complexity. Complementing dynamical with structural analysis may further increase our understanding of persistence in food webs. #
Twenty-five model food webs can be designed from five points (species) and five links (trophic in... more Twenty-five model food webs can be designed from five points (species) and five links (trophic interactions), if they contain a single top-predator (i.e. sink webs). According to a simple topological approach, we presented elsewhere a reliability theoretical analysis of this set of food web graphs. The question addressed here is how network flow reliability is related to the dynamical behavior and stability of these 'model communities'. We simulated the behavior of these webs and calculated their persistence, according to four models: (1) with symmetrical interaction coefficients between species; (2) with asymmetrical interaction coefficients and lower death rates for predators; and (3) with absolutely and (4) relatively perturbed, formerly persistent parameter sets of the asymmetrical model. We used both Lotka Á/Volterra (LV) and Holling II-type equations (with switching effect). Thus, we had eight persistence values for each web. Persistence (a dynamical property) and flow reliability (a structural property) were analyzed. We found that (1) reliable flow pattern is associated with high persistence in the Holling models, while the LV models predict no consistent correlations; (2) in asymmetrical situations, persistence is always much higher (in both LV and Holling models); and (3) the predictions of Holling models (versus LV models) are much less sensitive to local perturbations. Based on these results, we conclude that (1) reliable network flows can contribute to persistence only if switching is possible; (2) asymmetrical interactions increase persistence, independently of the switching effect but it indicates persistence in Holling II model; (3) switching makes the relationship much more predictable between structure and dynamics. Thus, the network design is less useful predictor of persistence without switching effect but well can ensure dynamical stability under the conditions of the Holling II model. We have presented how various dynamical models predict different behavior of modelled communities characterized by the same structure and complexity. Complementing dynamical with structural analysis may further increase our understanding of persistence in food webs. #
There is an increasing body of literature on the topological analysis of modules (motifs, buildin... more There is an increasing body of literature on the topological analysis of modules (motifs, building blocks) in different networks. Most of these results are of descriptive, comparative and statistical nature, while dynamical simulations of their behaviour are missing. We present a stochastic food web simulation and study the relative strength of different simple food web modules. We found that (1) the effects of prey groups on predators are significantly stronger than other effects, (2) indirect loops have strong effects only on mean population sizes, not on their variabilty, and (3) some short indirect interactions are not stronger than some longer ones. We believe that these findings may contribute to systems-based conservation practice in the future.
ABSTRACT A pályázat keretében végzett kutatásaink a következő elméleti témakörökben történtek: 1)... more ABSTRACT A pályázat keretében végzett kutatásaink a következő elméleti témakörökben történtek: 1) Párosodási típusok evolúciója térben explicit modellel 2) Korai evolúciós problémák vizsgálata 3) A diszperzió és a mutualizmus evolúciója 4) Metapopulációk erősen zajos környezetben 5) Az interferencia-kompetíció szerepe mikrobiális élet-közösségek diverzitásának fenntartásában 6) Táplálékhálózatok szerkezete és stabilitása. Ebben a hat témakörben összesen 38, a pályázat azonosító számának feltüntetésével megjelent publikáció született, melyek összesített impakt faktora 113.86. Mindegyik témában folytatjuk a kutatásokat. | We have accomplished research in the following theoretical topics with the support of the present grant: 1) The evolution of mating types in a spatially explicit model 2) Research on problems of early evolution 3) The evolution of dispersal and mutualism 4) The dynamics of metapopulations in very noisy environments 5) The role of interference competition in the maintenance of the diversity of microbial communities 6) The strucure and the stability of food webs We have published 38 papers on these six topics with the number of the grant mentioned in the Acknowledgements of the papers. The cumulative impact factor of these publications is 113.86. We are planning to continue research in all the six topics.
One source of complexity in ecological systems is the hierarchical organization of parallel biolo... more One source of complexity in ecological systems is the hierarchical organization of parallel biological processes. Our 'horizontal' knowledge describing different levels is quite massive, but the understanding of their vertical interactions is very poor. We present a toy model linking social networks, food webs and a landscape graph. Horizontal processes refer to population, community and metacommunity dynamics, while vertical processes connect the three organizational levels. The model is stochastic and individual-based. We parametrized it by using reasonable empirical values found in the literature. Sensitivity analysis shows how the parameters describing the dynamics of a particular species (e.g., probability of social tie formation with conspecific individuals, or migration rate) can affect metapopulation size and spatial heterogeneity of all food web species. Changing the values of various parameters at any of the three levels have commensurable effects on the population size of all species. In contrast to the general intuition, community dynamics do not dominate population biology; social and landscape processes can trigger greater effects than food web interactions. More rapidly changing social relationships lead to a decrease in social network cohesion, thus impairing the feeding efficiency of consumers. In food webs, trophic specialization provides an advantage when it contributes to avoid competition, being detrimental otherwise. Highest migration rates result in a more heterogeneous metapopulation distribution of the generalist consumer, indirectly supporting its specialist competitor. We discuss conceptual and methodological aspects of the model, demonstrating the importance of an integrative view. We also emphasize the relevance of vertical connections, suggesting how such a modelling framework could support conservation biology. Further studies should focus on methods to approximate external pressures with changes in model parameters, thus allowing to characterize possible impacts on ecological systems. 161 the individuals over large distances: in case of elephants, the spatial dynamics of the population is also related to the fine structure of the social network, at several levels . Barton et al. [7] have shown that social group coherence is related to predation pressure: the fragmentation of the social network of baboon groups can increase if the density of predators is lower.
In order to better understand several cellular processes, it is helpful to study how various comp... more In order to better understand several cellular processes, it is helpful to study how various components make up the system. This systems perspective is supported by several modelling tools including network analysis. Networks of protein-protein interactions (PPI networks) offer a way to depict, visualize and quantify the functioning and relative importance of particular proteins in cell function. The toolkit of network analysis ranges from the local indices describing individual proteins (as network nodes) to global indicators of system architecture, describing the total interaction system (as the whole network). We briefly introduce some of these network indices and present a case study where the connectedness and potential functional relationships between certain disease proteins are inferred. We argue that network analysis can be used, in general, to improve databases, to infer novel functions, to quantify positional importance and to support predictions in pathogenesis studies. ...
The Codes of Life: The Rules of Macroevolution, 2007
The origin of the genetic code is still not fully understood, despite considerable progress in th... more The origin of the genetic code is still not fully understood, despite considerable progress in the last decade. Far from being a frozen complete accident, the canonical genetic code is full of patterns that seem to open a window on its evolutionary history. In this chapter we rethink the hypothesis that the primary selective force in favour of the emergence of genetic coding was the added value by amino acids to the RNA world in the form of increased catalytic potential. We identify a novel pattern in the genetic code suggesting that the catalytic propensity of amino acids has considerably shaped its structure. This suggestion complements older ideas arguing in favour of a driving force to build the smallest stable oligopeptide structures, such as hairpins (β-turns stabilized by small β-sheets). We outline experiments to test some of the proposals.
Recent publications that have assessed the relationship between fishing and possible alterations ... more Recent publications that have assessed the relationship between fishing and possible alterations of direct and indirect trophic relationships within impacted ecosystems have detected strong ecological effects, such as trophic cascades and changes in ecosystem control equilibrium, either top-down or bottom-up (Barausse et al.
The study of gene and protein interaction networks has improved our understanding of the multiple... more The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify 'linker' proteins that bridge diverse cellular processes -integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key role in controlling the temporal changes in the localization of the polarity machinery. Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation. Detailed bibliographic inspection of other predicted 'linkers' also confirms the predictive power of the method. As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.
Ecological systems are complex assemblages of various species with interactions between them. The... more Ecological systems are complex assemblages of various species with interactions between them. The interactions can be even more important than the species themselves for understanding how the whole system is functioning and organized. For the representation of the topological space of interspecific relationships, graph theory is a suitable mathematical tool: the network perspective and the various techniques of network analysis are more and more elaborated and invading ecology. Beyond a static view on networks, fundamental questions can only be answered if dynamical analyses are also made, and now it is clear that structural and dynamical studies must not "compete" but strongly complement each other. Our aim is to give a menu of classical and more recently suggested network indices and to discuss what do we know about their relations to ecosystem dynamics. Since ecologists have very diverse problems, they need diverse techniques and a good insight in matching the adequate method to a particular problem. The main question is how to link certain graph properties to understanding and predicting the behaviour of an ecosystem. We wish to contribute to bridging the gap between extreme structural and extreme dynamical views.
Parasites are ubiquitous in ecological communities but it is only recently that they have been ro... more Parasites are ubiquitous in ecological communities but it is only recently that they have been routinely included in food web studies. Using recently published data and the tool of network analysis, we elucidate features associated with the pattern of parasitism in ecological communities. First we show here that parasitism is non-random in food webs. Second we demonstrate that parasite diversity, the number of parasite species harboured by a host species, is related to the network position of a host species. Specifically, a host species with high parasite diversity tends to have a wide diet range, occupy a network position close to many prey species, or occupy a network position that can better accumulate resources from species at lower trophic levels. Lastly our results also suggest that a host species with higher vulnerability to predators, being at a network position close to many predatory species, or being involved in many different food chains, tends to be important in parasite transmission.
Plant-derived natural products have important functions in ecological interactions. In some cases... more Plant-derived natural products have important functions in ecological interactions. In some cases these compounds are deployed to sites of pathogen challenge by vesicle-mediated trafficking. Polar vesicle trafficking of natural products, proteins and other, as yet uncharacterized, cargo is emerging as a common theme in investigations of diverse disease resistance mechanisms in plants. Root-derived natural products can have marked effects on interactions between plants and soilborne organisms, for example by serving as signals for initiation of symbioses with rhizobia and mycorrhizal fungi. They may also contribute to competitiveness of invasive plant species by inhibiting the growth of neighbouring plants (allelopathy). Very little is known about the mechanisms of release of natural products from aerial plant parts or from roots, although there are likely to be commonalities in these processes. There is increasing evidence to indicate that pathogens and symbionts can manipulate plant endomembrane systems to suppress host defence responses and facilitate accommodation within plant cells. The relationship between secretory processes and plant interactions forms the focus of this review, which brings together different aspects of the deployment of defence-related natural products by plants.
Recent investigations on the structure of complex networks have provided interesting results for ... more Recent investigations on the structure of complex networks have provided interesting results for ecologists. Being inspired by these studies, we analyse a well-defined set of small model food webs. The extinction probability caused by internal Lotka-Volterra dynamics is compared to the position of species. Simulations have revealed that some global properties of these food webs (e.g. the homogeneity of connectedness) and the positions of species therein (e.g. interaction pattern) make them prone to modelled biotic extinction caused by population dynamical effects. We found that: (a) homogeneity in the connectedness structure increases the probability of extinction events; (b) in addition to the number of interactions, their orientations also influence the future of species in a web. Since species in characteristic network positions are prone to extinction, results could also be interpreted as describing the properties of preferred states of food webs during community assembly. Our results may contribute to understanding the intimate relationship between pattern and process in ecology.
One of the main concerns of shrimp fisheries is the associated impact on ecosystem biodiversity, ... more One of the main concerns of shrimp fisheries is the associated impact on ecosystem biodiversity, particularly on fish assemblages that are poorly characterized yet likely very relevant to the health of the ecosystem. The continental shelf along the eastern coast of the mouth of the Gulf of California is a region of high biodiversity that harbors highly productive fisheries. This study aimed to analyze the changes in the soft bottom fish assemblages caught as bycatch in the shrimp fishery located in this region. Sampling was conducted with commercial trawls at 16 fixed stations during the 2006-2007 shrimp-fishing season. A total of 103 fish species from 80 genera and 47 families were collected. The ecological and taxonomic diversity as well as the composition and abundance of the fish community caught as bycatch in the shrimp trawl fishery were found to be significantly different in the autumn and winter. Ordination and similarity analyses also revealed differing patterns. Species abundance was strongly associated with sea bottom temperature, depth and latitude. The effects of these abiotic variables on the observed diversity patterns and the possible influences of the fishery are discussed.
We present a simple language tool, CoSBiLab LIME, for building ecosystem models for stochastic dy... more We present a simple language tool, CoSBiLab LIME, for building ecosystem models for stochastic dynamic simulation. The LIME language allows the user to give a biologically intuitive model description in a narrative style. After performing static analysis on the model structure, the software tool translates the model description into the BlenX programming language for stochastic dynamical simulation. These features facilitate the analysis of parallel, multiple ecological interactions in metacommunities. The software tool thus allows ecologists with no programming background to perform quite complicated, process-algebra-based simulations.
The development of approaches to estimate the vulnerability of biological communities and ecosyst... more The development of approaches to estimate the vulnerability of biological communities and ecosystems to extirpations and reductions of species is a central challenge of conservation biology. One key aim of this challenge is to develop quantitative approaches to estimate and rank interaction strengths and keystoneness of species and functional groups, i.e. to quantify the relative importance of species. Network analysis can be a powerful tool for this because certain structural aspects of ecological networks are good indicators of the mechanisms that maintain co-evolved, biotic interactions. A static view of ecological networks would lead us to focus research on highly-central species in food webs (topological key players in ecosystems). There are a variety of centrality indices, developed for several types of ecological networks (e.g. for weighted and un-weighted webs). However, truly understanding extinction and its community-wide effects requires the use of dynamic models. Deterministic dynamic models are feasible when population sizes are sufficiently large to minimize noise in the overall system. In models with small population sizes, stochasticity can be modelled explicitly. We present a stochastic simulation-based ecosystem model for identification of "dynamic key species" in situations where stochastic models are appropriate. To demonstrate this approach, we simulated ecosystem dynamics and performed sensitivity analysis using data from the Prince William Sound, Alaska ecosystem model. We then compare these results to those of purely topological analyses and deterministic dynamic (Ecosim) studies. We present the relationships between various topological and dynamic indices and discuss their biological relevance. The trophic group with the largest effect on others is nearshore demersals, the species mostly sensitive to others is halibut, and the group of both considerable effect on and sensitivity to others is juvenile herring. The most important trophic groups in our dynamical simulations appear to have intermediate trophic levels.
Twenty-five model food webs can be designed from five points (species) and five links (trophic in... more Twenty-five model food webs can be designed from five points (species) and five links (trophic interactions), if they contain a single top-predator (i.e. sink webs). According to a simple topological approach, we presented elsewhere a reliability theoretical analysis of this set of food web graphs. The question addressed here is how network flow reliability is related to the dynamical behavior and stability of these 'model communities'. We simulated the behavior of these webs and calculated their persistence, according to four models: (1) with symmetrical interaction coefficients between species; (2) with asymmetrical interaction coefficients and lower death rates for predators; and (3) with absolutely and (4) relatively perturbed, formerly persistent parameter sets of the asymmetrical model. We used both Lotka Á/Volterra (LV) and Holling II-type equations (with switching effect). Thus, we had eight persistence values for each web. Persistence (a dynamical property) and flow reliability (a structural property) were analyzed. We found that (1) reliable flow pattern is associated with high persistence in the Holling models, while the LV models predict no consistent correlations; (2) in asymmetrical situations, persistence is always much higher (in both LV and Holling models); and (3) the predictions of Holling models (versus LV models) are much less sensitive to local perturbations. Based on these results, we conclude that (1) reliable network flows can contribute to persistence only if switching is possible; (2) asymmetrical interactions increase persistence, independently of the switching effect but it indicates persistence in Holling II model; (3) switching makes the relationship much more predictable between structure and dynamics. Thus, the network design is less useful predictor of persistence without switching effect but well can ensure dynamical stability under the conditions of the Holling II model. We have presented how various dynamical models predict different behavior of modelled communities characterized by the same structure and complexity. Complementing dynamical with structural analysis may further increase our understanding of persistence in food webs. #
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Papers by Ferenc Jordán