Competition between unit-restricted fungi: a metapopulation model

We aimed to provide a theoretical framework for dynamic studies of competition between fungi living on divided and ephemeral resources. We previously adapted the seminal Skellam's patch-occupancy model (Skellam, 1951) to describe the population dynamics of one species of unit-restricted fungus whose mycelial growth occurs within resource units and which colonizes new resource units by spore dispersal (Gourbiere et al., 1999). In this study, we extended this model to describe the competition between a pair of unit-restricted fungal species that interact with each other inside units by decreasing their spore production. Accordingly, we designed a discrete-time metapopulation model where all patches go extinct at each generation and species interact by lowering their propagule production in jointly occupied patches. We showed that the two species easily coexist although there is no trade-off between their competitive and colonization abilities. Furthermore, the outcome of the competition process can depend on a founder effect. Founder effect determines either which species is excluded or the relative densities of each species when they coexist. We investigated the implications of these results on the distribution and abundance of fungal species along environmental gradients. This work bridges the gap between the mycological theory of "Resource Units" and the metapopulation theory, showing the specificity of fungal exploitation competition. We suggest that unit-restricted fungal species are appropriate biological models to test the theoretical results of the metapopulation theory, such as the appearance of alternative stable equilibria.     

Detecting local adaptation in a natural plant-pathogen metapopulation: a laboratory vs. field transplant approach

Antagonistic coevolution between hosts and parasites in spatially structured populations can result in local adaptation of parasites. Traditionally parasite local adaptation has been investigated in field transplant experiments or in the laboratory under a constant environment. Despite the conceptual importance of local adaptation in studies of (co)evolution, to date no study has provided a comparative analysis of these two methods. Here, using information on pathogen population dynamics, I tested local adaptation of the specialist phytopathogen, Podosphaera plantaginis, to its host, Plantago lanceolata at three different spatial scales: sympatric host population, sympatric host metapopulation and allopatric host metapopulations. The experiment was carried out as a field transplant experiment with greenhouse-reared host plants from these three different origins introduced into four pathogen populations. In contrast to results of an earlier study performed with these same host and parasite populations under laboratory conditions, I did not find any evidence for parasite local adaptation. For interactions governed by strain-specific resistance, field studies may not be sensitive enough to detect mean parasite population virulence. Given that parasite transmission potential may be mediated by the abiotic environment and genotype-by-environment interactions, I suggest that relevant environmental variation should be incorporated into laboratory studies of parasite local adaptation.     

Allele fixation in a dynamic metapopulation: Founder effects vs refuge effects

The fixation of mutant alleles has been studied with models assuming various spatial population structures. In these models, the structure of the metapopulation that we call the “landscape” (number, size and connectivity of subpopulations) is often static. However, natural populations are subject to repetitive population size variations, fragmentation and secondary contacts at different spatiotemporal scales due to geological, climatic and ecological processes. In this paper, we examine how such dynamic landscapes can alter mutant fixation probability and time to fixation. We consider three stochastic landscape dynamics: (i) the population is subject to repetitive bottlenecks, (ii) to the repeated alternation of fragmentation and fusion of demes with a constant population carrying capacity, (iii) idem with a variable carrying capacity. We show by deriving a variance, a coalescent and a harmonic mean population effective size, and with simulations that these landscape dynamics generate repetitive founder effects which counteract selection, thereby decreasing the fixation probability of an advantageous mutant but accelerate fixation when it occurs. For models (ii) and (iii), we also highlight an antagonistic “refuge effect” which can strongly delay mutant fixation. The predominance of either founder effects or refuge effects determines the time to fixation and mainly depends on the characteristic time scales of the landscape dynamics.     

A tale of two oxidation states: bacterial colonization of arsenic-rich environments

Microbial biotransformations have a major impact on contamination by toxic elements, which threatens public health in developing and industrial countries. Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society. Although this metalloid is ubiquitous on Earth, thus far no bacterium thriving in arsenic-contaminated environments has been fully characterized. In-depth exploration of the genome of the β-proteobacterium Herminiimonas arsenicoxydans with regard to physiology, genetics, and proteomics, revealed that it possesses heretofore unsuspected mechanisms for coping with arsenic. Aside from multiple biochemical processes such as arsenic oxidation, reduction, and efflux, H. arsenicoxydans also exhibits positive chemotaxis and motility towards arsenic and metalloid scavenging by exopolysaccharides. These observations demonstrate the existence of a novel strategy to efficiently colonize arsenic-rich environments, which extends beyond oxidoreduction reactions. Such a microbial mechanism of detoxification, which is possibly exploitable for bioremediation applications of contaminated sites, may have played a crucial role in the occupation of ancient ecological niches on earth.     

A new approach for designing disease intervention strategies in metapopulation models

We describe a new approach for investigating the control strategies of compartmental disease transmission models. The method rests on the construction of various alternative next-generation matrices, and makes use of the type reproduction number and the target reproduction number. A general metapopulation SIRS (susceptible–infected–recovered–susceptible) model is given to illustrate the application of the method. Such model is useful to study a wide variety of diseases where the population is distributed over geographically separated regions. Considering various control measures such as vaccination, social distancing, and travel restrictions, the procedure allows us to precisely describe in terms of the model parameters, how control methods should be implemented in the SIRS model to ensure disease elimination. In particular, we characterize cases where changing only the travel rates between the regions is sufficient to prevent an outbreak.     

Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine

Chloroplast microsatellites are becoming increasingly popular markers for population genetic studies in plants, but there has been little focus on their potential for demographic inference. In this work the utility of chloroplast microsatellites for the study of population expansions was explored. First, we investigated the power of mismatch distribution analysis and the F(S) test with coalescent simulations of different demographic scenarios. We then applied these methods to empirical data obtained for the Canary Island pine (Pinus canariensis). The results of the simulations showed that chloroplast microsatellites are sensitive to sudden population growth. The power of the F(S) test and accuracy of demographic parameter estimates, such as the time of expansion, were reduced proportionally to the level of homoplasy within the data. The analysis of Canary Island pine chloroplast microsatellite data indicated population expansions for almost all sample localities. Demographic expansions at the island level can be explained by the colonization of the archipelago by the pine, while population expansions of different ages in different localities within an island could be the result of local extinctions and recolonization dynamics. Comparable mitochondrial DNA sequence data from a parasite of P. canariensis, the weevil Brachyderes rugatus, supports this scenario, suggesting a key role for volcanism in the evolution of pine forest communities in the Canary Islands.     

Competition between n-alkane-assimilating yeasts and bacteria during colonization of sandy soil microcosms

An n-alkane-assimilating strain of Candida tropicalis was selected in sandy soil inoculated with microorganisms from contaminated sites. Competition experiments with n-alkane utilizers from different strain collections confirmed that yeasts overgrow bacteria in sandy soil. Acidification of the soil is one of the colonization factors useful for the yeasts. It can be counteracted by addition of bentonite, a clay mineral with high ion exchange capacity, but not, however, by kaolin. Strains of different yeast species showed different levels of competitiveness. Strains of Arxula adeninivorans, Candida maltosa, and Yarrowia lipolytica overgrew strains of C. tropicalis, C. shehatae or Pichia stipitis. Two strains of C. maltosa and Y. lipolytica coexisted during several serial transfers under microcosm conditions. Received: 20 October 1999 / Received revision: 26 January 2000 / Accepted: 27 January 2000     

A novel approach to investigate hypoxic microenvironment during rice colonization by Magnaporthe oryzae

Because molecular oxygen functions as the final acceptor of electrons during aerobic respiration and a substrate for diverse enzymatic reactions, eukaryotes employ various mechanisms to maintain cellular homeostasis under varying oxygen concentration. Human fungal pathogens change the expression of genes involved in virulence and oxygen-required metabolisms such as ergosterol (ERG) synthesis when they encounter oxygen limitation (hypoxia) during infection. The oxygen level in plant tissues also fluctuates, potentially creating hypoxic stress to pathogens during infection. However, little is known about how in planta oxygen dynamics impact pathogenesis. In this study, we investigated oxygen dynamics in rice during infection by Magnaporthe oryzae via two approaches. First, rice leaves infected by M. oryzae were noninvasively probed using a microscopic oxygen sensor. Second, an immunofluorescence assay based on a chemical probe, pimonidazole, was used. Both methods showed that oxygen concentration in rice decreased after fungal penetration. We also functionally characterized five hypoxia-responsive genes participating in ERG biosynthesis for their role in pathogenesis. Resulting insights and tools will help study the nature of in planta oxygen dynamics in other pathosystems.     

Competition in variable environments: experiments with planktonic rotifers

1. In a constant environment, competition often tends to reduce species diversity. However, several theories predict that temporal variation in the environment can slow competitive exclusion and allow competing species to coexist. This study reports on laboratory competition experiments in which two pairs of planktonic rotifer species competed for a phytoplankton resource under different conditions of temporal variability in resource supply.
2. For both species pairs, Keratella cochlearis dominated under all conditions of temporal variability, and the other species ( Brachionus calyciflorus or Synchaeta sp.) almost always went extinct. Increasing temporal variation in resource supply slowed competitive exclusion but did not change competitive outcome or allow coexistence.
3. Rotifers show a gleaner–opportunist trade-off, because gleaner species have low threshold resource levels ( R *) and low maximum population growth rates, while opportunist species have the opposite characteristics. In the competition experiments, the gleaner always won and the opportunists always lost. Thus, a gleaner–opportunist trade-off was not sufficient to facilitate coexistence under conditions of resource variability. Instead, the winning species had both the lowest R * and the greatest ability to store resources and ration their use during times of extreme resource scarcity.     

Competition and coexistence in plant communities: intraspecific competition is stronger than interspecific competition

Theory predicts that intraspecific competition should be stronger than interspecific competition for any pair of stably coexisting species, yet previous literature reviews found little support for this pattern. We screened over 5400 publications and identified 39 studies that quantified phenomenological intraspecific and interspecific interactions in terrestrial plant communities. Of the 67% of species pairs in which both intra‐ and interspecific effects were negative (competitive), intraspecific competition was, on average, four to five‐fold stronger than interspecific competition. Of the remaining pairs, 93% featured intraspecific competition and interspecific facilitation, a situation that stabilises coexistence. The difference between intra‐ and interspecific effects tended to be larger in observational than experimental data sets, in field than greenhouse studies, and in studies that quantified population growth over the full life cycle rather than single fitness components. Our results imply that processes promoting stable coexistence at local scales are common and consequential across terrestrial plant communities.     

A hierarchical deductive approach for functional types in disturbed ecosystems

Abstract. We propose a hierarchical approach for plant functional classification in disturbed ecosystems to be used for vegetation modelling and global plant trait comparisons. Our framework is based on the persistence of plants at different levels of organization. We assume that the main parameters to determine persistence in chronically disturbed ecosystems are those related to: I ndividual‐persistence capacity, P ropagule‐persistence capacity (persistence at the population level), C ompetitive capacity (persistence at the community level) and D ispersal capacity (persistence at the landscape level). The IPCD approach is illustrated for fire‐prone and grazed ecosystems from the Mediterranean region and Australia and by assuming a binary classification of the four traits determining persistence which give a total 16 possible functional types. The IPCD framework provides a simple structured and synthetic view from which more elaborated schemes can be developed.     

Models on prebiotic polymer competition: A deterministic approach

Two simple models are proposed and analysed, in which it is shown that the formation of a new polymer, resulting from an “error” in the template action mechanism of production of an old polymer, may compromise the stability of the initial system under specific conditions, in the context of prebiotic evolution. Autocatalysis is shown to be a “selective advantage”, enabling the “mutant” to dominate in concentration and even replace the initial polymer. The addition of a third molecule playing the role of a catalyst causes hysteresis effects.     

A metapopulation paradox: partial improvement of habitat may reduce metapopulation persistence

The adverse influence of habitat degradation on the survival of populations may sometimes be amplified by rapid evolution over ecological timescales. This phenomenon of evolutionary suicide has been described in theoretical as well as empirical studies. However, no studies have suggested that habitat improvement could possibly also trigger an evolutionary response that would result in a decline in population size. We use individual-based simulations to demonstrate the potential for such a paradoxical response. An increase in the quality, size, or stability of only a fraction of the habitat patches in a metapopulation may result in an evolutionary decline in the dispersal propensity of individuals, followed by a decrease in recolonization, a reduction in the number of patches occupied, a decline in overall population size, and even extinction. Thus, well-intended conservation efforts that ignore potential evolutionary consequences of habitat management may increase the extinction risk of populations.     

A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation

Dendritic metapopulations have been attributed unique properties by in silico studies, including an elevated genetic diversity relative to a panmictic population of equal total size. These predictions have not been rigorously tested in nature, nor has there been full consideration of the interacting effects among contemporary landscape features, colonization history and life history traits of the target species. We tested for the effects of dendritic structure as well as the relative importance of life history, environmental barriers and historical colonization on the neutral genetic structure of a longnose sucker (Catostomus catostomus) metapopulation in the Kogaluk watershed of northern Labrador, Canada. Samples were collected from eight lakes, genotyped with 17 microsatellites, and aged using opercula. Lakes varied in differentiation, historical and contemporary connectivity, and life history traits. Isolation by distance was detected only by removing two highly genetically differentiated lakes, suggesting a lack of migration–drift equilibrium and the lingering influence of historical factors on genetic structure. Bayesian analyses supported colonization via the Kogaluk's headwaters. The historical concentration of genetic diversity in headwaters inferred by this result was supported by high historical and contemporary effective sizes of the headwater lake, T‐Bone. Alternatively, reduced allelic richness in headwaters confirmed the dendritic structure's influence on gene flow, but this did not translate to an elevated metapopulation effective size. A lack of equilibrium and upstream migration may have dampened the effects of dendritic structure. We suggest that interacting historical and contemporary factors prevent the achievement of the idealized traits of a dendritic metapopulation in nature.     

Pathogen evolution in switching environments: A hybrid dynamical system approach

We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a version of the Fisher-Haldane-Wright equation while the switching between environments follows a Markov jump process. We investigate how the qualitative behavior of a simple single-host deterministic system changes when the stochastic switching process is added. In particular, we study the stability in probability of monomorphic equilibria. We prove that in a "constantly" fluctuating environment, the genotype with the highest mean fitness is asymptotically stable in probability while all others are unstable in probability. However, if the probability of host switching depends on the genotype composition of the population, polymorphism can be stably maintained.     

Competition systems with periodic coefficients: A geometric approach

The classical two-species competition system is modified to include coefficients which are time-periodic with the same period. We show first that all (nonnegative) solutions converge to a periodic one, having the same period, thus excluding subharmonics. The global structure of the set of all periodic solutions is then investigated. This is accomplished by developing a geometric theory of the discrete dynamical system defined by the iterates of the period map T. It turns out, in particular, that periodic solutions appear which have no counterpart in the corresponding time-averaged system: thus oscillations in the environment may cause the two species to coexist in an oscillatory regime even if the corresponding averaged system would force either of the two species to extinction.     

Competition and species packing in patchy environments

In models of competition in which space is treated as a continuum, and population size as continuous, there are no limits to the number of species that can coexist. For a finite number of sites, N, the results are different. The answer will, of course, depend on the model used to ask the question. In the Tilman-May-Nowak ordinary differential equation model, the number of species is asymptotically C log N with most species packed in at the upper end of the competitive hierarchy. In contrast, for metapopulation models with discrete individuals and stochastic spatial systems with various competition neighborhoods, we find a traditional species area relationship CN(a), with no species clumping along the phenotypic gradient. The exponent a is larger by a factor of 2 for spatially explicit models. In words, a spatial distribution of competitors allows for greater diversity than a metapopulation model due to the effects of recruitment limitation in their competition.     

Habitat loss alters effects of intransitive higher-order competition on biodiversity: a new metapopulation framework

Recent studies have suggested that intransitive competition, as opposed to hierarchical competition, allows more species to coexist. Furthermore, it is recognized that the prevalent paradigm, which assumes that species interactions are exclusively pairwise, may be insufficient. More importantly, whether and how habitat loss, a key driver of biodiversity loss, can alter these complex competition structures (and therefore species coexistence) remain unclear. We thus present a new, simple yet comprehensive metapopulation framework that can account for any competition pattern and more complex higher-order interactions (HOIs) among species. We find that competitive intransitivity increases community diversity and that HOIs generally enhance this effect. Essentially, intransitivity promotes species richness by preventing the dominance of a few species, unlike the hierarchical competition, while HOIs facilitate species coexistence through stabilizing community fluctuations. However, variation in species’ vital rates and habitat loss can weaken or even reverse such higher-order effects, as their interaction can lead to a more rapid decline in competitive intransitivity under HOIs. Thus, it is essential to correctly identify the most appropriate interaction model for a given system before models are used to inform conservation efforts. Overall, our simple model framework provides a more parsimonious explanation for biodiversity maintenance than the existing theory.