Community assembly: alternative stable states or alternative transient states?

The concept of alternative stable states has long been a dominant framework for studying the influence of historical contingency in community assembly. This concept focuses on stable states, yet many real communities are kept in a transient state by disturbance, and the utility of predictions for stable states in explaining transient states remains unclear. Using a simple model of plant community assembly, we show that the conditions under which historical contingency affects community assembly can differ greatly for stable versus transient states. Differences arise because the contribution of such factors as mortality rate, environmental heterogeneity and plant-soil feedback to historical contingency changes as community assembly proceeds. We also show that transient states can last for a long time relative to immigration rate and generation time. These results argue for a conceptual shift of focus from alternative stable states to alternative transient states for understanding historical contingency in community assembly.     

Alternative (un)stable states in a stochastic predator–prey model

Stochastic models sometimes behave qualitatively differently from their deterministic analogues. We explore the implications of this in ecosystems that shift suddenly from one state to another. This phenomenon is usually studied through deterministic models with multiple stable equilibria under a single set of conditions, with stability defined through linear stability analysis. However, in stochastic systems, some unstable states can trap stochastic dynamics for long intervals, essentially masquerading as additional stable states. Using a predator–prey model, we demonstrate that this effect is sufficient to make a stochastic system with one stable state exhibit the same characteristics as an analogous system with alternative stable states. Although this result is surprising with respect to how stability is defined by standard analyses, we show that it is well-anticipated by an alternative approach based on the system's “quasi-potential.” Broadly, understanding the risk of sudden state shifts will require a more holistic understanding of stability in stochastic systems.     

Does crossover interference count in Saccharomyces cerevisiae?

We previously proposed a "counting model" for meiotic crossover interference, in which double-strand breaks occur independently and a fixed number of noncrossovers occur between neighboring crossovers. Whereas in some organisms (group I) this simple model alone describes the crossover distribution, in other organisms (group II) an additional assumption--that some crossovers lack interference--improves the fit. Other differences exist between the groups: Group II needs double-strand breaks and some repair functions to achieve synapsis, while repair in group I generally occurs after synapsis is achieved; group II, but not group I, has recombination proteins Dmc1, Mnd1, and Hop2. Here we report experiments in msh4 mutants that are designed to test predictions of the revised model in a group II organism. Further, we interpret these experiments, the above-mentioned differences between group I and II meiosis, and other data to yield the following proposal: Group II organisms use the repair of leptotene breaks to promote synapsis by generating double-Holliday-junction intermediates that lock homologs together (pairing pathway). The possible crossover or noncrossover resolution products of these structures lack interference. In contrast, for both group I and group II, repair during pachytene (disjunction pathway) is associated with interference and generates only two resolution types, whose structures suggest that the Holliday junctions of the repair intermediates are unligated. A crossover arises when such an intermediate is stabilized by a protein that prevents its default resolution to a noncrossover. The protein-binding pattern required for interference depends on clustering of sites that have received, or are normally about to receive, meiotic double-strand breaks.     

Does mutual interference always stabilize predator–prey dynamics? A comparison of models

Based on a qualitative analysis of ODE systems, the dynamic properties of alternative predator-prey models with predator-dependent functional response have been compared in order to study the role that predator interference plays in the stabilisation of trophic systems. The models considered for interference have different mathematical expressions and different conceptual foundations. Despite these differences, they give essentially the same qualitative results: when interference is low, increasing it has a positive effect on asymptotic stability and thus on the resilience of the biological system. When it is high, it is the contrary (with logistic prey growth, increasing the interference parameter ensures stability but leads to very small predator densities). Possible consequences on the evolution of the interference level in real ecosystems are discussed.     

Are systems with strong underlying abiotic regimes more likely to exhibit alternative stable states?

Suding et al. (2004) demonstrate how conceptual advances in alternative ecosystem states theory have led to a greater understanding of why degraded systems are often resilient to restoration management. In their review they pose one (of several) ‘outstanding’ questions (Box 3 in Suding et al. 2004 ): “Are there predictable characteristics that indicate when a system will follow a successional pathway and/or that indicate the presence or absence of alternative ecosystem states?” We suggest that the persistence of alternative stable states might be predicted from simple consideration of assembly rules for systems structured along a gradient of environmental adversity. We raise the hypothesis that strongly abiotically‐ or disturbance‐structured assemblages, with nonrandom trait under‐dispersion ( Weiher and Keddy 1995 ), are more likely to exhibit catastrophic phase shifts in community structure than assemblages which are weakly structured by environmental adversity.     

Alternative stable states in host–phage dynamics

Bacteriophage are ubiquitous in nature, yet many central aspects of host–phage biology have not been integrated into mathematical models. We propose a novel model of host–phage population dynamics that accounts for the decreased ability of phages to lyse hosts as hosts approach their carrying capacity. In contrast to existing predator–prey-like models, we find a parameter regime in which phages cannot invade a host-only system but, nonetheless, can stably coexist with hosts at lower densities. The finding of alternative stable states suggests clear linkages with observed life history strategies of phages. In addition, we solve a limiting case of the proposed model and show that conservative predator-prey like systems do not inevitably exhibit population cycles. Finally, we discuss possible extensions of the present model and scenarios for experimental testing.     

Does aneuploidy cause cancer?

Aneuploidy has been recognized as a common characteristic of cancer cells for >100 years. Aneuploidy frequently results from errors of the mitotic checkpoint, the major cell cycle control mechanism that acts to prevent chromosome missegregation. The mitotic checkpoint is often compromised in human tumors, although not as a result of germline mutations in genes encoding checkpoint proteins. Less obviously, aneuploidy of whole chromosomes rapidly results from mutations in genes encoding several tumor suppressors and DNA mismatch repair proteins, suggesting cooperation between mechanisms of tumorigenesis that were previously thought to act independently. Cumulatively, the current evidence suggests that aneuploidy promotes tumorigenesis, at least at low frequency, but a definitive test has not yet been reported.     

Does species diversity limit productivity in natural grassland communities?

Theoretical analyses and experimental studies of synthesized assemblages indicate that under particular circumstances species diversity can enhance community productivity through niche complementarity. It remains unclear whether this process has important effects in mature natural ecosystems where competitive feedbacks and complex environmental influences affect diversity–productivity relationships. In this study, we evaluated diversity–productivity relationships while statistically controlling for environmental influences in 12 natural grassland ecosystems. Because diversity–productivity relationships are conspicuously nonlinear, we developed a nonlinear structural equation modeling (SEM) methodology to separate the effects of diversity on productivity from the effects of productivity on diversity. Meta-analysis was used to summarize the SEM findings across studies. While competitive effects were readily detected, enhancement of production by diversity was not. These results suggest that the influence of small-scale diversity on productivity in mature natural systems is a weak force, both in absolute terms and relative to the effects of other controls on productivity.     

Revealing the role of predator interference in a predator–prey system with disease in prey population

Predation on a species subjected to an infectious disease can affect both the infection level and the population dynamics. There is an ongoing debate about the act of managing disease in natural populations through predation. Recent theoretical and empirical evidence shows that predation on infected populations can have both positive and negative influences on disease in prey populations. Here, we present a predator–prey system where the prey population is subjected to an infectious disease to explore the impact of predator on disease dynamics. Specifically, we investigate how the interference among predators affects the dynamics and structure of the predator–prey community. We perform a detailed numerical bifurcation analysis and find an unusually large variety of complex dynamics, such as, bistability, torus and chaos, in the presence of predators. We show that, depending on the strength of interference among predators, predators enhance or control disease outbreaks and population persistence. Moreover, the presence of multistable regimes makes the system very sensitive to perturbations and facilitates a number of regime shifts. Since, the habitat structure and the choice of predators deeply influence the interference among predators, thus before applying predators to control disease in prey populations or applying predator control strategy for wildlife management, it is essential to carefully investigate how these predators interact with each other in that specific habitat; otherwise it may lead to ecological disaster.     

Does forest fragmentation cause an increase in forest temperature?

Forest fragmentation is considered by many to be a primary cause of the current biodiversity crisis. The underlying mechanisms are poorly known, but a potentially important one is associated with altered thermal conditions within the remaining forest patches, especially at forest edges. Yet, large uncertainty remains about the effect of fragmentation on forest temperature, as it is unclear whether temperature decreases from forest edge to forest interior, and whether this local gradient scales up to an effect of fragmentation (landscape attribute) on temperature. We calculated the effect size (correlation coefficient) of distance from forest edge on air temperature, and tested for differences among forest types surrounded by different matrices using meta-analysis techniques. We found a negative edge-interior temperature gradient, but correlation coefficients were highly variable, and significant only for temperate and tropical forests surrounded by a highly contrasting open matrix. Nevertheless, it is unclear if these local-scale changes in temperature can be scaled up to an effect of fragmentation on temperature. Although it may be valid when considering “fragmentation” as forest loss only, the landscape-scale inference is not so clear when we consider the second aspect of fragmentation, where a given amount of forest is divided into a large number of small patches (fragmentation per se). Therefore, care is needed when assuming that fragmentation changes forest temperature, as thermal changes at forest edges depend on forest type and matrix composition, and it is still uncertain if this local gradient can be scaled up to the landscape.     

Does distance matter? Variations in alternative 3′ splicing regulation

Alternative splicing constitutes a major mechanism creating protein diversity in humans. This diversity can result from the alternative skipping of entire exons or by alternative selection of the 5′ or 3′ splice sites that define the exon boundaries. In this study, we analyze the sequence and evolutionary characteristics of alternative 3′ splice sites conserved between human and mouse genomes for distances ranging from 3 to 100 nucleotides. We show that alternative splicing events can be distinguished from constitutive splicing by a combination of properties which vary depending on the distance between the splice sites. Among the unique features of alternative 3′ splice sites, we observed an unexpectedly high occurrence of events in which a polypyrimidine tract was found to overlap the upstream splice site. By applying a machine-learning approach, we show that we can successfully discriminate true alternative 3′ splice sites from constitutive 3′ splice sites. Finally, we propose that the unique features of the intron flanking alternative splice sites are indicative of a regulatory mechanism that is involved in splice site selection. We postulate that the process of splice site selection is influenced by the distance between the competitive splice sites.     

Does streptomycin cause an error catastrophe?

We have examined the interpretation that streptomycin kills a bacterial culture by initiating the so-called error catastrophe. In particular, we asked whether the increased translational error rate induced by the antibiotic gives rise to an autocatalytic loss of functional fidelity of the devices responsible for gene expression, which ultimately causes the death of the culture. We have analyzed the performance characteristics of one of these devices, namely the ribosome in streptomycin-treated bacteria. We find that, although the treated ribosomes are constructed from error-containing proteins, they are not significantly different in elongation rate and fidelity from those ribosomes taken from untreated bacteria. We conclude that the bacteriocidal effect of streptomycin is not due to the initiation of an error catastrophe.     

Does chromosome size affect map distance and genetic interference in budding yeast?

The hypothesis that chromosome size affects the rate and distribution of meiotic crossovers in budding yeast was tested. Map distance and interference were measured in the same genetic intervals present on either small (340 and 508 kb) or large (917 and 1085 kb) chromosomes, respectively. No differences were observed.     

Does phosphorus limitation promote species-rich plant communities?

It is known that the number of limiting nutrients may affect the species richness of plant communities, but it is unclear whether the type of nutrient limitation is also important. I place the results from a study in Patagonia (elsewhere in this issue) in the context of the number and types of nutrients that are limiting. I present four mechanisms through which N or P limitation may potentially influence species richness. These mechanisms are related to: (i) the number of forms in which P or N are present in soil and the plant traits needed to acquire them, (ii) the mechanisms and traits that control species competition and coexistence under N or P limitation, (iii) the regional species pools of plants capable of growing under N- and P-limited conditions, and (iv) the interaction between the type of nutrient limitation and community productivity. It appears likely that P limitation can favour a higher species richness than N limitation, in at least in a variety of low productive plant communities, but evidence to support this conclusion is so far lacking. The four mechanisms proposed here offer a framework for exploring whether the type of nutrient limitation per se, or an interaction with productivity, is a potential driver for variation in species diversity.     

An ecological perspective of allelochemical interference in land–water interface communities

Allelochemical interactions among aquatic macrophytes and between macrophytes and attached microbial assemblages (epiphyton) influence a number of ecological processes. The ecological importance of these interactions, however, is poorly understood; we hypothesize that paucity has resulted, in part, from (1) a narrow focus on exploration for herbicidal plant products from aquatic macrophytes, (2) the difficulties in distinguishing resource competition from allelopathic interference, and (3) a predominance of approaching aquatic allelopathy from a terrestrial perspective. Based upon recent thorough investigations of allelopathy among aquatic vascular plants, chemical compounds that influence competitive interactions among littoral organisms are amphiphilic compounds that tend to remain near the producing organism (e.g., polyphenolic compounds and volatile fatty acids). Production of these compounds may be influenced by relative availability of nutrients (particularly phosphorus and nitrogen), inorganic carbon, and light. Macrophyte strategies of clonal reproduction, in an effort to persist in these highly productive and competitive habitats, have contributed to reduced reliance upon sexual reproduction that is correlated with allelopathic autotoxicity among several dominant wetland plant species. Although few studies document the importance of allelochemical interactions in the wetland and littoral zones of aquatic ecosystems, abundant evidence supports the potential for significant effects on competition and community structure; effects of altered nutrient ratios and availability on plant chemical composition; and resultant effects on trophic interactions, particularly suppression of herbivory, competitive attached algae and cyanobacteria, and heterotrophic utilization of organic matter by bacteria and fungi.     

Does the alternative pathway ameliorate chilling injury in sensitive plant tissues?

Free radical processes have been observed in senescence and several membrane-associated disorders of plants including chilling, freezing, and desiccation injuries. The mitochondria of plant tissues exposed to low temperatures, and other abiotic and biotic stresses, produce superoxide and/or hydrogen peroxide when electron transport through the cytochrome pathway is impaired due to the energy state of the cell or to stress-induced physical changes in the membrane components. The superoxide and/or hydrogen peroxide produced can diffuse throughout the cell causing peroxidation of membrane lipids which results in membrane disruption, increased permeability and metabolic disturbances, and eventually the visible symptoms of chilling injury. The alternative pathway of electron transport in the mitochondria, which is induced by low temperatures in some plant tissues, can mediate these degradative processes by reducing the level of superoxide generated by the mitochondria.     

Analysis of stable states in global savannas: is the CART pulling the horse?

Multiple stable states, bifurcations and thresholds are fashionable concepts in the ecological literature, a recognition that complex ecosystems may at times exhibit the interesting dynamic behaviours predicted by relatively simple biomathematical models. Recently, several papers in Global Ecology and Biogeography, Proceedings of the National Academy of Sciences USA, Science and elsewhere have attempted to quantify the prevalence of alternate stable states in the savannas of Africa, Australia and South America, and the tundra–taiga–grassland transitions of the circum‐boreal region using satellite‐derived woody canopy cover. While we agree with the logic that basins of attraction can be inferred from the relative frequencies of ecosystem states observed in space and time, we caution that the statistical methodologies underlying the satellite product used in these studies may confound our ability to infer the presence of multiple stable states. We demonstrate this point using a uniformly distributed ‘pseudo‐tree cover’ database for Africa that we use to retrace the steps involved in creation of the satellite tree‐cover product and subsequent analysis. We show how classification and regression tree (CART)‐based products may impose discontinuities in satellite tree‐cover estimates even when such discontinuities are not present in reality. As regional and global remote sensing and geospatial data become more easily accessible for ecological studies, we recommend careful consideration of how error distributions in remote sensing products may interact with the data needs and theoretical expectations of the ecological process under study.