Fate of a mutant emerging at the initial stage of evolution

A simple system was constructed and used in the experimental elucidation of the fate of a mutant emerging in a population. ThreeEscherichia coli strains having the same genetic background except for their glutamine synthetase gene were used as model competitors. The difference in the enzyme gene were introduced by random mutation. Competition between these bacterial strains was carried out and observed in a continuous liquid culture. In most cases, the competitors stably coexist either in a steady state or in an oscillating state. In addition, the competition between the strains was found to be a deterministic process and not a stochastic one. These results showed that an emerging mutant in a population, be it a closely related one to the original members, can attain a state of stable coexistence even in a homogeneous environment. The ability of each of the emerging mutants to maintain its stable coexistence with the original population gives rise to the accumulation of various mutants in a population. Therefore, evolution starts from gradual accumulation of various mutants in the population, which in turn leads to the diversification of the population. As our experimental system is a minimum model for the various competitions in the natural ecosystem, the observed competitive coexistence is proposed to be a general phenomenon in nature.     

How small can the difference among competitors be for coexistence to occur

Closely related competitors comprising ofEscherichia coli strains having the same metabolic system and differing only with a few bases on the glutamine synthetase gene in the plasmid pKGN were previously shown to coexist in a chemostat. The differences among these closely related competitors can be considered large enough to allow coexistence as the level of enzyme activity is different. To bring the difference among competitors to the slightest possible, the mutation was introduced on the noncoding region of the plasmid pKGN harbored in the wild-type strain (strain W). The new strain, strain W’, carries the plasmid pKGN’ with a 4-base insertion at theHind III site in the polycloning site of pKGN. As the noncoding region is a nucleotide segment that is not translated into amino acids, the relatedness between strains W and W’ is the closest possible from the genetic point of view. Interestingly, though both strains are almost identical, they can coexist stably in a chemostat irrespective of the initial population size. These experimental results suggest that in the natural ecosystem, no matter how akin competitors are, coexistence is not impossible.     

Maintenance of clonal diversity in Dipsa bifurcata (Fallén, 1810) (Diptera: Lonchopteridae). I. Fluctuating seasonal selection moulds long-term coexistence

The deterministic maintenance of clonal diversity in thelytokous taxa can be seen as a model for understanding how environmental heterogeneity both can stabilize genetic diversity and can allow coexistence of competing species. We here analyze the temporal fluctuations in clonal diversity in the thelytokous Lonchopterid fly, Dipsa bifurcata (Fallén, 1810), at four localities in Sweden over an 8-year period. Estimated fitness values for clones are cyclical, synchronous among populations and correlated with seasonal changes in the environment. Differential winter viability and emergence from overwintering along with differential reproductive rate during the summer appear to be the selective mechanisms by which long-term clonal diversity is maintained. In a companion paper (Tomiuk et al, 2004), we present a model for the maintenance of clonal diversity through the mechanism of differential diapause among clones, utilizing fitness values estimated from the data presented here. In general, our results imply that fluctuating seasonal fitnesses can maintain stable genetic polymorphism within populations, as well as coexistence between closely related competitors, when coupled with differences in diapause phenology.     

代谢互养关系在维持微生物物种多样性中的作用

互养关系（cross-feeding）是微生物物种之间普遍存在的一种相互关系,其中物种利用环境中其他成员的代谢产物以促进自身生长的情形称为代谢互养关系,这种关系对物种间的竞争结果往往有很大影响,甚至会改变种群结构。为了研究代谢互养关系在维持微生物物种多样性中的作用,构建包含不同代谢互养关系的资源竞争模型,这些模型既体现了微生物物种竞争资源时种群密度及资源量的动态,也展示了物种利用其他竞争者的代谢资源对自身生存状况的影响。数值模拟结果显示：（1）考虑微生物中不同的代谢互养关系结构：两物种间单向互养、双向互养以及多物种间的互养,不同的互养关系都可以促进竞争物种稳定共存,竞争中处于劣势的物种通过利用其他竞争成员的代谢产物,打破外界资源量对其生长的限制,改变原本消亡的命运;而处于优势的物种则通过利用其他竞争成员的代谢产物,增大种群密度。（2）多物种竞争同一种有限资源时,不是所有物种都能共存,在四物种模拟中,原本处于最劣势的物种灭绝,其余三者共存。物种产生代谢资源对其本身是"不利"的,如果在模拟中物种利用代谢资源的能力相同,那么物种竞争外界资源的劣势就很可能无法被抵消。通过改变资源利用率发现只有互养关系中代谢资源的利用可以弥补劣势种在竞争外界资源时的不足,多物种才可以全部共存。（3）验证数值模拟结果的普遍性,分析参数变化对共存的影响,结果表明代谢互养关系促进的共存对代谢资源相关参数不敏感,参数的改变只影响平衡态时物种的种群密度。所以,代谢互养关系可以促进相互竞争的微生物物种共存,即微生物之间的互养关系很可能是维持物种多样性的一种机制。     

Operating parameters' effects on the outcome of pure and simple competition between two populations in configurations of two interconnected chemostats

It is known from the literature that two microbial populations competing purely and simply for a common substrate in a spatially inhomogeneous environment may under certain conditions coexist in a steady state. This paper studies pure and simple competition between two microbial species in three alternate configurations of two interconnected ideal chemostats and focuses on the effects of the operating parameters-dilution rate, substrate concentration in the feed to the vessels, recycle ratio, and volume ratio of the two vessels, splitting ratio of the external feed to the chemostats-on the coexistence of the two competitors. It is shown that the coexistence steady state is practically feasible in the sense that it occurs in a finite domain of the operating parameters space. Theoretical and numerical results are presented, some of them in the form of operating diagrams projected on the two-dimensional subspace. A comparison of the three possible configurations is offered.     

Blood flow and oxygen uptake increase with total power during five different knee-extension contraction rates.

Controversies exist regarding quantification of internal power (IP) generated by the muscles to overcome energy changes of moving body segments when external power (EP) is performed. The aim was to 1) use a kinematic model for estimation of IP during knee extension, 2) validate the model by independent calculation of IP from metabolic variables (IP(met)), and 3) analyze the relationship between total power (TP = EP + IP) and physiological responses. IP increased in a curvilinear manner (5, 7, 13, 21, and 34 W) with contraction rate (45, 60, 75, 90, and 105 contractions/min), but it was independent of EP. Correspondingly, IP(met) was 5, 7, 10, 19, and 28 W, supporting the kinematic model. Heart rate, pulmonary oxygen uptake, and leg blood flow plotted vs. TP fell on the same line independent of contraction rate, and muscular mechanical efficiency as well as delta efficiency remained remarkably constant across contraction rates. It is concluded that the novel metabolic validation of the kinematic model supports the model assumptions, and physiological responses proved to be closely related to TP, supporting the legitimacy of IP estimates.     

Metabolic modeling of Saccharomyces cerevisiae using the optimal control of homeostasis: a cybernetic model definition

A model is presented to describe the observed behavior of microorganisms that aim at metabolic homeostasis while growing and adapting to their environment in an optimal way. The cellular metabolism is seen as a network with a multiple controller system with both feedback and feedforward control, i.e., a model based on a dynamic optimal metabolic control. The dynamic network consists of aggregated pathways, each having a control setpoint for the metabolic states at a given growth rate. This set of strategies of the cell forms a true cybernetic model with a minimal number of assumptions. The cellular strategies and constraints were derived from metabolic flux analysis using an identified, biochemically relevant, stoichiometry matrix derived from experimental data on the cellular composition of continuous cultures of Saccharomyces cerevisiae. Based on these data a cybernetic model was developed to study its dynamic behavior. The growth rate of the cell is determined by the structural compounds and fluxes of compounds related to central metabolism. In contrast to many other cybernetic models, the minimal model does not consist of any assumed internal kinetic parameters or interactions. This necessitates the use of a stepwise integration with an optimization of the fluxes at every time interval. Some examples of the behavior of this model are given with respect to steady states and pulse responses. This model is very suitable for describing semiquantitatively dynamics of global cellular metabolism and may form a useful framework for including structured and more detailed kinetic models.     

Competition and coexistence with multiple life-history stages

Do complex life histories affect the conditions under which competitors can coexist? We investigated this using a two-species, two-stage Ricker model. With complex life cycles, the competition coefficients associated with each life-history stage suggest one of three competitive outcomes-coexistence, alternate stable states, or competitive exclusion-that depend on the relative magnitudes of intraspecific and interspecific competition. When the two stages suggest the same outcome, only that outcome can occur. When the stages suggest different outcomes, either one may prevail. It is also possible to have emergent outcomes, in which the outcome is not suggested by either stage. This can occur when the two stages suggest competitive exclusion by opposite species or when one stage suggests alternate stable states and the other suggests coexistence. Therefore, determining the mechanisms of coexistence in species with complex life histories may require consideration of competitive interactions within all life-history stages.     

Recycling‐mediated facilitation and coexistence based on plant size

We introduce nutrient recycling into a model where competitors differ in the scale at which they perceive their environment. In a two-resource system with both external nutrient inputs and recycling, larger consumers ("integrators") often generate resource distributions that favor their smaller ("nonintegrator") competitors, and vice versa. This occurs because recycling of integrator biomass reduces between-patch resource heterogeneity, whereas recycling of nonintegrator biomass does not. Combined, recycling and throughput can allow coexistence when it is not possible with either alone. With recycling, the presence of an integrator also may facilitate higher biomass of a co-occurring nonintegrator. Our model provides a context where recycling can generate negative feedback between competitors that differ in size and so promote coexistence. This is opposite to the positive recycling-mediated feedback commonly expected on the basis of litter chemistry differences between competitors. Effects of recycling and homogenization on nonintegrators may also be negative in our model, depending on the conformation of the system's resource supply points and the species' relative resource requirements. Our model suggests that the effects of plant size on competitive outcomes may depend critically on the degree of resource recycling found in the system and, reciprocally, that the effects of recycling may depend on plant size.     

Rock-scissors-paper game in a chaotic flow: the effect of dispersion on the cyclic competition of microorganisms

Laboratory experiments and numerical simulations have shown that the outcome of cyclic competition is significantly affected by the spatial distribution of the competitors. Short-range interaction and limited dispersion allows for coexistence of competing species that cannot coexist in a well-mixed environment. In order to elucidate the mechanisms that destroy species diversity we study the intermediate situation of imperfect mixing, typical in aquatic media, in a model of cyclic competition between toxin producing, sensitive and resistant phenotypes. It is found, that chaotic mixing, by changing the character of the spatial distribution, induces coherent oscillations in the populations. The magnitude of the oscillations increases with the strength of mixing, leading to the extinction of some species beyond a critical mixing rate. When mixing is non-uniform in space, coexistence can be sustained at much stronger mixing by the formation of partially isolated regions, that prevent global extinction. The heterogeneity of mixing may enable toxin producing and sensitive strains to coexist for very long time at strong mixing.     

A biochemically structured model for Saccharomyces cerevisiae.

A biochemically structured model for the aerobic growth of Saccharomyces cerevisiae on glucose and ethanol is presented. The model focuses on the pyruvate and acetaldehyde branch points where overflow metabolism occurs when the growth changes from oxidative to oxido-reductive. The model is designed to describe the onset of aerobic alcoholic fermentation during steady-state as well as under dynamical conditions, by triggering an increase in the glycolytic flux using a key signalling component which is assumed to be closely related to acetaldehyde. An investigation of the modelled process dynamics in a continuous cultivation revealed multiple steady states in a region of dilution rates around the transition between oxidative and oxido-reductive growth. A bifurcation analysis using the two external variables, the dilution rate, D, and the inlet concentration of glucose, S(f), as parameters, showed that a fold bifurcation occurs close to the critical dilution rate resulting in multiple steady-states. The region of dilution rates within which multiple steady states may occur depends strongly on the substrate feed concentration. Consequently a single steady state may prevail at low feed concentrations, whereas multiple steady states may occur over a relatively wide range of dilution rates at higher feed concentrations.     

Hutchinson revisited: Patterns of density regulation and the coexistence of strong competitors

Ecologists have long been searching for mechanisms of species coexistence, particularly since G.E. Hutchinson raised the ‘paradox of the plankton’. A promising approach to solve this paradox and to explain the coexistence of many species with strong niche overlap is to consider over-compensatory density regulation with its ability to generate endogenous population fluctuations.Previous work has analysed the role of over-compensation in coexistence based on analytical approaches. Using a spatially explicit time-discrete simulation model, we systematically explore the dynamics and conditions for coexistence of two species. We go beyond the analytically accessible range of models by studying the whole range of density regulation from under- to very strong over-compensation and consider the impact of spatial structure and temporal disturbances. In particular, we investigate how coexistence can emerge in different types of population growth models.We show that two strong competitors are able to coexist if at least one species exhibits over-compensation. Analysing the time series of population dynamics reveals how the differential responses to density fluctuations of the two competitors lead to coexistence: The over-compensator generates density fluctuations but is the inferior competitor at strong amplitudes of those fluctuations; the competitor, therefore, becomes frequent and dampens the over-compensator's amplitudes, but it becomes inferior under dampened fluctuations.These species interactions cause a dynamic alternation of community states with long-term persistence of both species. We show that a variety of population growth models is able to reproduce this coexistence although the particular parameter ranges differ among the models. Spatial structure influences the probability of coexistence but coexistence is maintained for a broad range of dispersal parameters.The flexibility and robustness of coexistence through over-compensation emphasize the importance of nonlinear density dependence for species interactions, and they also highlight the potential of applying more flexible models than the classical Lotka-Volterra equations in community ecology.     

Spatial mechanisms for coexistence of species sharing a common natural enemy

We examine the conditions under which spatial structure can mediate coexistence of apparent competitors. We use a spatially explicit, host-parasitoid metapopulation model incorporating local dynamics of Nicholson-Bailey type and global dispersal. Depending on the model parameters, the resulting system displays a plethora of asynchronous dynamical behaviors for which permanent or transient coexistence is observed. We identify a number of spatially mediated tradeoffs which apparent competitors can utilize and demonstrate that the dynamics of spatial coexistence can typically be understood from consideration of two and three patch systems. The phase relationships of species abundances are different for our model than for some other mechanisms of spatial coexistence. We discuss the implications of our findings relative to issues of community organization and biological conservation.     

Coexistence of two competitors on one resource and one inhibitor: a chemostat model based on bacteria and antibiotics

We present a continuous time model of the dynamics of two species competing for a single limiting resource in the presence of a substance that inhibits the growth of one of the species. Resource and inhibitor are both derived from external sources. These inputs, and all other model parameters, are assumed to be constant in space and time. There exist conditions that permit the stable coexistence of the competitors, provided that the sensitive species is more efficient in exploiting the limiting resource, and the resistant species removes the inhibitor from the environment. There exists a subset of these conditions wherein the sensitive species can become established if and only if the resistant species is already established. If the resistant species does not remove the inhibitor from the environment, then coexistence of sensitive and resistant species is structurally unstable. If the resistant species produces the inhibitor, then coexistence is dynamically unstable. We review several studies of bacterial competition in the presence of antibiotics that support these conclusions.     

Complexity and coexistence in a simple spatial model for arid savanna ecosystems

Tree–grass coexistence is broadly observed in tropical savannas. Recent studies indicate that, in arid savannas, such coexistence is stable and related to water availability. The role of different factors (from niche separation to demographic structure) has been explored. Nevertheless, spatial mechanisms of water–vegetation interactions have been rarely taken into account, despite their well-known importance for vegetation distribution. Here, we introduce a spatial model including tree and grass biomass dynamics, together with soil and surface water dynamics. We consider two water–vegetation feedbacks. Grasses increase water infiltration into the soil, while tree shadow limits evaporation, and both mechanisms increase soil water availability, leading to positive feedbacks. The infiltration feedback can also lead to spatial pattern formation. Despite the fact that trees and grasses compete for the same resource, namely water, we observe stable coexistence as a possible model outcome. The system displays a complex behavior, with multiple stable states and possible catastrophic shifts between states, e.g., patterned grassland, bare soil and forest. In our model, coexistence is always linked with multi-stability and spatial pattern formation, driven by grass infiltration feedback. Given such complex model solutions, we expect that, under real conditions, heterogeneities and disturbances, acting on the multi-stable states, may further foster coexistence.     

Integrating nested spatial scales: implications for the coexistence of competitors on a patchy resource

1. Intraspecific aggregation at a single spatial scale can promote the coexistence of competitors. This paper demonstrates how this same mechanism can be applied to the many systems that are patchy at two scales, with patches nested within 'superpatches'.
2. Data are presented from a field study showing that insects living in rotting fruits have aggregated distributions in the fruits under a single tree, and that the mean density and degree of aggregation varies significantly among trees. Observations in this system motivate the following models.
3. A model of competition has been developed between two species which explicitly represents spatial variation at two scales. By integrating the probability distributions for each scale, the marginal distributions of competitors over all patches can be found and used to calculate coexistence criteria. This model assumes global movement of the competitors.
4. Although spatial variation at a single scale may not be sufficient for coexistence, the total variation over all patches can allow coexistence. Variation in mean densities among superpatches and variation in the degree of aggregation among superpatches both promote coexistence, but act in different ways.
5. A second model of competition between two species is described which incorporates the effects of limited movement among superpatches. Limited movement among superpatches generally promotes coexistence, and also leads to correlations among aggregation and the mean densities of competitors.     

Ionic currents in the human serotonin transporter reveal inconsistencies in the alternating access hypothesis

We have investigated the conduction states of human serotonin transporter (hSERT) using the voltage clamp, cut-open frog oocyte method under different internal and external ionic conditions. Our data indicate discrepancies in the alternating access model of cotransport, which cannot consistently explain substrate transport and electrophysiological data. We are able simultaneously to isolate distinct external and internal binding sites for substrate, which exert different effects upon currents conducted by hSERT, in contradiction to the alternating access model. External binding sites of coupled Na ions are likewise simultaneously accessible from the internal and external face. Although Na and Cl are putatively cotransported, they have opposite effects on the internal face of the transporter. Finally, the internal K ion does not compete with internal 5-hydroxytryptamine for empty transporters. These data can be explained more readily in the language of ion channels, rather than carrier models distinguished by alternating access mechanisms: in a channel model of coupled transport, the currents represent different states of the same permeation path through hSERT and coupling occurs in a common pore.     

Variability in resource consumption rates and the coexistence of competing species

A model which incorporates random temporal variation in resource consumption rates is used to investigate the effects that such variation has on the coexistence of competitors. The analysis of the model and several extensions of it suggests that such variation in consumption rates will often allow two or more competitors to coexist while limited by the same resource. For variability to promote coexistence, it is necessary that the time scale of resource population dynamics be fast relative to the time scale of environmental change. Variability is especially likely to promote coexistence if there is a large variance in consumption rates, negative correlation between the consumption rates of different species, and a linear or concave relationship between resource consumption and per capita population growth. Many previous studies which have found coexistence of two or more species on one resource can be interpreted as examples of coexistence due to varying resource consumption rates.