FCS cell surface measurements--photophysical limitations and consequences on molecular ensembles with heterogenic mobilities.

BACKGROUND: Fluorescence Correlation Spectroscopy is a powerful method to analyze densities and diffusive behavior of molecules in membranes, but effects of photodegradation can easily be overlooked. METHOD: Based on experimental photophysical parameters, calculations were performed to analyze the consequences of photobleaching in fluorescence correlation spectroscopy (FCS) cell surface experiments, covering a range of standard measurement conditions. RESULTS: Cumulative effects of photobleaching can be prominent, although an absolute majority of the fluorescent molecules would pass the laser excitation beam without being photo-bleached. Given a distribution of molecules on a cell surface with different diffusive properties, the fraction of molecules that is actually analyzed depends strongly on the excitation intensities and measurement times, as well as on the size of the reservoir of freely diffusing molecules. Both the slower and the faster diffusing molecules can be disfavored. CONCLUSIONS: Apart from quantifying photobleaching effects, the calculations suggest that the effects can be used to extract additional information, for instance about the size of the reservoirs of free diffusion. By certain choices of measurement conditions, it may be possible to more specifically analyze certain species within a population, based on their different diffusive properties, different areas of free diffusion, or different kinetics of possible transient binding.     

Barriers to gene flow and ring species formation

Ring species are groups of organisms that dispersed along a ring‐shaped region in such a way that the two ends of the population that meet after many generations are reproductively isolated. They provide a rare opportunity to understand the role of spatial structuring in speciation. Here, we simulate the evolution of ring species assuming that individuals become sexually isolated if the genetic distance between them is above a certain threshold. The model incorporates two forms of dispersal limitation: exogenous geographic barriers that limit the population range and endogenous barriers that result in genetic structuring within the population range. As expected, species' properties that reduce gene flow within the population range facilitate the evolution of reproductive isolation and ring species formation. However, if populations are confined to narrow ranges by geographic barriers, ring species formation increases when local mating is less spatially restricted. Ring species are most likely to form if a population expands while confined to a quasi‐unidimensional range but preserving high mobility in the direction of the range expansion. These conditions are unlikely to be met or persist in real populations and may explain why ring species are rare.     

On evolutionary stability of carrying capacity driven dispersal in competition with regularly diffusing populations

Two competing populations in spatially heterogeneous but temporarily constant environment are investigated: one is subject to regular movements to lower density areas (random diffusion) while the dispersal of the other is in the direction of the highest per capita available resources (carrying capacity driven diffusion). The growth of both species is subject to the same general growth law which involves Gilpin–Ayala, Gompertz and some other equations as particular cases. The growth rate, carrying capacity and dispersal rate are the same for both population types, the only difference is the dispersal strategy. The main result of the paper is that the two species cannot coexist (unless the environment is spatially homogeneous), and the carrying capacity driven diffusion strategy is evolutionarily stable in the sense that the species adopting this strategy cannot be invaded by randomly diffusing population. Moreover, once the invasive species inhabits some open nonempty domain, it would spread over any available area bringing the native species diffusing randomly to extinction. One of the important technical results used in the proofs can be interpreted in the form that the limit solution of the equation with a regular diffusion leads to lower total population fitness than the ideal free distribution.     

具有年龄结构的食蚜蝇-蚜虫捕食模型

现有的具有年龄结构的捕食-食饵模型总是假设只有成年捕食者捕食猎物,这与实际情况不符。建立了一个幼年捕食者捕食食饵的具有年龄结构的食蚜蝇-蚜虫模型,应用微分方程定性理论,讨论了系统平衡点及其稳定性:其中平衡点E1(0,0,0)为不稳定的;满足一定条件时,边界平衡点E2(K,0,0)及正平衡点E3(x*,y1*,y2*)为局部渐近稳定的;且应用一致持续生存理论得到了系统永久持续生存的条件,为有害生物综合治理提供了理论依据。     

Human impact on the ecological performance of Potamogeton species in northwestern Germany

The changes in habitat quality of lowland rivers in Lower Saxony (Germany) during the past 40 years are outlined. Almost all chemical, physical, and morphological parameters have changed, resulting in most cases in an enhanced potential productivity, accompanied by a complex disturbance regime. Historical reconstruction of the change in river vegetation is presented to compare the frequency of macrophyte species 40 years ago with the situation of today. For a total of 289 sampling sites, the floristic change was exactly reconstructed. Nearly all species show a decline in frequency. This trend is also recognizable in Potamogeton, with the exception of two narrow-leaved species.An attempt is made to explain both decline and maintenance in terms of life history characters (vital attributes) allowing the species to react to the changing habitat conditions. The successful species are characterized by certain life history characteristics which enable them to survive under the current disturbance regime. Most important aspects of life history are the ability to reproduce by means of turions and other fragments, a long-lived, deep-rooting rhizome system, phenotypic plasticity of above-ground parts, synchronous shoot polymorphism, and the potential to regenerate quickly from remaining buds after disturbance. The decline of formerly frequent species can be attributed mainly to the lack of certain key characters; however, physiological characters also may be important. The extirpation of some rare species could also be caused by random fluctuations in small populations. The general importance of population ecological research, particularly demography, life history theory, and the modelling of clonal populations in conservation ecology is stressed.     

Resolving Cytosolic Diffusive States in Bacteria by Single-Molecule Tracking

The trajectory of a single protein in the cytosol of a living cell contains information about its molecular interactions in its native environment. However, it has remained challenging to accurately resolve and characterize the diffusive states that can manifest in the cytosol using analytical approaches based on simplifying assumptions. Here, we show that multiple intracellular diffusive states can be successfully resolved if sufficient single-molecule trajectory information is available to generate well-sampled distributions of experimental measurements and if experimental biases are taken into account during data analysis. To address the inherent experimental biases in camera-based and MINFLUX-based single-molecule tracking, we use an empirical data analysis framework based on Monte Carlo simulations of confined Brownian motion. This framework is general and adaptable to arbitrary cell geometries and data acquisition parameters employed in two-dimensional or three-dimensional single-molecule tracking. We show that, in addition to determining the diffusion coefficients and populations of prevalent diffusive states, the timescales of diffusive state switching can be determined by stepwise increasing the time window of averaging over subsequent single-molecule displacements. Time-averaged diffusion analysis of single-molecule tracking data may thus provide quantitative insights into binding and unbinding reactions among rapidly diffusing molecules that are integral for cellular functions.     

The limitation of species range: A consequence of searching along resource gradients

Ecological modelers have long puzzled over the spatial distribution of species. The random walk or diffusive approach to dispersal has yielded important results for biology and mathematics, yet it has been inadequate in explaining all phenomenological features. Ranges can terminate non-smoothly absent a complementary shift in the characteristics of the environment. Also unexplained is the absence of a species from nearby areas of adequate, or even abundant, resources. In this paper, I show how local searching behavior–keyed to a density-dependent fitness–can limit the speed and extent of a species’ spread. In contrast to standard diffusive processes, pseudo-rational movement facilitates the clustering of populations. It also can be used to estimate the speed of an expanding population range, explain expansion stall, and provides a mechanism by which a population can colonize seemingly removed regions — biogeographic islands in a continental framework. Finally, I discuss the effect of resource degradation and different resource impact/utilization curves on the model.     

Hitchhiking in space: Ancestry in adapting,spatially extended populations*

Selective sweeps reduce neutral genetic diversity. In sexual populations, this “hitchhiking” effect is thought to be limited to the local genomic region of the sweeping allele. While this is true in panmictic populations, we find that in spatially extended populations the combined effects of many unlinked sweeps can affect patterns of ancestry (and therefore neutral genetic diversity) across the whole genome. Even low rates of sweeps can be enough to skew the spatial locations of ancestors such that neutral mutations that occur in an individual living outside a small region in the center of the range have virtually no chance of fixing in the population. The fact that nearly all ancestry rapidly traces back to a small spatial region also means that relatedness between individuals falls off very slowly as a function of the spatial distance between them.     

Effects of cell motility and chemotaxis on microbial population growth.

A mathematical model is developed to elucidate the effects of biophysical transport processes (nutrient diffusion, cell motility, and chemotaxis) along with biochemical reaction processes (cell growth and death, nutrient uptake) upon steady-state bacterial population growth in a finite one-dimensional region. The particular situation considered is that of growth limitation by a nutrient diffusing from an adjacent phase not accessible to the bacteria. It is demonstrated that the cell motility and chemotaxis properties can have great influence on steady-state population size. In fact, motility effects can be as significant as growth kinetic effects, in a manner analogous to diffusion- and reaction-limited regimes in chemically reacting systems. In particular, the following conclusions can be drawn from our analysis for bacterial populations growing at steady-state in a confined, unmixed region: (a) Random motility may lead to decreased population density; (b) chemotaxis can allow increased population density if the chemotactic response is large enough; (c) a species with superior motility properties can outgrow a species with superior growth kinetic properties; (d) motility effects become greater as the size of the confined growth region increases; and (e) motility effects are diminished by significant mass-transfer limitation of the nutrient from the adjacent source phase. The relationships of these results for populations to previous conclusions for individual cells is discussed, and implications for microbial competition are suggested.     

Carrying capacity in a heterogeneous environment with habitat connectivity

A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non‐diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial diffusion increased total equilibrium population abundance in heterogeneous environments, with the effect size depending on the relationship between r and K. Refuting previous theory, however, we discovered that homogeneously distributed resources support higher total carrying capacity than heterogeneously distributed resources, even with species diffusion. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments.     

有色环境噪音对空间异质种群动态同步性的影响

随着种群动态和空间结构研究兴趣的增加,激发了大量的有关空间同步性的理论和实验的研究工作。空间种群的同步波动现象在自然界广泛存在,它的影响和原因引起了很多生态学家的兴趣。Moran定理是一个非常重要的解释。但以往的研究大多假设环境变化为空间相关的白噪音。越来越多的研究表明很多环境变化的时间序列具有正的时间自相关性,也就是说用红噪音来描述更加合理。因此,推广经典的Moran效应来处理空间相关红噪音的情形很有必要。利用线性的二阶自回归过程的种群模型,推导了两种群空间同步性与种群动态异质性和环境变化的时间相关性(即环境噪音的颜色)之间的关系。深入分析了种群异质性和噪音颜色对空间同步性的影响。结果表明种群动态异质性不利于空间同步性,但详细的关系比较复杂。而红色噪音的同步能力体现在两方面:一方面,本身的相关性对同步性有贡献;另一方面,环境变化时间相关性可以通过改变种群密度依赖来影响同步性,但对同步性的影响并无一致性的结论,依赖于种群的平均动态等因素。这些结果对理解同步性的机理、利用同步机理来制定物种保护策略和害虫防治都有重要的意义。     

The influence of generalist predators in spatially extended predator–prey systems

The presence of generalist predators is known to have important ecological impacts in several fields. They have wide applicability in the field of biological control. However, their role in the spatial distribution of predator and prey populations is still not clear. In this paper, the spatial dynamics of a predator–prey system is investigated by considering two different types of generalist predators. In one case, it is considered that the predator population has an additional food source and can survive in the absence of the prey population. In the other case, the predator population is involved in intraguild predation, i.e., the source of the additional food of the predator coincides with the food source of the prey population and thus both prey and predator populations compete for the same resource. The conditions for linear stability and Turing instability are analyzed for both the cases. In the presence of generalist predators, the system shows different pattern formations and spatiotemporal chaos which has important implications for ecosystem functioning not only in terms of their predictability, but also in influencing species persistence and ecosystem stability in response to abrupt environmental changes. This study establishes the importance of the consideration of spatial dynamics while determining optimal strategies for biological control through generalist predators.     

Caught between two Allee effects: Trade-off between reproduction and predation risk

Reproductive activities are often associated with conspicuous morphology or behaviour that could be exploited by predators. Individuals can therefore face a trade-off between reproduction and predation risk. Here we use simple models to explore population-dynamical consequences of such a trade-off for populations subject to a mate-finding Allee effect and an Allee effect due to predation. We present our results in the light of populations that belong to endangered species or pests and study their viability and resilience. We distinguish several qualitative scenarios characterized by the shape and strength of the trade-off and, in particular, identify conditions for which the populations survive or go extinct. Reproduction can be so costly that the population always goes extinct. In other cases, the population goes extinct only over a certain range of low, intermediate or high levels of reproductive activities. Moreover, we show that predator removal (e.g. in an attempt to save an endangered prey species) has the least effect on populations with low cost of reproduction in terms of predation and, conversely, predator addition (e.g. to eradicate a pest) is most effective for populations with high predation cost of reproduction. Our results indicate that a detailed knowledge of the trade-off can be crucial in applications: for some trade-off shapes, only intermediate levels of reproductive activities might guarantee population survival, while they can lead to extinction for others. We therefore suggest that the fate of populations subject to the two antagonistic Allee effects should be evaluated on a case-by-case basis. Although the literature offers no quantitative data on possible trade-off shapes in any taxa, indirect evidence suggests that the trade-off and both Allee effects can occur simultaneously, e.g. in the golden egg bug Phyllomorpha laciniata.     

Coexistence phenomena and global bifurcation structure in a chemostat-like model with species-dependent diffusion rates

We study the competition of two species for a single resource in a chemostat. In the simplest space-homogeneous situation, it is known that only one species survives, namely the best competitor. In order to exhibit coexistence phenomena, where the two competitors are able to survive, we consider a space dependent situation: we assume that the two species and the resource follow a diffusion process in space, on top of the competition process. Besides, and in order to consider the most general case, we assume each population is associated with a distinct diffusion constant. This is a key difficulty in our analysis: the specific (and classical) case where all diffusion constants are equal, leads to a particular conservation law, which in turn allows to eliminate the resource in the equations, a fact that considerably simplifies the analysis and the qualitative phenomena. Using the global bifurcation theory, we prove that the underlying 2-species, stationary, diffusive, chemostat-like model, does possess coexistence solutions, where both species survive. On top of that, we identify the domain, in the space of the relevant bifurcation parameters, for which the system does have coexistence solutions.     

Spatial and temporal synchrony in reptile population dynamics in variable environments

Resources are seldom distributed equally across space, but many species exhibit spatially synchronous population dynamics. Such synchrony suggests the operation of large-scale external drivers, such as rainfall or wildfire, or the influence of oasis sites that provide water, shelter, or other resources. However, testing the generality of these factors is not easy, especially in variable environments. Using a long-term dataset (13–22 years) from a large (8000 km²) study region in arid Central Australia, we tested firstly for regional synchrony in annual rainfall and the dynamics of six reptile species across nine widely separated sites. For species that showed synchronous spatial dynamics, we then used multivariate follow a multivariate auto-regressive state–space (MARSS) models to predict that regional rainfall would be positively associated with their populations. For asynchronous species, we used MARSS models to explore four other possible population structures: (1) populations were asynchronous, (2) differed between oasis and non-oasis sites, (3) differed between burnt and unburnt sites, or (4) differed between three sub-regions with different rainfall gradients. Only one species showed evidence of spatial population synchrony and our results provide little evidence that rainfall synchronizes reptile populations. The oasis or the wildfire hypotheses were the best-fitting models for the other five species. Thus, our six study species appear generally to be structured in space into one or two populations across the study region. Our findings suggest that for arid-dwelling reptile populations, spatial and temporal dynamics are structured by abiotic events, but individual responses to covariates at smaller spatial scales are complex and poorly understood.     

Quasi-Local Competition in Stage-Structured Metapopulations: A New Mechanism of Pattern Formation

A central question of ecology is what determines the presence and abundance of species at different locations. In cases of ecological pattern formation, population sizes are largely determined by spatially distributed interactions and may have very little to do with the habitat template. We find pattern formation in a single-species metapopulation model with quasi-local competition, but only if the populations have (at least) two age or stage classes. Quasi-local competition is modeled using an explicit resource competition model with fast resource dynamics, and assuming that adults, but not juveniles, spend a fraction of their foraging time in habitat patches adjacent to their home patch. Pattern formation occurs if one stage class depletes the common resource but the shortage of resource affects mostly the other stage. When the two stages are spatially separated due to quasi-local competition, this results in competitive exclusion between the populations. We find deep similarity between spatial pattern formation and population cycles due to competitive exclusion between cohorts of biennial species, and discuss the differences between the present mechanism and established ways of pattern formation such as diffusive instability and distributed competition with local Allee-effects.     

Analysis of Reaction-Diffusion Systems with Anomalous Subdiffusion

Reaction-diffusion equations are the cornerstone of modeling biochemical systems with spatial gradients, which are relevant to biological processes such as signal transduction. Implicit in the formulation of these equations is the assumption of Fick's law, which states that the local diffusive flux of species i is proportional to its concentration gradient; however, in the context of complex fluids such as cytoplasm and cell membranes, the use of Fick's law is based on empiricism, whereas evidence has been mounting that such media foster anomalous subdiffusion (with mean-squared displacement increasing less than linearly with time) over certain length scales. Particularly when modeling diffusion-controlled reactions and other systems where the spatial domain is considered semi-infinite, assuming Fickian diffusion might not be appropriate. In this article, two simple, conceptually extreme models of anomalous subdiffusion are used in the framework of Green's functions to demonstrate the solution of four reaction-diffusion problems that are well known in the biophysical context of signal transduction: fluorescence recovery after photobleaching, the Smolochowski limit for diffusion-controlled reactions in solution, the spatial range of a diffusing molecule with finite lifetime, and the collision coupling mechanism of diffusion-controlled reactions in two dimensions. In each case, there are only subtle differences between the two subdiffusion models, suggesting how measurements of mean-squared displacement versus time might generally inform models of reactive systems with partial diffusion control.     

Patterns of Patchy Spread in Deterministic and Stochastic Models of Biological Invasion and Biological Control

A few spatiotemporal models of population dynamics are considered in relation to biological invasion and biological control. The patterns of spread in one and two spatial dimensions are studied by means of extensive numerical simulations. We show that, in the case that population multiplication is damped by the strong Allee effect (when the population growth rate becomes negative for small population density), in a certain parameter range the spread can take place not via the intuitively expected circular expanding population front but via motion and interaction of separate patches. Alternatively, the patchy spread can take place in a system without Allee effect as a result of strong environmental noise. We then show that the phenomenon of deterministic patchy invasion takes place ‘at the edge of extinction’ so that a small change of controlling parameters either brings the species to extinction or restores the travelling population fronts. Moreover, we show that the regime of patchy invasion in two spatial dimensions actually takes place when the species go extinct in the corresponding 1-D system.     

Spatial (a)synchrony in population fluctuations of five plant species in fragmented habitats

The spatial scale at which populations show synchronous temporal fluctuations in abundance, relative to the spatial scale over which they can disperse, may influence the persistence of local and regional populations. There have been frequent demonstrations of spatial synchrony in population dynamics of animal populations. But few studies have investigated the degree of spatial synchrony in less mobile taxa, e.g. plants, where life history, dispersal and interaction with the environment would be different due to a sessile phase. This study has during three years investigated the synchrony in local population size changes in four short-lived species, and during a nine-year period for one long-lived species, in a semi-natural grassland landscape in southern Sweden. The spatial scale of this study was less than 15 km, which is quite small in comparison with other studies, but the temporal scale was of similar magnitude as the few studies on plant abundances and synchrony. When using detrended estimates of population size change, a significant pattern of decreasing synchrony with increasing distance was found for the two short-lived species that were most confined to manage semi-natural grasslands. Spatial synchrony was detected up to a few km. However, the species displayed synchrony in different years. The degree of synchrony can thus vary considerably across years and among species. Spatially autocorrelated weather conditions could partly explain the spatial scale of synchrony found during certain time intervals. However, the prevailing asynchrony suggests that local factors dominate the dynamics of the populations at the investigated scale.     

Density dependence forces divergent population growth rates and alters occupancy patterns of a central place foraging Antarctic seabird

Density‐dependent regulation is an important process in spatio‐temporal population dynamics because it can alter the effects of synchronizing processes operating over large spatial scales. Most frequently, populations are regulated by density dependence when higher density leads to reduced individual fitness and population growth, but inverse density dependence can also occur when small populations are subject to higher extinction risks. We investigate whether density‐dependent regulation influences population growth for the Antarctic breeding Adélie penguin Pygoscelis adeliae. Understanding the prevalence and nature of density dependence for this species is important because it is considered a sentinel species reflecting the impacts of fisheries and environmental change over large spatial scales in the Southern Ocean, but the presence of density dependence could introduce uncertainty in this role. Using data on population growth and indices of resource availability for seven regional Adélie penguin populations located along the East Antarctic coastline, we find compelling evidence that population growth is constrained at some locations by the amount of breeding habitat available to individuals. Locations with low breeding habitat availability had reduced population growth rates, higher overall occupancy rates, and higher occupancy of steeper slopes that are sparsely occupied or avoided at other locations. Our results are consistent with evolutionary models of avian breeding habitat selection where individuals search for high‐quality nest sites to maximize fitness returns and subsequently occupy poorer habitat as population density increases. Alternate explanations invoking competition for food were not supported by the available evidence, but strong conclusions on food‐related density dependence were constrained by the paucity of food availability data over the large spatial scales of this region. Our study highlights the importance of incorporating nonconstant conditions of species–environment relationships into predictive models of species distributions and population dynamics, and provides guidance for improved monitoring of fisheries and climate change impacts in the Southern Ocean.