生态系统多稳态研究进展

在多稳态的生态系统中,外力可能导致生态系统状态突然之间发生不可逆转的转变,从而达到一个新的平衡状态。但目前对多稳态理论的系统研究很少,如何使用预警信号来预测生态系统的状态转变依旧是个难题。通过多稳态理论的梳理提出了一个更加综合的多稳态定义,并以放牧模型为例,系统总结了多稳态理论的相关概念,将多稳态理论应用在生态系统演替和扰沌理论的解释中;通过对生态系统稳态转换预警信号的原理、优缺点和应用条件的分析,对不同尺度下多稳态的研究方法进行了归纳;最后提出了目前多稳态领域的研究问题和未来的研究重点。结果表明：（1）将时间和空间预警信号结合在一起,并量化正确预警信号的概率,对错误预警信号的比例进行加权,可能会提供更准确的稳态转换的预报。（2）定量观测试验适用于小尺度的研究,而较大尺度的研究则采用简化的模型来模拟研究,选择正确的尺度极有可能改变预警信号的可靠性。（3）结合多稳态理论研究生态系统临界转换和反馈控制机制,并将基于性状的特征指标和进化动力学纳入其中,是生态系统修复实践的重要研究方向。（4）将多稳态相关理论和生态保护管理政策的实践相结合,是多稳态理论未来应用的前景。本研究为多稳态理论和实践的深入研究提供科学支撑。     

Ontogenetic niche shift, food-web coupling, and alternative stable states

Several recent studies have shown that food web coupling by ontogenetic niche shifts can generate alternative stable states (ASS). However, these studies mainly considered cases where juvenile and adult stages are the top level consumers. The conditions under which ASS occur in more structurally diverse food web configurations have not been explored. In this study, I examine the influence of food-chain length and the trophic positions of juveniles and adults on the existence of ASS. Comprehensive model analysis showed that if both juveniles and adults are top predators, ASS are possible irrespective of their trophic level, because of overcompensation in reproduction and maturation due to strong density dependence, as previously predicted. However, the following potential food-web effects were found: ASS potential (1) disappears if either or both the juveniles and adults have a predator and (2) is once again observed if another predator is added on the stage-specific predator. These mechanisms involve (1) top–down control that relaxes intrastage food competition and (2) top–down cascade that intensifies the intrastage competition, respectively. Furthermore, it was illustrated that the environmental conditions under which ASS occurred varied in complex ways with the coupled food-web configurations. My results provide a novel concept that anthropogenic changes in local community structure (e.g., species extinction and invasion) propagate through space and may cause or prevent regime shifts in broad-scale community structure by altering the resilience to environmental perturbations.     

Alternative stable states generated by ontogenetic niche shift in the presence of multiple resource use

It has been suggested that when juveniles and adults use different resources or habitats, alternative stable states (ASS) may exist in systems coupled by an ontogenetic niche shift. However, mainly the simplest system, i.e., the one-consumer-two-resource system, has been studied previously, and little is known about the development of ASS existing in more complex systems. Here, I theoretically investigated the development of ASS caused by an ontogenetic niche shift in the presence of multiple resource use. I considered three independent scenarios; (i) additional resources, (ii) multiple habitats, and (iii) interstage resource sharing. The model analyses illustrate that relative balance between the total resource availability in the juvenile and adult habitats is crucial for the development of ASS. This balance is determined by factors such as local habitat productivity, subsidy inputs, colonization area, and foraging mobility. Furthermore, it is also shown that interstage resource sharing generally suppresses ASS. These results suggest that the anthropogenic impacts of habitat modifications (e.g., fragmentation and destruction) or interaction modifications (e.g., changes in ontogeny and foraging behavior) propagate through space and may cause or prevent regime shifts in the regional community structure.     

Geographic isolation facilitates the evolution of reproductive isolation and morphological divergence

Geographic isolation is known to contribute to divergent evolution, resulting in unique phenotypes. Oftentimes morphologically distinct populations are found to be interfertile while reproductive isolation is found to exist within nominal morphological species revealing the existence of cryptic species. These disparities can be difficult to predict or explain especially when they do not reflect an inferred history of common ancestry which suggests that environmental factors affect the nature of ecological divergence. A series of laboratory experiments and observational studies were used to address what role biogeographic factors may play in the ecological divergence of Hyalella amphipods. It was found that geographic isolation plays a key role in the evolution of reproductive isolation and divergent morphology and that divergence cannot be explained by molecular genetic variation.     

Multiplicity of stable states in freshwater systems

It is shown with the use of minimal models that several ecological relationships in freshwater systems potentially give rise to the existence of alternative equilibria over a certain range of nutrient values. The existence of alternative stable states has some implications for the management of such systems. An important consequence is that signs of eutrophication are only apparent after the occurrence of changes that are very difficult to reverse. Reduction of the nutrient level as a measure to restore such systems gives poor results, but biomanipulation as an additional measure can have significant effects, provided that the nutrient level has been reduced enough to allow the existence of a stable alternative clear water equilibrium.     

Characterisation of alternative stable vegetation assemblages in a mesic savannah in Kenya

The phenomenon of sharp boundaries between distinctive vegetation types occurring under the same climatic conditions has often been interpreted by plant ecologists to characterise alternative stable states (ASS). The phenomenon may be relevant in explaining two strikingly different vegetation formations (broad-leaved nonspiny Combretum and fine-leaved spiny Acacia) co-occurring in mesic savannah of southeastern Kenya. We hypothesise that the two vegetation within southeastern Kenya ecosystems represent ASS whose transition may be a response to soil characteristics switch. To explore our hypothesis, we analysed empirical field data of woody species and soil characteristics from 57 plots that included 25 from Combretum and 32 from Acacia vegetation formations. We compared floristic composition and soil characteristics between the two systems and correlated edaphic statuses and vegetation states. We encountered 2,749 woody plant individuals, representing 115 species, 87 genera and 40 families. We found that the two vegetation had discrete woody species composition and soil characteristics, and also a significant species–edaphic association. The results are consistent with the ASS theory demonstrating that soil characteristics are among the important micro-environmental filters driving and maintaining woody vegetation mosaics in the tropics. Importantly, understanding ASS has ramifications for sustainable utilisation of woody plant resources in East African savannahs.     

The ecological significance of time sense in animals

Time is a fundamental dimension of all biological events and it is often assumed that animals have the capacity to track the duration of experienced events (known as interval timing). Animals can potentially use temporal information as a cue during foraging, communication, predator avoidance, or navigation. Interval timing has been traditionally investigated in controlled laboratory conditions but its ecological relevance in natural environments remains unclear. While animals may time events in artificial and highly controlled conditions, they may not necessarily use temporal information in natural environments where they have access to other cues that may have more relevance than temporal information. Herein we critically evaluate the ecological contexts where interval timing has been suggested to provide adaptive value for animals. We further discuss attributes of interval timing that are rarely considered in controlled laboratory studies. Finally, we encourage consideration of ecological relevance when designing future interval-timing studies and propose future directions for such experiments.     

Information, discrimination and divergence in cytology. III. Optimization of classification of Papanicolaou smears

The performance of a cytology laboratory can be objectively quantitated as the total discrimination, a defined quantity of information. The total discrimination is dependent on the number of categories used in gynecologic cytology and on the corresponding histologic states; over-classification results in a higher rate of misinformation and reduced total discrimination. Total divergence is another measure of the association between cytologic categories and histologic states; in contrast to the total discrimination, the total divergence does not require a one-to-one correspondence between the cytologic categories and the histologic states. Using data from the Gynecologic Cytology Laboratory of the University of Minnesota, the total discrimination was maximized when gynecologic cytology used three categories of diagnosis, consisting of (1) normal, atypical benign or reactive atypia, (2) cervical intraepithelial neoplasia (CIN) and (3) all malignancies. The use of four categories, (1) normal, atypical benign or reactive atypia, (2) mild or moderate dysplasia, (3) severe dysplasia or squamous carcinoma in situ and (4) all malignancies, was almost equally informative. Observations on the total divergences resulted in similar conclusions. These findings generally support the recommendation of the consensus workshop sponsored by the National Cancer Institute (the Bethesda System nomenclature) to group all degrees of CIN into two large categories.     

Interactive effects of disturbance and dispersal on community assembly

The traditional debate on alternative community states has been over whether or not they exist. Studies of community assembly have examined the role of assembly history in driving community divergence, but the context in which assembly history becomes important is a continued topic of interest. In this study, we created communities of bacterivorous ciliated protists in laboratory microcosms and manipulated assembly history, disturbance frequency, and the presence of dispersal among local communities to investigate the mechanisms behind community divergence. Specifically, we sought to understand how the role of assembly history changed in response to disturbance, dispersal, and the combination of the two. Assembly history influenced the identity of the dominant species through priority effects, and dispersal and disturbance showed interactive effects on both alpha and beta diversity. Dispersal substantially increased alpha diversity, but only in the absence of disturbance, and it reduced beta diversity, but not in the presence of low or mixed disturbance. These results demonstrate that the role of assembly history and the strength of priority effects depend on community context, suggesting that understanding the interactions between various factors shaping community assembly is important for understanding how ecological communities are structured.     

Refugial isolation versus ecological gradients

Hypotheses for divergence and speciation in rainforests generally fall into two categories: those emphasizing the role of geographic isolation and those emphasizing the role of divergent selection along gradients. While a majority of studies have attempted to infer mechanisms based on the pattern of species richness and congruence of geographic boundaries, relatively few have tried to simultaneously test alternative hypotheses for diversification. Here we discuss four examples, taken from our work on diversification of tropical rainforest vertebrates, in which we examine patterns of genetic and morphological variation within and between biogeographic regions to address two alternative hypotheses. By estimating morphological divergence between geographically contiguous and isolated populations under similar and different ecological conditions, we attempt to evaluate the relative roles of geographic isolation and natural selection in population divergence. Results suggest that natural selection, even in the presence of appreciable gene flow, can result in morphological divergence that is greater than that found between populations isolated for millions of years and, in some cases, even greater than that found between congeneric, but distinct, species. The relatively small phenotypic divergence that occurs among long-term geographic isolates in similar habitats suggests that morphological divergence via drift may be negligible and/or that selection is acting to produce similar phenotypes in populations occupying similar habitats. Our results demonstrate that significant phenotypic divergence: (1) is not necessarily coupled with divergence in neutral molecular markers; and (2) can occur without geographic isolation in the presence of gene flow.     

Stability and coexistence in a lawn community: experimental assessment of the stability of the actual community

Calculation of a community matrix for a lawn, based on pairwise competition experiments between lawn species, had predicted that the community would be unstable, but that it was close to the stability/instability boundary. To test for stability in the actual community, three types of 'pulse' perturbation were applied: shading for six weeks, mechanical perturbation (removal of vegetation) and a herbicide specific to grasses. Following shade and mechanical perturbation, the abundances of the species recovered towards that of the undisturbed community, although full recovery of the whole community was not realised. For the herbicide perturbation, recovery was still quite incomplete after 4.5 years, apparently because the compensatory growth of dicots made it difficult for the grasses to reinvade. Based on species presence/absence, the lawn fully recovered from all three perturbations. The overall pattern of recovery of the lawn was consistent with the prediction of marginal instability derived from the community matrix analysis. However, care must be taken in the interpretation of these results, as a pre-requisite for valid application of community matrix theory is that the community should be at equilibrium, but in the lawn this assumption was violated. A transitive hierarchy of competitive dominance was identified in the pairwise competition experiments; however, this hierarchy was unrelated to the rankings of the species in field abundance in the undisturbed community. The problems in applying community matrix theory to real communities are reviewed. It is concluded that whilst the theory may have biological relevance to at least simple communities, such as the lawn system used here, difficulties in its practical application, and more importantly, the restrictive assumptions on which the theory is based, will limit its relevance in most natural systems. These results call into question the generality of a large volume of theoretical studies based on these methods.     

Host choice promotes reproductive isolation between host races of the larch budmoth Zeiraphera diniana

The chances for sympatric speciation are improved if ecological divergence leads to assortative mating as a by-product. This effect is known in parasites that find mates using host cues, but studies of larch- and pine-feeding races of the larch budmoth (Zeiraphera diniana, Lepidoptera: Tortricidae) suggest it may also occur when mate attraction is via sex pheromones that are independent of habitat. We have previously shown that females releasing pheromones on or near their own host attract more males of their own race than if placed on the alternative host. This host effect would enhance assortative mating provided adults preferentially alight on their native hosts. Here we investigate alighting preferences in natural mixed forest using a novel likelihood analysis of genotypic clusters based on three semidiagnostic allozyme loci. Both larch and pine females show a realized alighting preference for their own host of 86%. The equivalent preferences of males were 79% for the larch race and 85% for the pine race. These preferences are also detectable in small-scale laboratory experiments, where alighting preferences of larch and pine races towards their own hosts were, respectively, 67 and 66% in females and 69 and 63% in males. Pure larch race moths reared in the laboratory had alighting choice similar to moths from natural populations, while hybrids were intermediate, showing that alighting preferences were heritable and approximately additive. The field estimates of alighting preference, coupled with earlier work on mate choice, yield an estimated rate of natural hybridization between sympatric host races of 2.2-3.8% per generation. Divergent alighting choice enhances pheromone-mediated assortative mating today, and is likely to have been an important cause of assortative mating during initial divergence in host use. Because resources are normally 'coarse-grained' in space and time, assortative mating due to ecological divergence may be a more important catalyst of sympatric speciation than generally realized.     

Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex

Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter‐ and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.     

Regime shifts between free-floating plants and phytoplankton: a review

Field studies evidence shifts between phytoplankton and free-floating plant regimes; yet, it is unclear what drives these shifts and if they are critical transitions (alternative stable states). In this review, we synthesized field and experimental data on free-floating plants (of varying size and phylogenies) and phytoplankton regimes, to assess the effects of these producers on the environment. Nutrient-rich environments promote free-floating plants dominance—regardless of life form—which causes dark and anoxic environments, and nutrient release from sediments. This reinforces free-floating plants dominance, but controls phytoplankton biomass by strong shading (despite high nutrients and low grazing). Phytoplankton dominance renders turbid and oxygen-rich (when producing) environments. We also searched for case studies of regime shifts for free-floating plants and phytoplankton dominance. Most studies showed that when free-floating plants dominance was interrupted, phytoplankton biomass (usually Cyanobacteria) rose steeply. Likewise, when phytoplankton-dominated, the development of dense mats of free-floating plants covers usually controlled phytoplankton. Field evidence that suggests critical transitions include abrupt regime transitions in time and space; yet, evidence including indoor controlled experiments and mathematical models is needed for conclusive evidence of alternative stable states to be drawn.     

Marine reserves can enhance ecological resilience

The goals of ecosystem‐based management (EBM) include protecting ecological resilience, the magnitude of a perturbation that a community can withstand and remain in a given state. As a tool to achieve this goal, no‐take marine reserves may enhance resilience by protecting source populations or reduce it by concentrating fishing in harvested areas. Here, we test whether spatial management with marine reserves can increase ecological resilience compared to non‐spatial (conventional) management using a dynamic model of a simplified fish community with structured predation and competition that causes alternative stable states. Relative to non‐spatial management, reserves increase the resilience of the desired (predator‐dominated) equilibrium state in both stochastic and deterministic environments, especially under intensive fishing. As a result, spatial management also increases the feasibility of restoring degraded (competitor‐dominated) systems, particularly if combined with culling of competitors or stock enhancement of adult predators.     

Inheritance of epigenetic chromatin silencing

Maintenance of alternative chromatin states through cell divisions pose some fundamental constraints on the dynamics of histone modifications. In this paper, we study the systems biology of epigenetic inheritance by defining and analyzing general classes of mathematical models. We discuss how the number of modification states involved plays an essential role in the stability of epigenetic states. In addition, DNA duplication and the consequent dilution of marked histones act as a large perturbation for a stable state of histone modifications. The requirement that this large perturbation falls into the basin of attraction of the original state sometimes leads to additional constraints on effective models. Two such models, inspired by two different biological systems, are compared in their fulfilling the requirements of multistability and of recovery after DNA duplication. We conclude that in the presence of multiple histone modifications that characterize alternative epigenetic stable states, these requirements are more easily fulfilled.     

Repeated and predictable patterns of ecotypic differentiation during a biological invasion: lake–stream divergence in parapatric Swiss stickleback

The relative importance of ecological selection and geographical isolation in promoting and constraining genetic and phenotypic differentiation among populations is not always obvious. Interacting with divergent selection, restricted opportunity for gene flow may in some cases be as much a cause as a consequence of adaptation, with the latter being a hallmark of ecological speciation. Ecological speciation is well studied in parts of the native range of the three‐spined stickleback. Here, we study this process in a recently invaded part of its range. Switzerland was colonized within the past 140 years from at least three different colonization events involving different stickleback lineages. They now occupy diverse habitats, ranging from small streams to the pelagic zone of large lakes. We use replicated systems of parapatric lake and stream populations, some of which trace their origins to different invasive lineages, to ask (i) whether phenotypic divergence occurred among populations inhabiting distinct habitats, (ii) whether trajectories of phenotypic divergence follow predictable parallel patterns and (iii) whether gene flow constrains divergent adaptation or vice versa. We find consistent phenotypic divergence between populations occupying distinct habitats. This involves parallel evolution in several traits with known ecological relevance in independent evolutionary lineages. Adaptive divergence supersedes homogenizing gene flow even at a small spatial scale. We find evidence that adaptive phenotypic divergence places constraints on gene flow over and above that imposed by geographical distance, signalling the early onset of ecological speciation.     

Lizards as model organisms for linking phylogeographic and speciation studies

Lizards have been model organisms for ecological and evolutionary studies from individual to community levels at multiple spatial and temporal scales. Here we highlight lizards as models for phylogeographic studies, review the published population genetics/phylogeography literature to summarize general patterns and trends and describe some studies that have contributed to conceptual advances. Our review includes 426 references and 452 case studies: this literature reflects a general trend of exponential growth associated with the theoretical and empirical expansions of the discipline. We describe recent lizard studies that have contributed to advances in understanding of several aspects of phylogeography, emphasize some linkages between phylogeography and speciation and suggest ways to expand phylogeographic studies to test alternative pattern‐based modes of speciation. Allopatric speciation patterns can be tested by phylogeographic approaches if these are designed to discriminate among four alternatives based on the role of selection in driving divergence between populations, including: (i) passive divergence by genetic drift; (ii) adaptive divergence by natural selection (niche conservatism or ecological speciation); and (iii) socially‐mediated speciation. Here we propose an expanded approach to compare patterns of variation in phylogeographic data sets that, when coupled with morphological and environmental data, can be used to to discriminate among these alternative speciation patterns. [Correction made after online publication (28/07/2010): (minor deletion in the last line of the abstract)].     

Making predictive ecology more relevant to policy makers and practitioners

One of the aims of ecology is to aid policy makers and practitioners through the development of testable predictions of relevance to society. Here, we argue that this capacity can be improved in three ways. Firstly, by thinking more clearly about the priority issues using a range of methods including horizon scanning, identifying policy gaps, identifying priority questions and using evidence-based conservation to identify knowledge gaps. Secondly, by linking ecological models with models of other systems, such as economic and social models. Thirdly, by considering alternative approaches to generate and model data that use, for example, discrete or categorical states to model ecological systems. We particularly highlight that models are essential for making predictions. However, a key to the limitation in their use is the degree to which ecologists are able to communicate results to policy makers in a clear, useful and timely fashion.     

Extending the viability theory framework of resilience to uncertain dynamics,and application to lake eutrophication

Resilience, the capacity for a system to recover from a perturbation so as to keep its properties and functions, is of growing concern to a wide range of environmental systems. The challenge is often to render this concept operational without betraying it, nor diluting its content. The focus here is on building on the viability theory framework of resilience to extend it to discrete-time stochastic dynamical systems. The viability framework describes properties of the system as a subset of its state space. This property is resilient to a perturbation if it can be recovered and kept by the system after a perturbation: its trajectory can come back and stay in the subset. This is shown to reflect a general definition of resilience. With stochastic dynamics, the stochastic viability kernel describes the robust states, in which the system has a high probability of staying in the subset for a long time. Then, probability of resilience is defined as the maximal probability that the system reaches a robust state within a time horizon. Management strategies that maximize the probability of resilience can be found through dynamic programming. It is then possible to compute a range of statistics on the time for restoring the property. The approach is illustrated on the example of lake eutrophication and shown to foster the use of different indicators that are adapted to distinct situations. Its relevance for the management of ecological systems is also discussed.