Ecological models and the pitfalls of causality

After the disappointing experiences with complex ecological models in the days of the International Biological Program, dynamic modelling has never really recovered a convincing niche in applied ecology. Simple generic models have become the tool par excellence for the development of theory. However, the popularity of these abstract theoretical models among practical ecologists is marginal. It is argued that the antagonism against such models is largely due to a misconception about their possible role in the process of unravelling the functioning of ecological communities. We discuss the pitfalls of analyzing the driving causal relationships in real world ecosystems, and evaluate role for minimal models in this context.     

Does population ecology have general laws?

There is a widespread opinion among ecologists that ecology lacks general laws. In this paper I argue that this opinion is mistaken. Taking the case of population dynamics, I point out that there are several very general law-like propositions that provide the theoretical basis for most population dynamics models that were developed to address specific issues. Some of these foundational principles, like the law of exponential growth, are logically very similar to certain laws of physics (Newton's law of inertia, for example, is almost a direct analogue of exponential growth). I discuss two other principles (population self-limitation and resource-consumer oscillations), as well as the more elementary postulates that underlie them. None of the "laws" that I propose for population ecology are new. Collectively ecologists have been using these general principles in guiding development of their models and experiments since the days of Lotka, Volterra, and Gause.     

Does population ecology have general laws?

There is a widespread opinion among ecologists that ecology lacks general laws. In this paper the author argues that this opinion is mistaken. Taking the case of population dynamics, the author points out that there are several very general law-like propositions that provide the theoretical basis for most population dynamics models that were developed to address specific issues. Some of these foundational principles, like the law of exponential growth, are logically very similar to certain law of physics (Newton's law of intertia, for example, is almost a direct analogue of exponential growth). The author discusses two other principles (population self-limitation and resource-consumer oscillations), as well as the more elementary postulates that underlie them. None of the "laws" that the author proposes for population ecology are new. Collectively ecologists have been using these general principles in guiding development of their models and experiments since the days of Lotka, Volterra, and Gause.     

Defining ecology: Ecological theories,mathematical models,and applied biology in the 1960s and 1970s

Ever since the early decades of this century, there have emerged a number of competing schools of ecology that have attempted to weave the concepts underlying natural resource management and natural-historical traditions into a formal theoretical framework. It was widely believed that the discovery of the fundamental mechanisms underlying ecological phenomena would allow ecologists to articulate mathematically rigorous statements whose validity was not predicated on contingent factors. The formulation of such statements would elevate ecology to the standing of a rigorous scientific discipline on a par with physics. However, there was no agreement as to the fundamental units of ecology. Systems ecologists sought to identify the fundamental organization that tied the physical and biological components of ecosystems into an irreducible unit: the ecosystem was their fundamental unit. Population ecologists sought, instead, to identify the biological mechanisms regulating the abundance and distribution of plant and animal species: to these ecologists, the individual organism was the fundamental unit of ecology, and the physical environment was nothing more than a stage upon which the play of individuals in perennial competition took place. As Joel Hagen has pointed out, the two schools were thus dividied by fundamentally different and irreconcilable assumptions about the nature of ecosystems.Notwithstanding these divisive efforts to elevate the image of ecology, the discipline remained in the shadows of American academia until the mid-1960s, when systems ecologists succeeded in projecting ecology onto the national scene. They did so by seeking closer involvement with practical problems: they argued before Congress that their approach to the theoretical problems of ecology was uniquely suited to the solution of the impending environmental crisis. With the establishment of the International Biological Program, they succeeded in attracting unprecedented levels of funding for systems ecology research. Theoretical population ecologists, on the other hand, found themselves consigned to the outer regions of this new institutional landscape. The systems ecologists' successful capture of the limelight and the purse brought the divisions between them and population ecologists into sharper relief — hence the hardening of the division of ecology observed by Hagen.⁴⁵     

Modeling Taxa-Abundance Distributions in Microbial Communities using Environmental Sequence Data

We show that inferring the taxa-abundance distribution of a microbial community from small environmental samples alone is difficult. The difficulty stems from the disparity in scale between the number of genetic sequences that can be characterized and the number of individuals in communities that microbial ecologists aspire to describe. One solution is to calibrate and validate a mathematical model of microbial community assembly using the small samples and use the model to extrapolate to the taxa-abundance distribution for the population that is deemed to constitute a community. We demonstrate this approach by using a simple neutral community assembly model in which random immigrations, births, and deaths determine the relative abundance of taxa in a community. In doing so, we further develop a neutral theory to produce a taxa-abundance distribution for large communities that are typical of microbial communities. In addition, we highlight that the sampling uncertainties conspire to make the immigration rate calibrated on the basis of small samples very much higher than the true immigration rate. This scale dependence of model parameters is not unique to neutral theories; it is a generic problem in ecology that is particularly acute in microbial ecology. We argue that to overcome this, so that microbial ecologists can characterize large microbial communities from small samples, mathematical models that encapsulate sampling effects are required.     

植物-微生物互惠共生: 演化机制与生态功能

植物-微生物互惠共生是一种特殊的合作形式, 在整个生命和陆地生态系统的演化历史中起着至关重要的作用。在全球环境变化背景下, 植物和微生物间的互惠共生对生态系统功能的维持具有重要意义。尽管合作/互惠共生如此重要, 在生物学中却存在着对它的历史偏见与忽视。特别地, 尽管互惠共生的理论与建模发展已有较长的历史, 但不同学科分支间仍存在着多种不同的观点。本综述从两个看似对立的视角概述植物-微生物互惠共生的概念框架, 即微生物学家关心的微观机制和生态系统生态学家关注的宏观影响。宏观模型通常从一组过于简单的假设出发, 便于理论分析。但微观机制是开展定量预测的基础, 因此新一代基于过程的宏观模型需嵌入微观机制, 这对预测全球变化下的生态系统响应至关重要。此外, 希望本文也可以吸引更多学者关注合作/互惠的重要作用, 并将这一概念应用于解决其他生态学和社会学问题。     

H. A. GLEASON'S 'INDIVIDUALISTIC CONCEPT' AND THEORY OF ANIMAL COMMUNITIES: A CONTINUING CONTROVERSY

A tradition of natural history and of the lore of early twentieth-century ecology was that organisms lived together and interacted to form natural entities or communities. Before there was a recognizable science of ecology, Mobius (1877) had provided a name ‘biocoenosis’ for such entities. This concept persisted in the early decades of ecological science; at an extreme it was maintained that the community had integrating capabilities and organization like those of an individual organism, hence the term organismic community. In the 1950s- 1970s an alternative individualist concept, derived from the ideas of H. A. Gleason (1939), gained credence which held that communities were largely a coincidence of individualistic species characteristics, continuously varying environments and different probabilities of a species arriving on a given site. During the same period, however, a body of population based theory of animal communities became dominant which perpetuated the idea of patterns in nature based on biotic interactions among species resulting in integrated communities. This theory introduced an extended terminology and mathematical models to explain the organization of species into groups of compatible species governed by rules. In the late 1970s the premises and methods of the theory came under attack and a vigorous debate ensued. The alternatives proposed were, at an extreme, null models of random aggregations of species or stochastic, individualistic aggregations of species, sensu Gleason. Extended research and debate ensued during the 1980s resulting in an explosion of studies of animal communities and a plethora of symposia and volumes of collected works concerning the nature of animal communities. The inherent complexity of communities and the traditional differences among animal ecologists about how they should be defined and delimited, at what scale of taxa, space and time to study them, and appropriate methods of study and analysis have resulted in extended and as yet inconclusive discussions. Recent differences and discussions are considered under five general categories, evolution and community theory, individualistic concept, community definition, questions from community ecology and empirical studies. Communities are seen by some ecologists as entities of coevolving species and, in any case, it is necessary to integrate evolutionary ideas with the varied concepts of community. The individualistic concept of community, as a relative latecomer to discussions of animal community, is sometimes misconstrued as holding that communities are random assemblages of organisms without biotic interactions among species. Nevertheless, it has increasingly been accepted as supported by studies of diverse taxa and habitats. However, many other ecologists continue to argue for integrated, biotically controlled and evolved communities. Among the major difficulties of addressing the problems of community are problems of definition and terminology. One commentator noted that community ecology may be unique in the sciences because there is no consensus definition of community. One consequence of the lack of consensus definition is evident in the varied and diffuse questions posed in studies of community. Some critics of community ecology fault it for posing unanswerable questions. Recent empirical studies include various assessments about community ranging from deterministic, integrated and organismic to individualistic with various suggestions for compromise. The early emphasis on birds in studies of animal communities has expanded to obviate the argument that any position is constrained by the taxon studied. Insects, in general, are more prone to give rise to interpretation of a nonintegrated community. Parasite community studies have given rise to some distinctive categories and terminology. However, consensus is not achieved either within or among taxonomic groups or habitat groups. The extreme heterogeneity and complexity of communities (and of ecologists) has produced extended discussions of how to approach such multidimensional complexity. These discussions often turn on polarized positions of reductionism and experiment versus holism. Proponents of reductionism asserted that natural communities cannot be understood or their structure and organization predicted until experimental communities, or models thereof, are understood. Holists insisted that the inherent complexity and variability of communities cannot be elucidated in simplified experimental communities or in models. A more recent trend has urged pluralism, or, at least, mutual respect and dialogue, which are sometimes lacking, between proponents of these divergent approaches to communities. Recent work perpetuates the original dichotomy between integrated organismic community concept and individualistic non-integrated concept. The hope for a rule-governed community has extended to metarules and a new theory of community as divided into core species and satellite species is called into question. The problems of distinguishing between determinism and chance effects in community organization continue and the lost or fading hope of a general theory of community is revived in a search for rules that govern their assembly.     

The Hierarchical Structure of Ecosystems: Connections to Evolution

Ecologic systems, which are involved mainly in the processing of energy and materials, are actually nested one inside another—they are simultaneously parts and wholes. This fundamental hierarchical organization is easy to detect in nature but has been undervalued by ecologists as a source of new insights about the structure and development of ecosystems and as a means of understanding the crucial connections between ecologic processes and large-scale evolutionary patterns. These ecologic systems include individual organisms bundled into local populations, populations as functional components of local communities or ecosystems, local systems making up the working parts of larger regional ecosystems, and so on, right up to the entire biosphere. Systems at any level of organization can be described and interpreted based on aspects of scale (size, duration, and “membership” in more inclusive entities), integration (all the vital connections both at a particular focal level and across levels of hierarchical organization), spatiotemporal continuity (the “life history” of each system), and boundaries (either membranes, skins, or some other kind of border criterion). Considering hierarchical organization as a general feature of ecologic systems could reinvigorate theoretical ecology, provide a realistic scaling framework for paleoecologic studies, and – most importantly – forge new and productive connections between ecology and evolutionary theory.     

Challenges in modelling complexity of fungal entomopathogens in semi-natural populations of insects

The use of fungal entomopathogens as microbial control agents has driven studies into their ecology in crop ecosystems. Yet, there is still a lack of understanding of the ecology of these insect pathogens in semi-natural habitats and communities. We review the literature on prevalence of fungal entomopathogens in insect populations and highlight the difficulties in making such measurements. We then describe the theoretical host-pathogen models available to examine the role that fungal entomopathogens could play in regulating insect populations in semi-natural habitats, much of the inspiration for which has been drawn from managed systems, particularly forests. We further emphasise the need to consider the complexity, and particularly the heterogeneity, of semi-natural habitats within the context of theoretical models and as a framework for empirical studies. We acknowledge that fundamental gaps in understanding fungal entomopathogens from an ecological perspective coupled with a lack of empirical data to test theoretical predictions is impeding progress. There is an increasing need, especially under current rapid environmental change, to improve our understanding of the role of fungi in insect population dynamics beyond the context of forestry and agriculture.     

The anarchist's guide to ecological theory. Or, we don't need no stinkin' laws

Several ecologists have recently suggested that ecology has several laws. This conclusion contrasts with the views of some philosophers of science, who have suggested that biology cannot have laws. I argue that the debate has been confused because two very different types of law can be recognised: correlative and causal laws. Once we recognise that there is a difference, the argument against causal laws becomes stronger, and instead I suggest that ecologists should recognise that they can and do produce generalisations that are used to build models – nomological machines – that describe the ecological systems they are studying.     

What is the role of predation on stability of natural communities? A theoretical investigation.

A basic question in ecology concerns the role of species interaction on dynamics of natural communities. In this framework, ecologists have considered predation, competition, mutualism, the three most important interactions, highlighting their specific effects on distribution and abundance of species, providing knowledge about phenomena like coexistence and extinction. This paper seeks to identify the effects of predation on stability of natural communities by mathematical models. Simple multispecies community models, organized in trophic levels, are analyzed by means of a qualitative technique, loop analysis, combined with a computer calculation procedure. Results do not support the hypothesis of predation as a stabilizing factor. Rather, the outcomes of the analysis suggest that predation may or may not stabilize a community. This depends on the predator's behaviour and on the network of the community.     

生态化学计量学研究进展

生态化学计量学结合生物学、化学和物理学等基本原理,研究能量和碳、氮、磷等化学元素在生态系统中,特别是各种生态系统过程(如竞争、捕食、寄生、共生等)参与者中的变化,以及它们之间的动态平衡,并分析这种平衡对生态系统的影响。目前,C∶N∶P化学计量学研究已深入到生态学的各个层次(细胞、个体、种群、群落、生态系统)及区域等不同尺度。近年来,由于认识到化学计量学研究可以把生态实体的各个层次在元素水平上统一起来,因此生态化学计量学已成为许多生态系统的新兴研究工具。其中,C∶N∶P化学计量学是各种生态过程研究中的核心内容。论述了生态化学计量学在物种、群落、生态系统等各层次的应用现状,并指出了C∶N∶P化学计量学研究的应用前景和发展趋势,以期引起同行的重视并推动该领域的进一步发展。     

The scope of mission-orientation in Dutch fresh-water ecology

In response to growing concern about environmental problems ecologists have engaged in a variety of mission-oriented efforts in which they claim to have taken into account the objective of helping to solve environmental problems in their research strategies or research programmes. The significance of these efforts is evaluated here in terms of both the theoretical development of the field of ecology and its orientation towards social objectives.Three examples of mission-orientation are analyzed on the basis of a case-study of Dutch fresh-water ecology; (1) ecosystems research within the framework of the International Biological Programme; (2) landscape ecology, and (3) ecological research on the management of fresh-water resources. These examples demonstrate that in principle the scope of missionorientation in ecology can be broad. In Dutch fresh-water ecology, however, two specific approaches have become particularly institutionalized. The ecologists tended to opt either for theory-centered approaches close to the type of research carried out by ecologists developing the field regardless of any societal mission or for problem-centered approaches without much emphasis on theory development. Types of mission-orientation which can be placed between these extremes have been established only to a limited extent in Dutch fresh-water ecology.     

Understanding movement data and movement processes: current and emerging directions

Animal movement has been the focus on much theoretical and empirical work in ecology over the last 25 years. By studying the causes and consequences of individual movement, ecologists have gained greater insight into the behavior of individuals and the spatial dynamics of populations at increasingly higher levels of organization. In particular, ecologists have focused on the interaction between individuals and their environment in an effort to understand future impacts from habitat loss and climate change. Tools to examine this interaction have included: fractal analysis, first passage time, Lévy flights, multi‐behavioral analysis, hidden markov models, and state‐space models. Concurrent with the development of movement models has been an increase in the sophistication and availability of hierarchical bayesian models. In this review we bring these two threads together by using hierarchical structures as a framework for reviewing individual models. We synthesize emerging themes in movement ecology, and propose a new hierarchical model for animal movement that builds on these emerging themes. This model moves away from traditional random walks, and instead focuses inference on how moving animals with complex behavior interact with their landscape and make choices about its suitability.     

Regional effects as important determinants of local diversity in both marine and terrestrial systems

Community ecologists have struggled to create unified theories across diverse ecosystems, but it has been difficult to acertain whether marine and terrestrial communities differ in the mechanisms responsible for structure and dynamics. One apparent difference between marine and terrestrial ecology is that the influence of regional processes on local populations and communities is better established in the marine literature. We examine three potential explanations: 1) influential early studies emphasized local interactions in terrestrial communities and regional dispersal in marine communities. 2) regional‐scale processes are actually more important in marine than in terrestrial communities. 3) recruitment from a regional species pool is easier to study in marine than terrestrial communities. We conclude that these are interrelated, but that the second and especially the third explanations are more important than the first. We also conclude that in both marine and terrestrial systems, there are ways to improve our understanding of regional influences on local community diversity. In particular, we advocate examining local vs regional diversity relationships at localities within environmentally similar regions that differ in their diversity either because of their sizes or their varying degrees of isolation from a species source.     

Idealized, Inaccurate but Successful: A Pragmatic Approach to Evaluating Models in Theoretical Ecology

Ecologists attempt to understand the diversity of life with mathematical models. Often, mathematical models contain simplifying idealizations designed to cope with the blooming, buzzing confusion of the natural world. This strategy frequently issues in models whose predictions are inaccurate. Critics of theoretical ecology argue that only predictively accurate models are successful and contribute to the applied work of conservation biologists. Hence, they think that much of the mathematical work of ecologists is poor science. Against this view, I argue that model building is successful even when models are predictively inaccurate for at least three reasons: models allow scientists to explore the possible behaviors of ecological systems; models give scientists simplified means by which they can investigate more complex systems by determining how the more complex system deviates from the simpler model; and models give scientists conceptual frameworks through which they can conduct experiments and fieldwork. Critics often mistake the purposes of model building, and once we recognize this, we can see their complaints are unjustified. Even though models in ecology are not always accurate in their assumptions and predictions, they still contribute to successful science.     

A complex speciation-richness relationship in a simple neutral model

Speciation is the "elephant in the room" of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities. We focus on the relationship between speciation, richness, and the spatial structure of communities. We find a strong opposition between speciation and local richness, with speciation being more common in isolated communities and local richness being higher in more connected communities. Unlike previous models, we also find a transition to a positive relationship between speciation and local richness when dispersal is low and the number of communities is small. We use several measures of centrality to characterize the effect of network structure on diversity. The degree, the simplest measure of centrality, is the best predictor of local richness and speciation, although it loses some of its predictive power as connectivity grows. Our framework shows how a simple neutral model can be combined with network theory to reveal complex relationships between speciation, richness, and the spatial organization of populations.     

Beyond simple adaptation: Incorporating other evolutionary processes and concepts into eco-evolutionary dynamics

Studies of eco-evolutionary dynamics have integrated evolution with ecological processes at multiple scales (populations, communities and ecosystems) and with multiple interspecific interactions (antagonistic, mutualistic and competitive). However, evolution has often been conceptualised as a simple process: short-term directional adaptation that increases population growth. Here we argue that diverse other evolutionary processes, well studied in population genetics and evolutionary ecology, should also be considered to explore the full spectrum of feedback between ecological and evolutionary processes. Relevant but underappreciated processes include (1) drift and mutation, (2) disruptive selection causing lineage diversification or speciation reversal and (3) evolution driven by relative fitness differences that may decrease population growth. Because eco-evolutionary dynamics have often been studied by population and community ecologists, it will be important to incorporate a variety of concepts in population genetics and evolutionary ecology to better understand and predict eco-evolutionary dynamics in nature.     

Levels of organization in biology: on the nature and nomenclature of ecology's fourth level

Viewing the universe as being composed of hierarchically arranged systems is widely accepted as a useful model of reality. In ecology, three levels of organization are generally recognized: organisms, populations, and communities (biocoenoses). For half a century increasing numbers of ecologists have concluded that recognition of a fourth level would facilitate increased understanding of ecological phenomena. Sometimes the word "ecosystem" is used for this level, but this is arguably inappropriate. Since 1986, I and others have argued that the term "landscape" would be a suitable term for a level of organization defined as an ecological system containing more than one community type. However, "landscape" and "landscape level" continue to be used extensively by ecologists in the popular sense of a large expanse of space. I therefore now propose that the term "ecoscape" be used instead for this fourth level of organization. A clearly defined fourth level for ecology would focus attention on the emergent properties of this level, and maintain the spatial and temporal scale-free nature inherent in this hierarchy of organizational levels for living entities.