The unified neutral theory of biodiversity: do the numbers add up?

Hubbell's unified neutral theory is a zero-sum ecological drift model in which population sizes change at random in a process resembling genetic drift, eventually leading to extinction. Diversity is maintained within the community by speciation. Hubbell's model makes predictions about the distribution of species abundances within communities and the turnover of species from place to place (beta diversity). However, ecological drift cannot be tested adequately against these predictions without independent estimates of speciation rates, population sizes, and dispersal distances. A more practical prediction from ecological drift is that time to extinction of a population of size N is approximately 2N generations. I test this prediction here using data for passerine birds (Passeriformes). Waiting times to speciation and extinction were estimated from genetic divergence between sister populations and a lineage-through-time plot for endemic South American suboscine passerines. Population sizes were estimated from local counts of birds in two large forest plots extrapolated to the area of wet tropical forest in South America and from atlas data on European passerines. Waiting times to extinction (ca. 2 Ma) are much less than twice the product of average population size (4.0 and 14.4 x 10(6) individuals in South America and Europe) and generation length (five and three years) for songbirds, that is, 40 and 86 Ma, respectively. Thus, drift is too slow to account for turnover in regional avifaunas. Presumably, other processes, involving external drivers, such as climate and physiographic change, and internal drivers, such as evolutionary change in antagonistic interactions, predominate. Hubbell's model is historical and geographic, and his perspective importantly links local and regional process and pattern. Ecological reality can be added to the mix while retaining Hubbell's concept of continuity of communities in space and time.     

Compositional divergence and convergence in arbuscular mycorrhizal fungal communities

In spite of the controversy that they have generated, neutral models provide ecologists with powerful tools for creating dynamic predictions about beta-diversity in ecological communities. Ecologists can achieve an understanding of the assembly rules operating in nature by noting when and how these predictions are met or not met. This is particularly valuable for those groups of organisms that are challenging to study under natural conditions (e.g., bacteria and fungi). Here, we focused on arbuscular mycorrhizal fungal (AMF) communities and performed an extensive literature search that allowed us to synthesize the information in 19 data sets with the minimal requisites for creating a null hypothesis in terms of community dissimilarity expected under neutral dynamics. In order to achieve this task, we calculated the first estimates of neutral parameters for several AMF communities from different ecosystems. Communities were shown either to be consistent with neutrality or to diverge or converge with respect to the levels of compositional dissimilarity expected under neutrality. These data support the hypothesis that divergence occurs in systems where the effect of limited dispersal is overwhelmed by anthropogenic disturbance or extreme biological and environmental heterogeneity, whereas communities converge when systems have the potential for niche divergence within a relatively homogeneous set of environmental conditions. Regarding the study cases that were consistent with neutrality, the sampling designs employed may have covered relatively homogeneous environments in which the effects of dispersal limitation overwhelmed minor differences among AMF taxa that would lead to environmental filtering. Using neutral models we showed for the first time for a soil microbial group the conditions under which different assembly processes may determine different patterns of beta-diversity. Our synthesis is an important step showing how the application of general ecological theories to a model microbial taxon has the potential to shed light on the assembly and ecological dynamics of communities.     

Adaptive speciation theory: a conceptual review

Speciation—the origin of new species—is the source of the diversity of life. A theory of speciation is essential to link poorly understood macro-evolutionary processes, such as the origin of biodiversity and adaptive radiation, to well understood micro-evolutionary processes, such as allele frequency change due to natural or sexual selection. An important question is whether, and to what extent, the process of speciation is ‘adaptive’, i.e., driven by natural and/or sexual selection. Here, we discuss two main modelling approaches in adaptive speciation theory. Ecological models of speciation focus on the evolution of ecological differentiation through divergent natural selection. These models can explain the stable coexistence of the resulting daughter species in the face of interspecific competition, but they are often vague about the evolution of reproductive isolation. Most sexual selection models of speciation focus on the diversification of mating strategies through divergent sexual selection. These models can explain the evolution of prezygotic reproductive isolation, but they are typically vague on questions like ecological coexistence. By means of an integrated model, incorporating both ecological interactions and sexual selection, we demonstrate that disruptive selection on both ecological and mating strategies is necessary, but not sufficient, for speciation to occur. To achieve speciation, mating must at least partly reflect ecological characteristics. The interaction of natural and sexual selection is also pivotal in a model where sexual selection facilitates ecological speciation even in the absence of diverging female preferences. In view of these results, it is counterproductive to consider ecological and sexual selection models as contrasting and incompatible views on speciation, one being dominant over the other. Instead, an integrative perspective is needed to achieve a thorough and coherent understanding of adaptive speciation.     

Coexistence of the niche and neutral perspectives in community ecology

The neutral theory for community structure and biodiversity is dependent on the assumption that species are equivalent to each other in all important ecological respects. We explore what this concept of equivalence means in ecological communities, how such species may arise evolutionarily, and how the possibility of ecological equivalents relates to previous ideas about niche differentiation. We also show that the co-occurrence of ecologically similar or equivalent species is not incompatible with niche theory as has been supposed, because niche relations can sometimes favor coexistence of similar species. We argue that both evolutionary and ecological processes operate to promote the introduction and to sustain the persistence of ecologically similar and in many cases nearly equivalent species embedded in highly structured food webs. Future work should focus on synthesizing niche and neutral perspectives rather than dichotomously debating whether neutral or niche models provide better explanations for community structure and biodiversity.     

Neutral modelling of agricultural landscapes by tessellation methods—Application for gene flow simulation

Neutral landscape models are not frequently used in the agronomical domain, whereas they would be very useful for studying given agro-ecological or physical processes. Contrary to ecological neutral landscape models, agricultural models have to represent and manage geometrical patches and thus should rely on tessellation methods. We present a three steps approach that aimed at simulating such landscapes. Firstly, we characterized the geometry of three real field patterns; secondly, we generated simulated field patterns with two tessellation methods attempting to control the value of some of the observed characteristics and, thirdly, we evaluated the simulated field patterns. For this evaluation, we considered that good simulated field patterns should capture characteristics of real landscapes that are important for the targeted agro-ecological process. Real landscapes and landscapes simulated using either a Voronoi or a rectangular tessellation were thus compared when used as input data within a gene flow model. The results showed that neither tessellation method captured field shapes correctly, thus leading to over or (small) under estimation of gene flow. The Voronoi tessellation, though, performed better than the rectangular tessellation. Possible research directions are proposed to improve the simulated patterns, including the use of post-processing, the control of cell orientation or the implementation of other tessellation techniques.     

Marine biology: the role of accommodation in shaping marine biodiversity

A review of evidence from two kinds of studies conducted in the marine environment suggests a species relationship not previously recognized as being consistent and widespread. In the first instance, observations on species invading from a more diverse ecosystem into a less diverse ecosystem indicate that successful colonizations take place because space is yielded by their ecological equivalents. In the second instance, widespread studies show that any community, rich or poor, located in tropical or cold waters, is vulnerable to invasions by species from a larger, more diverse region. Furthermore, the species richness of a community apparently depends upon that of the region to which it belongs. Together, these observations indicate the existence of a general rule which states that if an invader becomes established, it is permitted to do so by an accommodation on the part of the species that occupies the preferred ecological space. Paleontological data on invasions provide evidence of speciation following accommodation. This leads to the recognition of a three-step process: invasion to accommodation to speciation (IAS). This process, which may be called the IAS mechanism, may have contributed to historical rises of global biodiversity.     

Migratory orientation of red-eyed vireos,Vireo olivaceus,in relation to energetic condition and ecological context

How and when migrants integrate directional information from different sources may depend not only on the bird’s internal state, including fat stores, but also on the ecological context during passage. We designed experiments to (1) examine the influence of stored fat on the decision to migrate and on the choice of migratory direction and (2) investigate how the integration of orientation cue information is tied to energetic status in relation to migration across an ecological barrier. Migratory orientation of red-eyed vireos (Vireo olivaceus) at twilight was recorded using two different techniques, orientation cage experiments and free-flight release tests, during both fall and spring migration. During fall migration, the amount of stored fat proved decisive for directional selections of the vireos. Fat birds chose directions in accordance with migration across the Gulf of Mexico. Lean birds oriented either parallel to the coast line (cage tests) or moved inland (free-flight releases). Whereas only fat birds showed significant responses to experimental deflections of the geomagnetic field, lean birds displayed a tendency to shift their activity in the expected direction, making it difficult to evaluate the prediction that use of the magnetic compass is context dependent. Fat loads also had a significant effect on the decision to migrate, i.e., fat individuals were more likely to embark on migration than were lean birds (true for both cage and release experiments). During spring migration, a majority of experimental subjects were classified as lean, following their arrival after crossing the Gulf of Mexico, and oriented in seasonally appropriate directions. The vireos also showed significant responses to experimental deflections of the geomagnetic field regardless of their energetic status. Free-flight release experiments during spring migration revealed a significant difference in mean directions between clear sky and overcast tests. The difference may indicate a compensatory response to wind drift or possibly a need for celestial cues to calibrate the magnetic compass. Finally, this is the first demonstration of magnetic compass orientation in a North American vireo. Received: 15 December 1995/Accepted after revision: 24 March 1996     

Network-based exploration and visualisation of ecological data

Networks – structured graphs consisting of sets of nodes connected by edges – provide a rich framework for data visualisation and exploratory analyses. Although rarely used for the visualisation of ecological data, networks are well suited to this purpose, including data that one might not normally think of as a network. We present a simple method for transforming a data matrix into network format, and show how this can be used as the basis for interactive exploratory analyses of ecological data.The method is demonstrated using a database of marine zooplankton samples acquired in the Southern Ocean. The network analyses revealed zooplankton community structures that are in good agreement with previously published results. Variations in community structure were observed to be related to the temporal and spatial pattern of sampling, as well as to physical environmental factors such as sea ice cover. The analyses also revealed a number of errors in the data, including taxon identification errors and instrument failures.The method allows the analyst to generate networks from different combinations of variables in the data set, and to examine the effects of varying parameters such as the scales of spatial, temporal, and taxonomic aggregation. This flexibility allows the analyst to rapidly gain a number of perspectives on the data and provides a powerful mechanism for exploration.     

A critique of statistical aspects of ecological studies in spatial epidemiology

In this article, the mathematical assumptions of a number of commonly used ecological regression models are made explicit, critically assessed, and related to ecological bias. In particular, the role and interpretation of random effects models are examined. The modeling of spatial variability is considered and related to an underlying continuous spatial field. The examination of such a field with respect to the modeling of risk in relation to a point source highlights an inconsistency in commonly used approaches. A theme of the paper is to examine how plausible individual-level models relate to those used in practice at the aggregate level. The individual-level models acknowledge confounding, within-area variability in exposures and confounders, measurement error and data anomalies and so we can examine how the area-level versions consider these aspects. We briefly discuss designs that efficiently sample individual data and would appear to be useful in environmental settings.     

The effects of direct and indirect constraints on biological communities

Human activities are expected to result in a diversity of directional or stochastic constraints that affect species either directly or by indirectly impacting their resources. However, there is no theoretical framework to predict the complex and various effects of these constraints on ecological communities. We developed a dynamic model that mimics the use of different resource types by a community of competing species. We investigated the effects of different environmental constraints (affecting either directly the growth rate of species or having indirect effects on their resources) on several biodiversity indicators. Our results indicate that (i) in realistic community models (assuming uneven resource requirements among species) the effects of perturbations are strongly buffered compared to neutral models; (ii) the species richness of communities can be maximized for intermediate levels of direct constraints (unimodal response), even in the absence of trade-off between competitive ability and tolerance to constraints; (iii) no such unimodal response occurs with indirect constraints; (iv) an increase in the environmental (e.g., climatic) variance may have different effects on community biomass and species richness.     

A review of recent developments in lake modelling

This paper reviews the lake models published the last five years, mainly in Ecological Modelling. The review shows that structurally dynamic modelling and coupling between hydrodynamic and ecological models are applied increasingly. A number of processes that have not been included in lake models before have been proposed. It has been shown that these additional processes in specific case studies are significant, for instance the competition between phytoplankton and macrophytes or cyanobacteria growth and growth of mussels. It is recommended to study these models for the development of models for case studies where these processes are relevant.     

Reconciling empirical ecology with neutral community models

Neutral community models embody the idea that individuals are ecologically equivalent, having equal fitness over all environmental conditions, and describe how the spatial dynamics and speciation of such individuals can produce a wide range of patterns of distribution, diversity, and abundance. Neutral models have been controversial, provoking a rush of tests and comments. The debate has been spurred by the suggestion that we should test mechanisms. However, the mechanisms and the spatial scales of interest have never clearly been described, and consequently, the tests have often been only peripherally relevant. At least two mechanisms are present in spatially structured neutral models. Dispersal limitation causes clumping of a species, which increases the strength of intraspecific competition and reduces the strength of interspecific competition. This may prolong coexistence and enhance local and regional diversity. Speciation is present in some neutral models and gives a donor-controlled input of new species, many of which remain rare or are short lived, but which directly add to species diversity. Spatial scale is an important consideration in neutral models. Ecological equivalence and equal fitness have implicit spatial scales because dispersal limitation and its emergent effects operate at population levels, and populations and communities are defined at a chosen spatial scale in recent neutral models; equality is measured relative to a metacommunity, and this necessitates defining the spatial scale of that metacommunity. Furthermore, dispersal has its own scales. Thorough empirical tests of neutral models will require both tests of mechanisms and pattern-producing ability, and will involve coupling theoretical models and experiments.     

种群水平生态风险评价方法概述及其在环境管理中的应用

生态风险评价的目的是保护生态系统功能的完整性、稳定性和持久性,为环境风险管理提供理论依据。然而,目前常见的用于保护生物的化学污染物浓度阈值大多是以个体水平的毒性试验结果为基础,忽略了物种在时间和空间相互作用等因素,不能够完全保护生态环境安全和生态系统功能的延续性。本文从生态风险评价的概念、目的和意义引出种群水平生态风险评价在环境管理应用的重要性,综述了种群水平生态风险评价的科学问题(如密度依赖、遗传变异和空间结构等),归纳了种群水平风险评价主要模型方法及其应用(如Euler-Lotka方程、预测矩阵、个体模型、空间模型和动态能量预算模型等),列举了各国现有法律法规中关于种群水平生态风险评价的规定,以期为种群水平生态风险评价方法研究及在环境管理中的应用提供有益借鉴。     

State-of-the-art of ecological modelling with emphasis on development of structural dynamic models

The paper deals with two major problems in ecological modelling today, namely how to get reliable parameters? and how to build ecosystem properties into our models? The use of new mathematical tools to answer these questions is mentioned briefly, but the main focus of the paper is on development of structural dynamic models which are models using goal functions to reflect a current change of the properties of the biological components in the models. These changes of the properties are due to the enormous adaptability of the biological components to the prevailing conditions. All species in an ecosystem attempt to obtain most biomass, i.e. to move as far away as possible from thermodynamic equilibrium which can be measured by the thermodynamic concept exergy. Consequently, exergy has been proposed as a goal function in ecological models with dynamic structure, meaning currently changed properties of the biological components and in model language currently changed parameters. An equation to compute an exergy index of a model is presented. The theoretical considerations leading to this equation are not presented here but references to literature where the basis theory can be found are given. Two case studies of structural dynamic modelling are presented: a shallow lake where the structural dynamic changes have been determined before the model was developed, and the application of biomanipulation in lake management, where the structural dynamic changes are generally known. Moreover. it is also discussed how the same idea of using exergy as a goal function in ecological modelling may be applied to facilitate the estimation of parameters.     

Appreciating Ecological Complexity: Habitat Contours as a Conceptual Landscape Model

Abstract:  Organisms respond to their surroundings at multiple spatial scales, and different organisms respond differently to the same environment. Existing landscape models, such as the "fragmentation model" (or patch-matrix-corridor model) and the "variegation model," can be limited in their ability to explain complex patterns for different species and across multiple scales. An alternative approach is to conceptualize landscapes as overlaid species-specific habitat contour maps. Key characteristics of this approach are that different species may respond differently to the same environmental conditions and at different spatial scales. Although similar approaches are being used in ecological modeling, there is much room for habitat contours as a useful conceptual tool. By providing an alternative view of landscapes, a contour model may stimulate more field investigations stratified on the basis of ecological variables other than human-defined patches and patch boundaries. A conceptual model of habitat contours may also help to communicate ecological complexity to land managers. Finally, by incorporating additional ecological complexity, a conceptual model based on habitat contours may help to bridge the perceived gap between pattern and process in landscape ecology. Habitat contours do not preclude the use of existing landscape models and should be seen as a complementary approach most suited to heterogeneous human-modified landscapes.     

Ecosystem states: Creating a data-derived, ecosystem-scale ecological response model that is explicit in space and time

Increasing difficulties associated with balancing consumptive demands for water and achieving ecological benefits in aquatic ecosystems provide opportunities for new ecosystem-scale ecological response models to assist managers. Using an Australian estuary as a case study, we developed a novel approach to create a data-derived state-and-transition model. The model identifies suites of co-occurring birds, fish, benthic invertebrates and aquatic macrophytes (as ‘states’) and the changing physico-chemical conditions that are associated with each (‘transitions’). The approach first used cluster analysis to identify sets of co-occurring biota. Differences in the physico-chemical data associated with each state were identified using classification trees, with the biotic distinctness of the resultant statistical model tested using analysis of similarities. The predictive capacity of the model was tested using new cases. Two models were created using different time-steps (annual and quarterly) and then combined to capture both longer-term trends and more-recent declines in ecological condition. We identified eight ecosystem states that were differentiated by a mix of water-quantity and water-quality variables. Each ecosystem state represented a distinct biotic assemblage under well-defined physico-chemical conditions. Two ‘basins of attraction’ were identified, with four tidally-influenced states, and another four independent of tidal influence. Within each basin, states described a continuum of relative health, manifest through declining taxonomic diversity and abundances. The main threshold determining relative health was whether freshwater flows had occurred in the region during the previous 339 days. Canonical analyses of principal coordinates tested the predictive capacity of the model and demonstrated that the variance in the environmental data set was well captured (87%) with 52% of the variance in the biological data set also captured. The latter increased to >80% when long- and short-term biological data were analysed separately, indicating that the model described the available data for the Coorong well. This approach thus created a data-derived, multivariate model, where neither states nor transitions were determined a priori. The approach did not over-fit the data, was robust to patchy or missing data, the choice of initial clustering technique and random errors in the biological data set, and was well-received by local natural resource managers. However, the model did not capture causal relationships and requires additional testing, particularly during future episodes of ecological recovery. The approach shows significant promise for simplifying management definitions of ecological condition and, via scenario analyses, can be used to assist in manager decision-making of large, complex aquatic ecosystems in the future.     

Community-scale analysis of the farmland abandonment occurrence process in the mountain region of Ladakh,India

Farmland abandonment has been a significant issue in mountain regions. Thus, many studies have attempted to uncover its driving factors. Most existing studies take a large- or meso-scale view of mountain regions, and there are a few studies that provide community-level analysis. Therefore, it is unclear how ecological and sociopolitical factors are actually combined to influence farmland abandonment at a community level. Thus, we conducted a field survey in the mountain village of Ladakh, northern India, beginning in 2009 and tried to understand the farmland abandonment occurrence process from the viewpoint of traditional altitudinal models of land use. Using data collected during the survey, a relationship between altitude and farmland abandonment was established. However, this relationship was complex, combining traditional forms of land use system in the village. The altitudinal model of land use was very common in mountain regions; thus, discussions of current land use issues should be based on an understanding of such traditional altitudinal systems.     

Modeling an exploited rocky coastal ecosystem: Bahia Tortugas, Mexico

A trophic structure model of the rocky coastal ecosystem in Bahia Tortugas, Mexico was constructed using Ecopath software to represent the main biomass flows in the system. Data for the model came from field observations (biomass estimates, stomach contents, and ecological observations for sea snails, abalones, lobster, some demersal finfishes, and macroalgae) carried out through ten field trips from 2006 to 2008. The results provide a snapshot of how the ecosystem operates. The model considers 23 functional groups. The total system throughput was 553 t/km²/year, 57% corresponds to internal consumption, 28% to respiration, 14% becomes detritus, and only 1% is removed through commercial fishing. The model suggests that even for exploited populations, predation and competition are heavier stresses than current fishing effort; however, because spiny lobster showed the second highest keystoneness’ index value, increasing fishing pressure on this group could strongly impact the entire ecosystem. We believe that this model has the potential to support management by allowing the exploration of the potential impacts of different fishing decisions at ecosystem level.     

Species and speciation in poikilothermal animals

On the basis of current scientific information related to intraspecific and interspecific variability of eco-physiological properties at the individual (organismic) and subindividual (tissues, cells, and molecules) levels and his own experimental data, the author comes to the conclusion that eco-physiological adaptation is one of the major processes determining speciation. During sequential multi-step adaptation at the most sensitive and plastic levels of organisation (whole organisms and their labile cells and proteins) to changed abiotic (physico-chemical) environmental factors, the latter directly affect the conservative proteins and polynucleotides that maintain the species' genetic information. Transition from phenotypical to genotypical changes may be achieved if the organisms have attained the limit of their phenotypical plasticity, via selection at cellular and molecular levels. The high rate of cellular mytotic division and a promiment rise in the speed of interrelated DNA-RNA protein synthesis under sudden and profound environmental changes may account for the high rates of speciation indicative of cataclysmic climatic changes. Evolutionary morphological changes are considered to follow physiological changes. The adaptive nature of morphological peculiarities in higher taxonomic categories (type, class, order, family; more seldom genus) may be accounted for by the selection of phenotypes possessing morphological peculiarities best suited to the ecological niches of the species concerned. These peculiarities (although often neutral to physiological changes that have determined the speciation) are transferred from species to species, manifesting both historical relationship and morphological unity. The suggested scheme of speciation is in accord with the conceptions of the intermittent character of speciation, which can proceed only if extreme, directed, climatic changes cover a larger portion of the species' area. As the organisms' organisation becomes more complex during phylogenesis, intraspecific variability decreases; this trend manifests itself in the progressive stabilization of body shape and other morphological properties, and in the increase of eco-physiological stability of cells and proteins.