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.     

Ecomanagement of biodiversity and ecosystem functioning in the Mediterranean Sea: concerns and strategies

Marine biodiversity is generally higher in benthic than in pelagic systems, and in coastal than in open sea systems. Sediments are the most human-impacted domain and therefore represent the target zone for both the study and actions needed for the preservation of biodiversity. Losses of marine diversity, higher (or simply more evident) in coastal areas, are generally the result of conflicting uses of coastal habitats. Large difficulties arise from the analysis and evaluation of the actual biodiversity, especially when different environments are compared, as often studies on biodiversity are dependent upon the distribution of the specialists. On the other hand, losses of marine biodiversity might be underestimated, due to the limited knowledge of the ecosystems' functioning, of the species inhabiting various habitats and of the still limited capacity to assess microbial biodiversity, which represents the largest fraction of the global marine biodiversity. Finally, claimed losses of biodiversity might be just apparent, as the sea floor is a bank of resting stages of various plankton species that are likely to spend even decades in the sediment before reactivating and inducing unattended blooms in the water column. The Mediterranean Sea displays high species diversity, but might reach the highest values in terms of adaptive strategies and functional diversity. Moreover, the Mediterranean Sea represents also a key area for the study of the relative influences of the natural and anthropogenic changes on biodiversity and its consequences on ecosystem functioning. Habitat destruction, over-fishing, contaminants, eutrophication, introduction of alien species, and climate changes are producing increasingly evident changes in community structure and biodiversity of this warm and miniature ocean. We summarized the main effects of different disruptive agents on the marine biodiversity of the Mediterranean Sea, with special attention on the biodiversity relevance in ecosystem functioning and possible implications in bio-geochemical cycles. The present overview aims at focusing and synthesizing the most important factors potentially affecting the interactions between biodiversity and ecosystem functioning in the Mediterranean in order to better define possible strategies of conservation and eco-management.     

有机农业与常规农业对农田生物多样性影响的比较研究进展

一些研究者认为,有机农业不仅在理念上而且在实践上,都有助于促进农田生物多样性的维持和保护.为了促进我国科学界对有机农业与农田生物多样性关联性研究的关注,综述了有机农业对农田生态系统内杂草、地表节肢动物、土壤生物以及鸟类等不同生物类群种类、数量及其多样性的影响.     

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.     

Distinguishing stressors acting on land bird communities in an urbanizing environment

Urbanization has profound influences on ecological communities, but our understanding of causal mechanisms is limited by a lack of attention to its component stressors. Published research suggests that at landscape scales, habitat loss and fragmentation are the major drivers of community change, whereas at local scales, human activity and vegetation management are the primary stressors. Little research has focused on whether urbanization stressors may supplant natural factors as dominant forces structuring communities. We used model selection to determine the relative importance of urban development, human activity, local and landscape vegetation, topography, and geographical location in explaining land bird species richness, abundance, and dominance. We analyzed the entire community and groups of species based on ecological characteristics, using data collected in remnant forests along a gradient of urban development in the Lake Tahoe basin, California and Nevada, USA. Urbanization stressors were consistently among the principal forces structuring the land bird community. Strikingly, disturbance from human activity was the most important factor for richness in many cases, surpassing even habitat loss from development. Landscape-scale factors were consistently more important than local-scale factors for abundance. In demonstrating considerable changes in land bird community structure, our results suggest that ecosystem function in urban areas may be severely compromised. Such changes compel local- and landscape-scale management, focused research, and long-term monitoring to retain biodiversity in urban areas to the extent possible.     

Neutral theory and the evolution of ecological equivalence

Since the publication of the unified neutral theory in 2001, there has been much discussion of the theory, pro and con. The hypothesis of ecological equivalence is the fundamental yet controversial idea behind neutral theory. Assuming trophically similar species are demographically alike (symmetric) on a per capita basis is only an approximation, but it is equivalent to asking: How many of the patterns of ecological communities are the result of species similarities, rather than of species differences? The strategy behind neutral theory is to see how far one can get with the simplification of assuming ecological equivalence before introducing more complexity. In another paper, I review the empirical evidence that led me to hypothesize ecological equivalence among many of the tree species in the species-rich tropical forest on Barro Colorado Island (BCI). In this paper, I develop a simple model for the evolution of ecological equivalence or niche convergence, using as an example evolution of the suite of life history traits characteristic of shade tolerant tropical tree species. Although the model is simple, the conclusions from it seem likely to be robust. I conclude that ecological equivalence for resource use are likely to evolve easily and often, especially in species-rich communities that are dispersal and recruitment limited. In the case of the BCI forest, tree species are strongly dispersal- and recruitment-limited, not only because of restricted seed dispersal, but also because of low recruitment success due to heavy losses of the seedling stages to predators and pathogens and other abiotic stresses such as drought. These factors and the high species richness of the community strongly reduce the potential for competitive exclusion of functionally equivalent or nearly equivalent species.     

Host-plant genotypic diversity mediates the distribution of an ecosystem engineer

Ecosystem engineers affect ecological communities by physically modifying the environment. Understanding the factors determining the distribution of engineers offers a powerful predictive tool for community ecology. In this study, we examine whether the goldenrod bunch gall midge (Rhopalomyia solidaginis) functions as an ecosystem engineer in an old-field ecosystem by altering the composition of arthropod species associated with a dominant host plant, Solidago altissima. We also examine the suite of factors that could affect the distribution and abundance of this ecosystem engineer. The presence of bunch galls increased species richness and altered the structure of associated arthropod communities. The best predictors of gall abundance were host-plant genotype and plot-level genotypic diversity. We found positive, nonadditive effects of genotypic diversity on gall abundance. Our results indicate that incorporating a genetic component in studies of ecosystem engineers can help predict their distribution and abundance, and ultimately their effects on biodiversity.     

A paradox of the ciliates? High ciliate diversity in a resource-poor environment

Ecological theory predicts that low productivity systems should have low biodiversity. However, despite the oligotrophic status of the Gulf of Aqaba (Northern Red Sea) ciliate species richness was unexpectedly high. In addition, phytoplankton, as main ciliate prey, was made up by only few genera, indicating a significant niche overlap among the grazers. Up to 97% of the ciliates were from the same taxonomic group and of the same size range, implying very similar food niches. Ciliate diversity was highest at times of lowest chlorophyll concentrations, during the period of stable abiotic conditions, but relatively high genetic diversity within the ciliate prey, notably among the cyanobacteria Synechococcus and Prochlorococcus. In the absence of disturbance and with little predation pressure, the alternate explanations for the observed ciliate diversity are either very fine niche partitioning by the ciliates, or their competitive equivalence resulting in a random assortment of species immigrating from a larger metacommunity, in accordance with Hubbell’s, (The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, 2001) neutral model. While the use of species abundance distributions (SAD’s) is far from definitive, the theoretical SAD’s that best fit the Gulf of Aqaba ciliate data was most often not that expected by neutral theory.     

Use of Community‐Composition Data to Predict the Fecundity and Abundance of Species

Abstract: Species distribution models are critical tools for the prediction of invasive species spread and conservation of biodiversity. The majority of species distribution models have been built with environmental data. Community ecology theory suggests that species co‐occurrence data could also be used to predict current and potential distributions of species. Species assemblages are the products of biotic and environmental constraints on the distribution of individual species and as a result may contain valuable information for niche modeling. We compared the predictive ability of distribution models of annual grassland plants derived from either environmental or community‐composition data. Composition‐based models were built with the presence or absence of species at a site as predictors of site quality, whereas environment‐based models were built with soil chemistry, moisture content, above‐ground biomass, and solar radiation as predictors. The reproductive output of experimentally seeded individuals of 4 species and the abundance of 100 species were used to evaluate the resulting models. Community‐composition data were the best predictors of both the site‐specific reproductive output of sown individuals and the site‐specific abundance of existing populations. Successful community‐based models were robust to omission of data on the occurrence of rare species, which suggests that even very basic survey data on the occurrence of common species may be adequate for generating such models. Our results highlight the need for increased public availability of ecological survey data to facilitate community‐based modeling at scales relevant to conservation.     

Biodiversity mediates productivity through different mechanisms at adjacent trophic levels

Biodiversity may enhance productivity either because diverse communities more often contain productive species (selection effects) or because they show greater complementarity in resource use. Our understanding of how these effects influence community production comes almost entirely from studies of plants. To test whether previous results apply to higher trophic levels, we first used simulations to derive expected contributions of selection and complementarity to production in competitive assemblages defined by either neutral interactions, dominance, or a trade-off between growth and competitive ability. The three types of simulated assemblages exhibited distinct interaction signatures when diversity effects were partitioned into selection and complementarity components. We then compared these signatures to those of experimental marine communities. Diversity influenced production in fundamentally different ways in assemblages of macroalgae, characterized by growth-competition trade-offs, vs. in herbivores, characterized by dominance. Forecasting the effects of changing biodiversity in multitrophic ecosystems will require recognizing that the mechanism by which diversity influences functioning can vary among trophic levels in the same food web.     

Habitat structure and complexity as determinants of biodiversity in blue mussel beds on sublittoral rocky shores

Habitat-forming, ecosystem engineer species are common in most marine systems. Still, much uncertainty exists about how individual and population-level traits of these species contribute to ecosystem processes and how engineering species jointly affect biodiversity. In this manipulative field experiment, we examined how biodiversity in marginal blue mussel beds is affected by blue mussel (1) body size, density and patch context and (2) presence of fucoid and algal structures. In the study area, bladder-wrack (Fucus vesiculosus), filamentous algae and blue mussels (Mytilus edulis) coexist at shallow depths in a variety of patch configurations and offer complex habitats with a high variability of resources. We hypothesized that complexity in terms of mussel bed structure and algal presence determines species composition and abundance. Results from the experiment were compared with macrofaunal communities found in natural populations of both engineering species. Results show that the physical structure and blue mussel patch context are important determinants for species composition and abundance. Results further show that the presence of algal structures positively affects diversity in blue mussel habitats due to increased surface availability and complexity that these algae offer. This study shows that blue mussel beds at the very margin of their distribution have an indisputable function for promoting and maintaining biodiversity and suggest that facilitative effects of habitat-modifying species are important on Baltic Sea rocky shores with fundamental importance to community structure.     

Effects of Urban Development on Ant Communities: Implications for Ecosystem Services and Management

Abstract:  Research that connects the effects of urbanization on biodiversity and ecosystem services is lacking. Ants perform multifarious ecological functions that stabilize ecosystems and contribute to a number of ecosystem services. We studied responses of ant communities to urbanization in the Lake Tahoe basin by sampling sites along a gradient of urban land development. We sampled ant communities, measured vegetation characteristics, quantified human activities, and evaluated ant-community responses by grouping ants into service-providing units (SPUs), defined as a group of organisms and their populations that perform specific ecosystem services, to provide an understanding of urbanization impacts on biodiversity and their delivery of ecosystem services. Species richness and abundance peaked at intermediate levels of urban development, as did the richness of 3 types of ant SPUs (aerators, decomposers, and compilers). With increasing land development aerator and decomposer ants significantly declined in abundance, whereas compiler ants significantly increased in abundance. Competing models demonstrated that precipitation was frequently among the strongest influences on ant community structure; however, urban development and human activities also had a strong, negative influence on ants, appearing in most models with ΔAIC_c < 2 for species richness and abundance patterns of SPUs and generalists. Response diversity was observed within SPUs, which suggests that the corresponding ecosystem services were maintained until development reached 30–40%. Our data provide evidence that ecosystem functions, such as water infiltration and soil productivity, may be diminished at sites subject to greater levels of urbanization and that conserving ant communities and the ecosystem services they provide could be an important target in land-use planning and conservation efforts.     

Predicting landscape-scale biodiversity recovery by natural tropical forest regrowth

Natural forest regrowth is a cost-effective, nature-based solution for biodiversity recovery, yet different socioenvironmental factors can lead to variable outcomes. A critical knowledge gap in forest restoration planning is how to predict where natural forest regrowth is likely to lead to high levels of biodiversity recovery, which is an indicator of conservation value and the potential provisioning of diverse ecosystem services. We sought to predict and map landscape-scale recovery of species richness and total abundance of vertebrates, invertebrates, and plants in tropical and subtropical second-growth forests to inform spatial restoration planning. First, we conducted a global meta-analysis to quantify the extent to which recovery of species richness and total abundance in second-growth forests deviated from biodiversity values in reference old-growth forests in the same landscape. Second, we employed a machine-learning algorithm and a comprehensive set of socioenvironmental factors to spatially predict landscape-scale deviation and map it. Models explained on average 34% of observed variance in recovery (range 9–51%). Landscape-scale biodiversity recovery in second-growth forests was spatially predicted based on socioenvironmental landscape factors (human demography, land use and cover, anthropogenic and natural disturbance, ecosystem productivity, and topography and soil chemistry); was significantly higher for species richness than for total abundance for vertebrates (median range-adjusted predicted deviation 0.09 vs. 0.34) and invertebrates (0.2 vs. 0.35) but not for plants (which showed a similar recovery for both metrics [0.24 vs. 0.25]); and was positively correlated for total abundance of plant and vertebrate species (Pearson r = 0.45, p = 0.001). Our approach can help identify tropical and subtropical forest landscapes with high potential for biodiversity recovery through natural forest regrowth.     

DNA宏条形码(metabarcoding)技术在浮游植物群落监测研究中的应用

保护生物多样性和生态系统健康是维持生态系统功能和实现人类可持续发展的必要条件。浮游植物作为水生生态系统的初级生产者发挥着重要的生态功能,同时有毒藻类的爆发也会威胁水生态安全。然而,基于形态学的物种鉴定方法难以满足日益增长的水生态环境监测的需求。DNA条形码技术利用基因组特定基因的DNA序列来鉴别生物物种,目前已被广泛用于快速物种鉴别。然而其在水生生态系统浮游植物群落的监测中才刚刚起步。由于浮游植物物种多样性高,单基因DNA条形码往往难以识别所有浮游植物种类;近年来,采用多基因条形码、全叶绿体基因组序列的超级条形码,以及特定DNA条形码方法在浮游植物种类鉴别中有很大潜力。本文综述了浮游植物DNA条形码技术在物种鉴别研究方面的进展,以及DNA宏条形码技术(DNA metabarcoding)在水生浮游植物环境监测的应用现状及前景。     

DNA宏条形码（metabarcoding）技术在浮游植物群落监测研究中的应用

保护生物多样性和生态系统健康是维持生态系统功能和实现人类可持续发展的必要条件。浮游植物作为水生生态系统的初级生产者发挥着重要的生态功能,同时有毒藻类的爆发也会威胁水生态安全。然而,基于形态学的物种鉴定方法难以满足日益增长的水生态环境监测的需求。DNA条形码技术利用基因组特定基因上、短的DNA序列来鉴别生物物种,目前已广泛用于快速物种鉴别。然而其在水生生态系统浮游植物群落的监测中才刚刚起步。由于浮游植物物种多样性高,单基因DNA条形码往往不足以识别所有浮游植物种类;近年来,采用多基因条形码、全叶绿体基因组序列的超级条形码,以及特定DNA条形码方法在单物种和群落水平上区分浮游植物种类的潜力很大。本文综述了浮游植物DNA条形码技术在物种鉴别研究方面的进展,以及DNA宏条形码技术（DNA metabarcoding）在水生浮游植物环境监测的应用现状及前景。     

Exploring alternative states in ecological systems with a qualitative analysis of community feedback

Demonstrating and predicting the existence of alternative states in natural communities remains a challenge for ecologists and is essential for resource managers. Positive feedback is often presented as central in maintaining alternative ecosystem states, but no formal approach relates this part of theory to real world applications. Through qualitative modelling of community response to long-term perturbations, we define generic mechanistic links between positive feedback and the occurrence of alternative states. Positive feedback diminishes a system's overall resistance to change, and can create and maintain correlations in the relative abundance of variables that coincide with alternative states.Through specific models of the dynamics of Tasmanian rocky-reef communities, which are affected by climate and fishing and persist within alternative states, we demonstrate the ability of our theoretical framework to predict alternative states in ecosystems and inform management intervention. A qualitative knowledge of community structure permits a thorough analysis of system feedback and an assessment of the potential for an ecosystem to exhibit alternative states. We illustrate the usefulness of the approach to inform management priorities, and to focus monitoring and field research on the key drivers of ecosystem dynamics.     

The comparative evidence relating to functional and neutral interpretations of biological communities

Neutral and functional theories provide rival interpretations of community patterns involving distribution, abundance, and diversity. One group of patterns describes the overall properties of species or sites, and derives principally from the frequency distribution of abundance among species. According to neutral theory, these patterns are determined by the number of individuals of novel type appearing each generation in the community, whereas functional theory relates them to the distribution of the extent of niches. A second group of patterns describes the spatial attributes of communities, and derives principally from the decay of similarity in species composition with distance. Neutral theory interprets these patterns as consequences of local dispersal alone, whereas the functional interpretation is that more distant sites are likely to be ecologically different. Neutral theory often provides good predictions of community patterns, yet is at variance with a wide range of experimental results involving the manipulation of environments or communities. One explanation for this discrepancy is that spatially explicit models where selection is generally weak, or where selection acts strongly on only a few species at each site, have essentially the same output as neutral models with respect to the distribution of abundance and the decay of similarity. Detecting a non-neutral signal in survey data requires careful spatial or phylogenetic analysis; we emphasize the potential utility of incorporating phylogenetic information in order to detect functional processes that lead to ecological variation among clades.     

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.     

Multiple functions increase the importance of biodiversity for overall ecosystem functioning

Biodiversity is proposed to be important for the rate of ecosystem functions. Most biodiversity-ecosystem function studies, however, consider only one response variable at a time, and even when multiple variables are examined they are analyzed separately. This means that a very important aspect of biodiversity is overlooked: the possibility for different species to carry out different functions at any one time. We propose a conceptual model to explore the effects of species loss on overall ecosystem functioning, where overall functioning is defined as the joint effect of many ecosystem functions. We show that, due to multifunctional complementarity among species, overall functioning is more susceptible to species loss than are single functions. Modeled relationships between species richness and overall ecosystem functioning using five empirical data sets on monocultures reflected the range of effects of species loss on multiple functions predicted by the model. Furthermore, an exploration of the correlations across functions and the degree of redundancy within functions revealed that multifunctional redundancy was generally lower than single-function redundancy in these empirical data sets. We suggest that by shifting the focus to the variety of functions maintained by a diversity of species, the full importance of biodiversity for the functioning of ecosystems can be uncovered. Our results are thus important for conservation and management of biota and ecosystem services.