The community ecology of pathogens: coinfection,coexistence and community composition

Disease and community ecology share conceptual and theoretical lineages, and there has been a resurgence of interest in strengthening links between these fields. Building on recent syntheses focused on the effects of host community composition on single pathogen systems, we examine pathogen (microparasite) communities using a stochastic metacommunity model as a starting point to bridge community and disease ecology perspectives. Such models incorporate the effects of core community processes, such as ecological drift, selection and dispersal, but have not been extended to incorporate host–pathogen interactions, such as immunosuppression or synergistic mortality, that are central to disease ecology. We use a two‐pathogen susceptible‐infected (SI) model to fill these gaps in the metacommunity approach; however, SI models can be intractable for examining species‐diverse, spatially structured systems. By placing disease into a framework developed for community ecology, our synthesis highlights areas ripe for progress, including a theoretical framework that incorporates host dynamics, spatial structuring and evolutionary processes, as well as the data needed to test the predictions of such a model. Our synthesis points the way for this framework and demonstrates that a deeper understanding of pathogen community dynamics will emerge from approaches working at the interface of disease and community ecology.     

The challenges that spatial context present for synthesizing community ecology across scales

Accurately characterizing spatial patterns on landscapes is necessary to understand the processes that generate biodiversity, a problem that has applications in ecological theory, conservation planning, ecosystem restoration, and ecosystem management. However, the measurement of biodiversity patterns and the ecological and evolutionary processes that underlie those patterns is highly dependent on the study unit size, boundary placement, and number of observations. These issues, together known as the modifiable areal unit problem, are well known in geography. These factors limit the degree to which results from different metacommunity and macro‐ecological studies can be compared to draw new inferences, and yet these types of comparisons are widespread in community ecology. Using aquatic community datasets, we demonstrate that spatial context drives analytical results when landscapes are sub‐divided. Next, we present a framework for using resampling and neighborhood smoothing to standardize datasets to allow for inferential comparisons. We then provide examples for how addressing these issues enhances our ability to understand the processes shaping ecological communities at landscape scales and allows for informative meta‐analytical synthesis. We conclude by calling for greater recognition of issues derived from the modifiable areal unit problem in community ecology, discuss implications of the problem for interpreting the existing literature, and identify tools and approaches for future research.     

Plant genetics shapes inquiline community structure across spatial scales

Recent research in community genetics has examined the effects of intraspecific genetic variation on species diversity in local communities. However, communities can be structured by a combination of both local and regional processes and to date, few community genetics studies have examined whether the effects of instraspecific genetic variation are consistent across levels of diversity. In this study, we ask whether host-plant genetic variation structures communities of arthropod inquilines within distinct habitat patches – rosette leaf galls on tall goldenrod ( Solidago altissima ). We found that genetic variation determined inquiline diversity at both local and regional spatial scales, but that trophic-level responses varied independently of one another. This result suggests that herbivores and predators likely respond to heritable plant traits at different spatial scales. Together, our results show that incorporating spatial scale is essential for predicting the effects of genetically variable traits on different trophic levels and levels of diversity within the communities that depend on host plants.     

Local dispersal can facilitate coexistence in the presence of permanent spatial heterogeneity

Abstract In the presence of permanent spatial heterogeneity, local dispersal, especially short‐range dispersal, can facilitate coexistence by concentrating low‐density species in the areas where their rates of increase are higher. We present a framework for predicting the effects of local dispersal on coexistence for arbitrary forms of dispersal and arbitrary spatial patterns of environmental variation. Using the lottery model as an example, we find that local dispersal contributes to coexistence by enhancing the effects of environmental variation on scales longer than typical dispersal distances, which can be characterized solely by the variance of the dispersal kernel. Higher moments of the dispersal kernel are not important.     

Variation in invertebrate–bryophyte community structure at different spatial scales along altitudinal gradients

Aim This study assessed changes in diversity and assemblage composition in bryophytes and their associated invertebrates along altitudinal gradients in Australia and New Zealand. The importance of altitude in shaping these communities and for the diversity of both invertebrates and bryophytes was examined at different spatial scales, including local, altitudinal, regional and biogeographical. Location Samples were taken from four Australasian mountain ranges between 42° and 43°S: Mt Field and Mt Rufus, Tasmania, Australia, and Otira Valley and Seaward Kaikoura Mountains, South Island, New Zealand. Methods On both Tasmanian mountains, five altitudes were assessed (250, 500, 750, 1000 and 1250 m). At each location (mountain/altitude combination) two sites were chosen and six samples were taken. Six altitudes were assessed on New Zealand mountains (Otira: 250, 500, 750, 1000, 1250 and 1500 m; Kaikoura: 1130, 1225, 1325, 1425, 1525 and 2000 m). Bryophyte substrate was collected, and all samples were stored in 70% ethanol. Invertebrates were extracted from bryophytes using kerosene‐phase separation and all invertebrates were identified to family. At each location in Tasmania, all bryophyte species within six 25‐cm² grids per site were collected and identified to species. Bryophytes from New Zealand were identified to species from the invertebrate sample substrate because of sampling constraints. Results Altitude did have a significant effect on diversity, however, no general trend was found along the altitudinal gradient on the four mountains. There were distinct differences in diversity between biogeographical regions, mountains, altitudes and sites. In Tasmania, Mt Field had the highest diversity in invertebrates and bryophytes at 750 m. In contrast, Mt Rufus had consistent low invertebrate and bryophyte diversity along the entire altitudinal gradient. There were also distinctive differences between locations in the composition of invertebrate and bryophyte communities in Tasmania. Along the two altitudinal gradients in New Zealand, Otira had highest diversity for both invertebrates and bryophytes at low altitudes, whereas Kaikoura had highest invertebrate and lowest bryophyte diversity at the highest altitude. Main conclusions There was an effect of altitude, however, there were no consistent changes in diversity or composition on the four different mountains. There was considerable local and regional variation, and, despite a strong sampling design, no underlying altitudinal trends were detectable. This study demonstrates the importance of examining a range of spatial scales if patterns in community structure along altitudinal gradients are to be studied. The implications of this study are discussed with reference to survey design, taxonomic resolution, climate change and conservation of habitat.     

The merging of community ecology and phylogenetic biology

The increasing availability of phylogenetic data, computing power and informatics tools has facilitated a rapid expansion of studies that apply phylogenetic data and methods to community ecology. Several key areas are reviewed in which phylogenetic information helps to resolve long-standing controversies in community ecology, challenges previous assumptions, and opens new areas of investigation. In particular, studies in phylogenetic community ecology have helped to reveal the multitude of processes driving community assembly and have demonstrated the importance of evolution in the assembly process. Phylogenetic approaches have also increased understanding of the consequences of community interactions for speciation, adaptation and extinction. Finally, phylogenetic community structure and composition holds promise for predicting ecosystem processes and impacts of global change. Major challenges to advancing these areas remain. In particular, determining the extent to which ecologically relevant traits are phylogenetically conserved or convergent, and over what temporal scale, is critical to understanding the causes of community phylogenetic structure and its evolutionary and ecosystem consequences. Harnessing phylogenetic information to understand and forecast changes in diversity and dynamics of communities is a critical step in managing and restoring the Earth's biota in a time of rapid global change.     

Tree heterogeneity,resource availability,and larger scale processes regulating arboreal ant species richness

Abstract Processes acting on different spatial and temporal scales may influence local species richness. Ant communities are usually described as interactive and therefore determined by local processes. In this paper we tested two hypotheses linked to the question of why there is local variation in arboreal ant species richness in the Brazilian savanna (‘cerrado’). The hypotheses are: (i) there is a positive relationship between ant species richness and tree species richness, used as a surrogate of heterogeneity; and (ii) there is a positive relationship between ant species richness and tree density, used as a surrogate of resource availability. Arboreal ants were sampled in two cerrado sites in Brazil using baited pitfall traps and manual sampling, in quadrats of 20 m × 50 m. Ant species richness in each quadrat was used as the response variable in regression tests, using tree species richness and tree density as explanatory variables. Ant species richness responded positively to tree species richness and density. Sampling site also influenced ant species richness, and the relationship between tree density and tree species richness was also positive and significant. Tree species richness may have influenced ant species richness through three processes: (i) increasing the variety of resources and allowing the existence of a higher number of specialist species; (ii) increasing the amount of resources to generalist species; and (iii) some other unmeasured factor may have influenced both ant and tree species richness. Tree density may also have influenced ant species richness through three processes: (i) increasing the amount of resources and allowing a higher ant species richness; (ii) changing habitat conditions and dominance hierarchies in ant communities; and (iii) increasing the area and causing a species–area pattern. Processes acting on larger scales, such as disturbance, altitude and evolutionary histories, as well as sampling effect may have caused the difference between sites.     

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar com-munity are ecologically equivalent, Hubbell's neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and spe-ciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory.     

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar community are ecologically equivalent, Hubbell’s neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and speciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory. __________ Translated from Journal of Plant Ecology, 2006, 30(5): 868–877 [译自:植物生态学报]     

Plant physiological ecology: An essential link for integrating across disciplines and scales in plant ecology

A sizeable number of scientists and funding organisations are of the opinion that the relevance of plant physiological ecology as an important discipline has declined to the point that it is no longer considered as one of the important topics of ecological research. Plant physiological ecology is typically associated with the autecological plant research conducted during the latter portion of the 20th century or, even worse, simply with gas exchange measurements. However, taking a closer look, it becomes obvious that, by focusing on the intermediate integration levels (individuals, populations), this discipline represents an essential link between the high integration levels (communities, ecosystems, biosphere) and the disciplines at the bottom of the complexity hierarchy (physiology, molecular biology). In this paper we show that the principal question of all ongoing community and ecosystem level research – What is the mechanistic background of vegetation composition, biodiversity structure and dynamics and how is this linked to fluxes of matter at the community and higher levels of organisation? – can only be answered if the mechanism of interactions between the relevant organisms are understood. In consequence, the classical discipline of plant physiological ecology will continuously develop into a truly interdisciplinary experimental ecology of interactions and its importance will rather increase than diminish. Promising activities of this kind are already underway. Scientists needed for this new direction should have a rather broad scientific perspective, including knowledge and experience in fields outside of typical ecological research, instead of being specialists for single ecophysiological aspects.     

The partitioning of macroinvertebrate diversity across multiple spatial scales in the upper Modder River System,South Africa

A method for assessing the alpha and beta diversity components of a macroinvertebrate community across numerous spatial scales is presented. Findings were not empirically linked to ecological questions as the purpose of this study was primarily the demonstration of a diversity partitioning method. Sampling was carried out at three sites on the upper Modder River in the Free State Province, South Africa between April 2008 and January 2009. Communities were analysed by investigating the relative frequency of species in specific biotopes, a Similarity Profile (SIMPROF) and cluster analyses of the Bray‐Curtis similarities between samples, and the partitioning of species richness and Shannon diversity across multiple spatial scales. Findings revealed that sites showed significant clustering (SIMPROF P < 0.05; <20% Bray‐Curtis similarity), and the species frequencies indicated preference to selected microhabitats. Species richness and Shannon diversity of macroinvertebrates differed significantly (5% confidence levels) from randomly simulated values for sampling sites, biotopes and seasons indicating that diversity is clustered and not homogeneously distributed. The diversity partitioning could have potential in diversity assessment for conservation biology, land management and environmental impact assessments.     

村落文化林与非文化林多尺度物种多样性加性分配

文化林是指村民按照文化传统、风俗习惯或宗教信仰自觉保护和管理的森林,具有一定社会文化功能。目前国内外对文化林物种多样性研究主要为定性描述,缺乏对文化林和非文化林生物多样性的定量比较及差异来源分析。利用物种多样性加性分配方法,将总的Gamma 多样性分成样格内的Alpha多样性以及样格间、样方间和林型间Beta多样性,对中国亚热带地区3个村落文化林的乔木层、灌木层、草本层和藤本层进行物种多样性的多尺度分析。调查发现:(1)文化林共有维管束植物296种,以苦槠,樟和米槠为优势种,非文化林共有维管束植物189种,以杉木、马尾松和毛竹为优势种。文化林乔木层和灌木层物种数显著高于非文化林,草本层和藤本层物种数差异不显著。(2)Beta多样性随尺度增大而增加,林型间Beta多样性最高,占区域总Gamma多样性的41.9%-62.8%,其次是样方间Beta多样性(18.6%-31.9%),对区域多样性贡献最小为样格内Alpha和样格间Beta多样性。(3)林型间的多样性对区域物种多样性的贡献中,文化林占主导作用,乔木层占54.4%-81.0%,灌木层占51.2%-60.2%,草本层占42.9%-64.1%,藤本层占49.9%-62.2%。(4) 物种累积-面积曲线表明,在各个尺度上,文化林物种多样性始终高于非文化林,从而在相同面积下保护了更多的物种。加性分配模型在多个空间尺度上阐明了Alpha和Beta多样性的变化,突出了文化林对区域物种多样性的贡献,对保护对象和保护范围的决策以及生物多样性的保护与恢复具有重要意义。     

Dispersal, spatial scale, and species diversity in a hierarchically structured experimental landscape

Although there has been growing interest in the effect of dispersal on species diversity, much remains unknown about how dispersal occurring at multiple scales influences diversity. We used an experimental microbial landscape to determine whether dispersal occurring at two different scales - among local communities and among metacommunities - affects diversity differently. At the local scale, dispersal initially had a positive effect and subsequently a neutral effect on diversity, whereas at the metacommunity and landscape scales, dispersal showed a consistently negative effect. The timing in which dispersal affected beta diversity also differed sharply between local communities and metacommunities. These patterns were explained by scale- and time-dependent effects of dispersal in allowing spread of species and in removing spatial refuges from predators. Our results suggest that the relative contribution of opposing mechanisms by which dispersal affects diversity changes considerably over time and space in hierarchical landscapes in which dispersal occurs at multiple scales.     

Plant species richness and community productivity: why the mechanism that promotes coexistence matters

This paper stresses that the mechanism of coexistence is the key to understanding the relationship between species richness and community productivity. Using model plant communities, we explored two general kinds of mechanisms based on resource heterogeneity and recruitment limitation, with and without any trade-off between reproductive and competitive abilities. We generated different levels of species richness by changing model parameters, in particular the number of species in the regional pool, the degree of recruitment limitation, and the level of heterogeneity. Different diversity–productivity patterns are obtained with different coexistence mechanisms, indicating there is no reason to expect any general relationship between species richness and productivity. We discuss these results in the context of the within-site and across-site aspects of the relationship between species richness and productivity. Furthermore, we extend these results to hypothesize the relationship between species richness and productivity for other coexistence mechanisms not explicitly considered here.     

Pervasive effects of dispersal limitation on within- and among-community species richness in agricultural landscapes

Aim To determine whether the effect of habitat fragmentation and habitat heterogeneity on species richness at different spatial scales depends on the dispersal ability of the species assemblages and if this results in nested species assemblages. Location Agricultural landscapes distributed over seven temperate Europe countries covering a range from France to Estonia. Methods We sampled 16 local communities in each of 24 agricultural landscapes (16 km²) that differ in the amount and heterogeneity of semi‐natural habitat patches. Carabid beetles were used as model organisms as dispersal ability can easily be assessed on morphological traits. The proximity and heterogeneity of semi‐natural patches within the landscape were related to average local (alpha), between local (beta) and landscape (gamma) species richness and compared among four guilds that differ in dispersal ability. Results For species assemblages with low dispersal ability, local diversity increased as the proximity of semi‐natural habitat increased, while mobile species showed an opposite trend. Beta diversity decreased equally for all dispersal classes in relation to proximity, suggesting a homogenizing effect of increased patch isolation. In contrast, habitat diversity of the semi‐natural patches affected beta diversity positively only for less mobile species, probably due to the low dispersal ability of specialist species. Species with low mobility that persisted in highly fragmented landscapes were consistently present in less fragmented ones, resulting in nested assemblages for this mobility class only. Main conclusions The incorporation of dispersal ability reveals that only local species assemblages with low dispersal ability show a decrease of richness as a result of fragmentation. This local species loss is compensated at least in part by an increase in species with high dispersal ability, which obscures the effect of fragmentation when investigated across dispersal groups. Conversely, fragmentation homogenizes the landscape fauna for all dispersal groups, which indicates the invasion of non‐crop habitats by similar good dispersers across the whole landscape. Given that recolonization of low dispersers is unlikely, depletion of these species in modern agricultural landscapes appears temporally pervasive.     

Increased community compositional dissimilarity alleviates species loss following nutrient enrichment at large spatial scales

Aims Anthropogenic activities have drastically increased nutrient availability, resulting in declines in species richness in many plant communities. However, most previous studies have explored only species-loss patterns and mechanisms over small sampling areas, so their results might overestimate species loss at larger spatial scales. The aim of this research was to explore species diversity change patterns and species-loss rates at multiple scales in alpine meadow communities following nutrient enrichment. Specifically, we asked two closely related questions: (i) do changes in species diversity and species-loss patterns differ among spatial scales? and (ii) how does community compositional dissimilarity and species turnover change among spatial scale?