Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods

Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should have a higher probability of occurring on adjacent islands. In contrast to UNTB, if certain groups have traits that permit them to disperse to islands better than other taxa, then phylogeny may be more predictive of which taxa will occur on islands. Taking surveys of 54 island snake communities in the Eastern Nearctic along with mainland communities that have abundance data for each species, we use phylogenetic assembly methods and UNTB estimates to predict island communities. Species richness is predicted by island area, whereas turnover from the mainland to island communities is random with respect to phylogeny. Community structure appears to be ecologically neutral and abundance on the mainland is the best predictor of presence on islands. With regard to young and proximate islands, where allopatric or cladogenetic speciation is not a factor, we find that simple neutral models following UNTB and ETIB predict the structure of island communities.     

Coexistence of insect species competing for a pulsed resource: toward a unified theory of biodiversity in fluctuating environments

Background

One major challenge in understanding how biodiversity is organized is finding out whether communities of competing species are shaped exclusively by species-level differences in ecological traits (niche theory), exclusively by random processes (neutral theory of biodiversity), or by both processes simultaneously. Communities of species competing for a pulsed resource are a suitable system for testing these theories: due to marked fluctuations in resource availability, the theories yield very different predictions about the timing of resource use and the synchronization of the population dynamics between the competing species. Accordingly, we explored mechanisms that might promote the local coexistence of phytophagous insects (four sister species of the genus Curculio) competing for oak acorns, a pulsed resource.

Methodology/Principal Findings

We analyzed the time partitioning of the exploitation of oak acorns by the four weevil species in two independent communities, and we assessed the level of synchronization in their population dynamics. In accordance with the niche theory, overall these species exhibited marked time partitioning of resource use, both within a given year and between different years owing to different dormancy strategies between species, as well as distinct demographic patterns. Two of the four weevil species, however, consistently exploited the resource during the same period of the year, exhibited a similar dormancy pattern, and did not show any significant difference in their population dynamics.

Conclusions/Significance

The marked time partitioning of the resource use appears as a keystone of the coexistence of these competing insect species, except for two of them which are demographically nearly equivalent. Communities of consumers of pulsed resources thus seem to offer a promising avenue for developing a unifying theory of biodiversity in fluctuating environments which might predict the co-occurrence, within the same community, of species that are ecologically either very similar, or very different.     

Seed arrival, ecological filters, and plant species richness: a meta-analysis

Theoretical models predict that effects of dispersal on local biodiversity are influenced by the size and composition of the species pool, as well as ecological filters that limit local species membership. We tested these predictions by conducting a meta-analysis of 28 studies encompassing 62 experiments examining effects of propagule supply (seed arrival) on plant species richness under contrasting intensities of ecological filters (owing to disturbance and resource availability). Seed arrival increased local species richness in a wide range of communities (forest, grassland, montane, savanna, wetland), resulting in a positive mean effect size across experiments. Mean effect size was 70% higher in disturbed relative to undisturbed communities, suggesting that disturbance increases recruitment opportunities for immigrating species. In contrast, effect size was not significantly influenced by nutrient or water availability. Among seed-addition experiments, effect size was positively correlated with species and functional diversity within the pool of added seeds (species evenness and seed-size diversity), primarily in disturbed communities. Our analysis provides experimental support for the general hypothesis that species pools and local environmental heterogeneity interactively structure plant communities. We highlight empirical gaps that can be addressed by future experiments and discuss implications for community assembly, species coexistence, and the maintenance of biodiversity.     

Movement‐mediated community assembly and coexistence

Organismal movement is ubiquitous and facilitates important ecological mechanisms that drive community and metacommunity composition and hence biodiversity. In most existing ecological theories and models in biodiversity research, movement is represented simplistically, ignoring the behavioural basis of movement and consequently the variation in behaviour at species and individual levels. However, as human endeavours modify climate and land use, the behavioural processes of organisms in response to these changes, including movement, become critical to understanding the resulting biodiversity loss. Here, we draw together research from different subdisciplines in ecology to understand the impact of individual‐level movement processes on community‐level patterns in species composition and coexistence. We join the movement ecology framework with the key concepts from metacommunity theory, community assembly and modern coexistence theory using the idea of micro–macro links, where various aspects of emergent movement behaviour scale up to local and regional patterns in species mobility and mobile‐link‐generated patterns in abiotic and biotic environmental conditions. These in turn influence both individual movement and, at ecological timescales, mechanisms such as dispersal limitation, environmental filtering, and niche partitioning. We conclude by highlighting challenges to and promising future avenues for data generation, data analysis and complementary modelling approaches and provide a brief outlook on how a new behaviour‐based view on movement becomes important in understanding the responses of communities under ongoing environmental change.     

Assessing the role of the spatial scale in the analysis of lagoon biodiversity. A case-study on the macrobenthic fauna of the Po River Delta

The analysis of benthic assemblages is a valuable tool to describe the ecological status of transitional water ecosystems, but species are extremely sensitive and respond to both microhabitat and seasonal differences. The identification of changes in the composition of the macrobenthic community in specific microhabitats can then be used as an “early warning” for environmental changes which may affect the economic and ecological importance of lagoons, through their provision of Ecosystem Services. From a conservational point of view, the appropriate definition of the spatial aggregation level of microhabitats or local communities is of crucial importance. The main objective of this work is to assess the role of the spatial scale in the analysis of lagoon biodiversity. First, we analyze the variation in the sample coverage for alternative aggregations of the monitoring stations in three lagoons of the Po River Delta. Then, we analyze the variation of a class of entropy indices by mixed effects models, properly accounting for the fixed effects of biotic and abiotic factors and random effects ruled by nested sources of variability corresponding to alternative definitions of local communities. Finally, we address biodiversity partitioning by a generalized diversity measure, namely the Tsallis entropy, and for alternative definitions of the local communities. The main results obtained by the proposed statistical protocol are presented, discussed and framed in the ecological context.     

The coherence problem with the Unified Neutral Theory of Biodiversity

The Unified Neutral Theory of Biodiversity (UNTB), proposed as an alternative to niche theory, has been viewed as a theory that species coexist without niche differences, without fitness differences, or with equal probability of success. Support is claimed when models lacking species differences predict highly aggregated metrics, such as species abundance distributions (SADs) or species area distributions (SARs). Here, I summarize why UNTB generates confusion, and is not actually relevant to niche theory (i.e. an explanation for why and how many species coexist). Equal probability is not a theory, but lack of one; it does not include or exclude any process relevant to coexistence of competitors. Models lacking explicit species can make useful predictions, but this does not support neutral theory. I provide s suggestions that could help reduce confusion generated by the debate.     

Biodiversity in microbial communities: system scale patterns and mechanisms

The relationship between anthropogenic impact and the maintenance of biodiversity is a fundamental question in ecology. The emphasis on the organizational level of biodiversity responsible for ecosystem processes is shifting from a species-centred focus to include genotypic diversity. The relationship between biodiversity measures at these two scales remains largely unknown. By stratifying anthropogenic effects between scales of biodiversity of bacterial communities, we show a statistically significant difference in diversity based on taxonomic scale. Communities with intermediate species richness show high genotypic diversity while speciose and species-poor communities do not. We propose that in species-poor communities, generally comprising stable yet harsh conditions, physiological tolerance and competitive trade-offs limit both the number of species that occur and the loss of genotypes due to decreases in already constrained fitness. In species-rich communities, natural environmental conditions result in well-defined community structure and resource partitioning. Disturbance of these communities disrupts niche space, resulting in lower genotypic diversity despite the maintenance of species diversity. Our work provides a model to inform future research about relationships between species and genotypic biodiversity based on determining the biodiversity consequences of changing environmental context.     

Grass greenness and grass height promote the resource partitioning among reintroduced Burchell's zebra and blue wildebeest in southern Mozambique

Differences in the selection of habitat and specific dietary items support resource partitioning and coexistence of sympatric African grazing herbivores, such as zebra and wildebeest. In Maputo Special Reserve (MSR), southern Mozambique, these two species were extirpated during the civil war (1977–1992); since 2010, they have been reintroduced into the Reserve. Identifying the resource selection by reintroduced species and how these species coexist, while utilising the same resources, is both of ecological interest and important for the management of wildlife communities and parks. This is a key application of our research. Therefore, the present study investigated resource partitioning between Burchell's zebra (Equus burchelli, Smuts 1832) and blue wildebeest (Connochaetes taurinus, Burchell 1823) in the MSR. We conducted the study from July 2016 to June 2017. The data were collected by direct observation, driving the vehicle along the reserve's roads that covered the vegetation communities where zebras and wildebeest are known to commonly occur. The composition of the diet and specific features of the grass grazed by the two species, including greenness, height, and the number of stems, were assessed. The widely available grass, Aristida barbicollis, contributed most to the diet of both herbivores. The dietary overlap between the two herbivores was higher during the dry season (95%) than wet season (86%). Resources partitioning appears to be determined, principally, by the height and greenness of the grass, with the zebra grazing taller grass, which may facilitate the access of the wildebeest to the greener, lower proportion of the forage. That results follow the expectation that, among native herbivores, overlap in resource use is not expected based on evolutionary segregation.     

Habitat selection and coexistence of invasive cockroach species (Dictyoptera) in sugar-cane fields on Réunion island

Selection of habitat has a profound influence on interactions among species and the assembly of ecological communities. We investigated habitat preferences to understand how different cockroach species coexist in sugar-cane fields on Réunion island.Cockroach populations belonging to a guild of seven species were surveyed during one annual cycle in eight sugar-cane fields that differed by several environmental factors, in order to investigate ecological features of cockroach species and their patterns of coexistence.Structure variations of the cockroach communities were analyzed at the field scale, at the sample unit scale, and according to variations of environmental conditions related to the annual sugar-cane growth cycle. A canonical correspondence analysis (CCA) was used to elucidate relationships between species diversity, population abundance and environmental characteristics.The examination of partitioning at different spatial and temporal scales evidenced that each species occupied a particular type of habitat. The main factors influencing spatial habitat selection were at the sample unit scale: presence of ants, edge effect, soil moisture and granulometry, at the field scale: irrigation, annual rainfall, altitude and age of the field. Although a pair of species shared the same type of habitat, annual population peaks of each species did not coincide in time. This suggests that resource partitioning is based both on ecological factors and interspecific competition.Factors enhancing cockroach coexistence and factors favoring population outbursts are discussed as well as specific invasive capacities of these cockroaches and the role of the cockroach community in the sugar-cane trophic web.     

The nested assembly of plant facilitation networks prevents species extinctions

Facilitation is a positive interaction assembling ecological communities and preserving global biodiversity. Although communities acquire emerging properties when many species interact, most of our knowledge about facilitation is based on studies between pairs of species. To understand how plant facilitation preserves biodiversity in complex ecological communities, we propose to move from the study of pairwise interactions to the network approach. We show that facilitation networks behave as mutualistic networks do, characterized by a nonrandom, nested structure of plant-plant interactions in which a few generalist nurses facilitate a large number of species while the rest of the nurses facilitate only a subset of them. Consequently, generalist nurses shape a dense and highly connected network. Interestingly, such generalist nurses are the most abundant species in the community, making facilitation-shaped communities strongly resistant to extinction, as revealed by coextinction simulations. The nested structure of facilitative networks explains why facilitation, by preventing extinction, preserves biodiversity.     

Landscape moderation of biodiversity patterns and processes - eight hypotheses

Understanding how landscape characteristics affect biodiversity patterns and ecological processes at local and landscape scales is critical for mitigating effects of global environmental change. In this review, we use knowledge gained from human-modified landscapes to suggest eight hypotheses, which we hope will encourage more systematic research on the role of landscape composition and configuration in determining the structure of ecological communities, ecosystem functioning and services. We organize the eight hypotheses under four overarching themes. Section A: 'landscape moderation of biodiversity patterns' includes (1) the landscape species pool hypothesis-the size of the landscape-wide species pool moderates local (alpha) biodiversity, and (2) the dominance of beta diversity hypothesis-landscape-moderated dissimilarity of local communities determines landscape-wide biodiversity and overrides negative local effects of habitat fragmentation on biodiversity. Section B: 'landscape moderation of population dynamics' includes (3) the cross-habitat spillover hypothesis-landscape-moderated spillover of energy, resources and organisms across habitats, including between managed and natural ecosystems, influences landscape-wide community structure and associated processes and (4) the landscape-moderated concentration and dilution hypothesis-spatial and temporal changes in landscape composition can cause transient concentration or dilution of populations with functional consequences. Section C: 'landscape moderation of functional trait selection' includes (5) the landscape-moderated functional trait selection hypothesis-landscape moderation of species trait selection shapes the functional role and trajectory of community assembly, and (6) the landscape-moderated insurance hypothesis-landscape complexity provides spatial and temporal insurance, i.e. high resilience and stability of ecological processes in changing environments. Section D: 'landscape constraints on conservation management' includes (7) the intermediate landscape-complexity hypothesis-landscape-moderated effectiveness of local conservation management is highest in structurally simple, rather than in cleared (i.e. extremely simplified) or in complex landscapes, and (8) the landscape-moderated biodiversity versus ecosystem service management hypothesis-landscape-moderated biodiversity conservation to optimize functional diversity and related ecosystem services will not protect endangered species. Shifting our research focus from local to landscape-moderated effects on biodiversity will be critical to developing solutions for future biodiversity and ecosystem service management.     

Mathematical modeling of the population dynamics of a distinct interactions type system with local dispersal

Distinct biotic interactions in multi-species communities are a ubiquitous force in the natural ecosystem, and this force is an essential determinant of community stability and species coexistence outcomes. We conduct numerical simulations and bifurcation analysis of partial differential equations to gain better understanding and ecological insights into how predation (a), predator handling time (h), and local dispersal affect multi-species community dynamics. This system consists of resource-mutualist-exploiter-competitor interactions and local dispersal. From the inspection of our numerical simulations and co-dimension one bifurcation analysis findings, we discover several critical values that correspond to transcritical bifurcation, subcritical and supercritical Hopf bifurcations. This occurs as we vary the bifurcation parameters a and h in this complex ecological system under symmetric and asymmetric dispersal scenarios. Furthermore, the interplay between these local bifurcation points results in an exciting co-dimension two bifurcations, i.e., Bogdanov-Takens and cusp bifurcation points, respectively, which act as the synchronization points in this complex ecological system. From an ecological viewpoint, we find that (i) the effect of the no-dispersal scenario supports the maintenance of species biodiversity when the predation strength is moderate; (ii) symmetric dispersal induces both subcritical and supercritical Hopf bifurcation and support species diversity for moderate predation strength; and (iii) asymmetric dispersal promotes species diversity as it simplifies the bifurcation changes in dynamics by eliminating the subcritical bifurcations that trigger uncertainty, and this dispersal mechanism mediates species coexistence outcomes. Fundamentally, stable limit cycles have been reported as predator handling time varies in some ecological models; however, we observed in our bifurcation analysis the emergence of the unstable limit cycle as predator handling time changes. We discover that intense predator handling time destabilizes this complex ecological community. In general, our results demonstrate the influential roles of predation, predator handling time, and local dispersal in determining this system’s coexistence dynamics. This knowledge provides a better understanding of species conservation and biological control management.     

片段化森林群落构建的生态过程及其检验方法

鉴于全球森林均呈现片段化(破碎化)的分布状态, 理解片段化森林群落构建的过程很有必要。该文通过综述群落构建的主要生态过程如生态漂变、扩散、选择和物种形成等在片段化森林群落构建中的相对作用, 发现因片段化森林形成方式的不同, 重构群落(片段化生境中通过次生演替重新形成的森林群落)和解构群落(原有森林被片段化后形成的森林群落)在不同演替阶段所受到的主要生态过程的相对作用有所不同。虽然利用基于群落内物种分布格局推测构建过程(如物种多度分布、零模型结合β多样性的方法、功能特征的收敛和发散等)、人工控制实验、群落结构动态分析等方法对片段化森林中群落构建的过程进行了有效的检验, 但是针对片段化森林群落构建过程的实验性研究仍然不足。未来有待在理论模型、群落构建过程的检验以及理论与物种保护相结合等方面继续开展深入的研究。     

Ecological succession in long-term experimentally evolved biofilms produces synergistic communities

Many biofilm populations are known for their exceptional biodiversity, but the relative contributions of the forces that could produce this diversity are poorly understood. This uncertainty grows in the old, well-established communities found on many natural surfaces and in long-term, chronic infections. If the prevailing interactions among species within biofilms are positive, productivity should increase with diversity, but if they tend towards competition or antagonism, productivity should decrease. Here, we describe the parallel evolution of synergistic communities derived from a clone of Burkholderia cenocepacia during ∼1500 generations of biofilm selection. This long-term evolution was enabled by a new experimental method that selects for daily cycles of colonization, biofilm assembly and dispersal. Each of the six replicate biofilm populations underwent a common pattern of adaptive morphological diversification, in which three ecologically distinct morphotypes arose in the same order of succession and persisted. In two focal populations, mixed communities were more productive than any monoculture and each variant benefited from the mixture. These gains in output resulted from asymmetrical cross-feeding between ecotypes and the expansion and partitioning of biofilm space that constructed new niches. Therefore, even in the absence of starting genetic variation, prolonged selection for surface colonization generates a dynamic of ecological succession that enhances productivity.     

Species integrity in trees

From California sequoia, to Australian eucalyptus, to the outstanding diversity of Amazonian forests, trees are fundamental to many processes in ecology and evolution. Trees define the communities that they inhabit, are host to a multiplicity of other organisms and can determine the ecological dynamics of other plants and animals. Trees are also at the heart of major patterns of biodiversity such as the latitudinal gradient of species diversity and thus are important systems for studying the origin of new plant species. Although the role of trees in community assembly and ecological succession is partially understood, the origin of tree diversity remains largely opaque. For instance, the relative importance of differing habitats and phenologies as barriers to hybridization between closely related species is still largely uncharacterized in trees. Consequently, we know very little about the origin of trees species and their integrity. Similarly, studies on the interplay between speciation and tree community assembly are in their infancy and so are studies on how processes like forest maturation modifies the context in which reproductive isolation evolves. In this issue of Molecular Ecology, Lindtke et al. (2014) and Lagache et al. (2014) overcome some traditional difficulties in studying mating systems and sexual isolation in the iconic oaks and poplars, providing novel insights about the integrity of tree species and on how ecology leads to variation in selection on reproductive isolation over time and space.     

More species,but all do the same: contrasting effects of flood disturbance on ground beetle functional and species diversity

The role of habitat disturbance on biodiversity is central as it promotes changes in ecological systems. That said, still little is known about the functional consequences of such changes. Functional diversity can be used to revealing more mechanistically the disturbance effects on communities by considering the richness and the distribution of traits among the species. Here we analyzed the response of functional and species diversity of ground beetles to flood disturbance to better understand the functioning of alluvial invertebrate communities. Ground beetles were sampled in periodically flooded grasslands along the Elbe River in Germany. We used generalized linear mixed effects models to unveil the relationships between flood disturbance, species and functional diversity, respectively. We measured different components of functional diversity (functional richness, evenness, dispersion, and divergence) and analyzed species diversity by means of rarefied species richness, abundances, evenness and Simpson's diversity. We found contrasting relationships in that most species diversity measures peaked at highest disturbance levels, while most functional diversity measures decreased with increasing disturbance intensities. Inversed relationships between species and functional diversity are rarely observed, as most studies report on positive correlations. We explain increasing species diversity with a higher amount of resources available in highly disturbed sites. Decreasing functional diversity is best explained through the convergence of species traits by flood disturbance and uneven resource exploitation in highly disturbed plots (low functional evenness), suggesting strong impacts from functionally different generalist species in floodchannels. We show that the amount of resources available, and how these resources are exploited, play major roles in the functioning of floodplain ground beetle communities.     

The macroecology of reef fish agonistic behaviour

Understanding the interplay between processes operating at large and small spatiotemporal scales in shaping biotic interactions remains challenging. Recent studies illustrate how phenotypic specialization, species life-history traits and/or resource partitioning recurrently underlie the structure of mutualistic interactions in terrestrial ecosystems along large latitudinal gradients of biodiversity. However, we know considerably less about how local processes interact with large-scale patterns of biodiversity in modulating biotic interactions in the marine realm. Considering agonistic behaviour as a proxy for contest competition, we empirically investigate whether the structure of reef fish agonistic interactions is conserved across a 34 000-km longitudinal gradient of biodiversity. By sampling coral reefs using standardized remote underwater video, we found recurrent patterns of fish agonistic behaviour in disparate communities distributed across five biogeographic provinces of the Pacific and Atlantic oceans. While the sheer number of species increases with regional richness, the number of aggressive disputes at the habitat scale is similar across communities. We then combined generalized linear models and network theory to reveal that, the emergent structure of local agonistic networks is not modular but instead recurrently display a nested structure, with a core of highly interactive site-attached herbivores of the Pomacentridae family. Therefore, despite the increase in the number of species involved in agonistic interactions toward speciose communities, the network structure is conserved along the longitudinal richness gradient because local disputes are mostly driven by closely-related, functionally-similar species. These findings suggest that evolutionary and local processes interact in modulating reef fish agonistic behaviour and that fine-scale niche-partitioning can structure the ecological networks in marine ecosystems.     

Multiple facets of stream macroinvertebrate alpha diversity are driven by different ecological factors across an extensive altitudinal gradient

Environmental filtering and spatial structuring are important ecological processes for the generation and maintenance of biodiversity. However, the relative importance of these ecological drivers for multiple facets of diversity is still poorly understood in highland streams. Here, we examined the responses of three facets of stream macroinvertebrate alpha diversity to local environmental, landscape‐climate and spatial factors in a near‐pristine highland riverine ecosystem. Taxonomic (species richness, Shannon diversity, and evenness), functional (functional richness, evenness, divergence, and Rao's Quadratic entropy), and a proxy of phylogenetic alpha diversity (taxonomic distinctness and variation in taxonomic distinctness) were calculated for macroinvertebrate assemblages in 55 stream sites. Then Pearson correlation coefficient was used to explore congruence of indices within and across the three diversity facets. Finally, multiple linear regression models and variation partitioning were employed to identify the relative importance of different ecological drivers of biodiversity. We found most correlations between the diversity indices within the same facet, and between functional richness and species richness were relatively strong. The two phylogenetic diversity indices were quite independent from taxonomic diversity but correlated with functional diversity indices to some extent. Taxonomic and functional diversity were more strongly determined by environmental variables, while phylogenetic diversity was better explained by spatial factors. In terms of environmental variables, habitat‐scale variables describing habitat complexity and water physical features played the primary role in determining the diversity patterns of all three facets, whereas landscape factors appeared less influential. Our findings indicated that both environmental and spatial factors are important ecological drivers for biodiversity patterns of macroinvertebrates in Tibetan streams, although their relative importance was contingent on different facets of diversity. Such findings verified the complementary roles of taxonomic, functional and phylogenetic diversity, and highlighted the importance of comprehensively considering multiple ecological drivers for different facets of diversity in biodiversity assessment.     

β-Diversity and Species Accumulation in Antarctic Coastal Benthos: Influence of Habitat,Distance and Productivity on Ecological Connectivity

High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in β-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100''s of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and β–diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on β-diversity at scales <290 km, while the effects of productivity were low and significant only at scales >40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance.