Metacommunity‐scale biodiversity regulation and the self‐organised emergence of macroecological patterns

There exist a number of key macroecological patterns whose ubiquity suggests that the spatio‐temporal structure of ecological communities is governed by some universal mechanisms. The nature of these mechanisms, however, remains poorly understood. Here, we probe spatio‐temporal patterns in species richness and community composition using a simple metacommunity assembly model. Despite making no a priori assumptions regarding biotic spatial structure or the distribution of biomass across species, model metacommunities self‐organise to reproduce well‐documented patterns including characteristic species abundance distributions, range size distributions and species area relations. Also in agreement with observations, species richness in our model attains an equilibrium despite continuous species turnover. Crucially, it is in the neighbourhood of the equilibrium that we observe the emergence of these key macroecological patterns. Biodiversity equilibria in models occur due to the onset of ecological structural instability, a population‐dynamical mechanism. This strongly suggests a causal link between local community processes and macroecological phenomena.     

Species residency status affects model selection and hypothesis testing in freshwater community ecology

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Effect of landscape context on fish metacommunity structuring in stream networks

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Elements of metacommunity structure and community‐environment relationships in stream organisms

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Dynamic disequilibrium: a long-term, large-scale perspective on the equilibrium model of island biogeography

• 1 The equilibrium model of island biogeography developed in the 1960s by MacArthur and Wilson has provided an excellent framework in which to investigate the dynamics of species richness in island and island‐like systems. It is comparable in many respects to the Hardy–Weinberg equilibrium model used in genetics as the basis for defining a point of reference, thus allowing one to discover the factors that prevent equilibrium from being achieved. Hundreds of studies have used the model effectively, especially those dealing with brief spans of time and limited geographical areas. In spite of this utility, however, there are important limitations to the MacArthur–Wilson model, especially when we consider long‐term and large‐scale circumstances.
• 2 Although their general theory is more complex, the MacArthur–Wilson equilibrium model treats colonization and extinction as the only two processes that are relevant to determining species richness. However, it is likely that phylogenetic diversification (phylogenesis) often takes place on the same time‐scale as colonization and extinction; for example, colonization, extinction, and phylogenesis among mammals on oceanic and/or old land‐bridge islands in South‐east Asia are all measured in units of time in the range of 10 000–1 million years, most often in units of 100 000 years.
• 3 Phylogenesis is not a process that can be treated simply as ‘another form of colonization’, as it behaves differently than colonization. It interacts in a complex manner with both colonization and extinction, and can generate patterns of species richness almost independently of the other two processes. In addition, contrary to the implication of the MacArthur–Wilson model, extinction does not drive species richness in highly isolated archipelagoes (those that receive very few colonists) to progressively lower values; rather, phylogenesis is a common outcome in such archipelagoes, and species richness rises over time. In some specific instances, phylogenesis may have produced an average of 14 times as many species as direct colonization, and perhaps 36 species from one such colonization event. Old, stable, large archipelagoes should typically support not just endemic species but endemic clades, and the total number of species and the size of the endemic clades should increase with age of the archipelago.
• 4 The existence of long‐term equilibrium in actual island archipelagoes is unlikely. The land masses that make up island archipelagoes are intrinsically unstable because the geological processes that cause their formation are dynamic, and substantial changes can occur (under some circumstances) on a time‐scale comparable to the processes of colonization, phylogenesis, and extinction. Large‐scale island‐like archipelagoes on continents also are unstable, in the medium term because of global climatic fluctuations, and in the long term because of the geologically ephemeral existence of, for example, individual mountain ranges.
• 5 Examples of these phenomena using the mammals of South‐east Asia, especially the Philippines, make it clear that the best conceptual model of the long‐term dynamics of species richness in island archipelagoes would be one in which colonization, extinction, and phylogenesis are recognized to be of equivalent conceptual importance. Furthermore, we should expect species richness to be always in a dynamic state of disequilibrium due to the constantly changing geological/geographical circumstances in which that diversity exists, always a step or two out of phase with the constantly changing equilibrium point for species richness.

     

Do metacommunity theories explain spatial variation in fish assemblage structure in a pristine tropical river?

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Factors determining mammal species richness on habitat islands and isolates: habitat diversity, disturbance, species interactions and guild assembly rules

• 1 For over three decades the equilibrium theory of island biogeography has galvanized studies in ecological biogeography. Studies of oceanic islands and of natural habitat islands share some similarities to continental studies, particularly in developed regions where habitat fragmentation results from many land uses. Increasingly, remnant habitat is in the form of isolates created by the clearing and destruction of natural areas. Future evolution of a theory to predict patterns of species abundance may well come from the application of island biogeography to habitat fragments or isolates.
• 2 In this paper we consider four factors other than area and isolation that influence the number and type of mammal species coexisting in one place: habitat diversity, habitat disturbance, species interactions and guild assembly rules. In all examples our data derive from mainland habitat, fragmented to differing degrees, with different levels of isolation.
• 3 Habitat diversity is seen to be a good predictor of species richness. Increased levels of disturbance produce a relatively greater decrease in species richness on smaller than on larger isolates. Species interactions in the recolonization of highly disturbed sites, such as regenerating mined sites, is analogous to island colonization. Species replacement sequences in secondary successions indicate not just how many, but which species are included. Lastly, the complement of species established on islands, or in insular habitats, may be governed by guild assembly rules. These contributions may assist in taking a renewed theory into the new millennium.

     

Mass–abundance scaling in avian communities is maintained after tropical selective logging

1. Selective logging dominates forested landscapes across the tropics. Despite the structural damage incurred, selectively logged forests typically retain more biodiversity than other forest disturbances. Most logging impact studies consider conventional metrics, like species richness, but these can conceal subtle biodiversity impacts. The mass–abundance relationship is an integral feature of ecological communities, describing the negative relationship between body mass and population abundance, where, in a system without anthropogenic influence, larger species are less abundant due to higher energy requirements. Changes in this relationship can indicate community structure and function changes.
2. We investigated the impacts of selective logging on the mass–abundance scaling of avian communities by conducting a meta‐analysis to examine its pantropical trend. We divide our analysis between studies using mist netting, sampling the understory avian community, and point counts, sampling the entire community.
3. Across 19 mist‐netting studies, we found no consistent effects of selective logging on mass–abundance scaling relative to primary forests, except for the omnivore guild where there were fewer larger‐bodied species after logging. In eleven point‐count studies, we found a more negative relationship in the whole community after logging, likely driven by the frugivore guild, showing a similar pattern.
4. Limited effects of logging on mass–abundance scaling may suggest high species turnover in logged communities, with like‐for‐like replacement of lost species with similar‐sized species. The increased negative mass–abundance relationship found in some logged communities could result from resource depletion, density compensation, or increased hunting; potentially indicating downstream impacts on ecosystem functions.
5. Synthesis and applications. Our results suggest that size distributions of avian communities in logged forests are relatively robust to disturbance, potentially maintaining ecosystem processes in these forests, thus underscoring the high conservation value of logged tropical forests, indicating an urgent need to focus on their protection from further degradation and deforestation.

     

Sharing detection heterogeneity information among species in community models of occupancy and abundance can strengthen inference

1. The estimation of abundance and distribution and factors governing patterns in these parameters is central to the field of ecology. The continued development of hierarchical models that best utilize available information to inform these processes is a key goal of quantitative ecologists. However, much remains to be learned about simultaneously modeling true abundance, presence, and trajectories of ecological communities.
2. Simultaneous modeling of the population dynamics of multiple species provides an interesting mechanism to examine patterns in community processes and, as we emphasize herein, to improve species‐specific estimates by leveraging detection information among species. Here, we demonstrate a simple but effective approach to share information about observation parameters among species in hierarchical community abundance and occupancy models, where we use shared random effects among species to account for spatiotemporal heterogeneity in detection probability.
3. We demonstrate the efficacy of our modeling approach using simulated abundance data, where we recover well our simulated parameters using N‐mixture models. Our approach substantially increases precision in estimates of abundance compared with models that do not share detection information among species. We then expand this model and apply it to repeated detection/non‐detection data collected on six species of tits (Paridae) breeding at 119 1 km² sampling sites across a P. montanus hybrid zone in northern Switzerland (2004–2020). We find strong impacts of forest cover and elevation on population persistence and colonization in all species. We also demonstrate evidence for interspecific competition on population persistence and colonization probabilities, where the presence of marsh tits reduces population persistence and colonization probability of sympatric willow tits, potentially decreasing gene flow among willow tit subspecies.
4. While conceptually simple, our results have important implications for the future modeling of population abundance, colonization, persistence, and trajectories in community frameworks. We suggest potential extensions of our modeling in this paper and discuss how leveraging data from multiple species can improve model performance and sharpen ecological inference.

     

Eutrophication decreases distance decay of similarity in diatom communities

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Linking life history strategies and historical baseline information shows effects of altered flow regimes and impoundments on freshwater mussel assemblages

1. Human impacts on aquatic ecosystems are causing shifts in the composition and distribution of species, leading to subsequent changes in community structure. However, these changes may not be fully realised because of inadequate baseline information. In Texas, such baseline information is generally lacking for cryptic aquatic species such as unionid mussels, which will be likely to impede identification of impacted populations, potential causal factors, and the setting or achieving of management goals.
2. The Navasota River, located in central Texas, is an exception, having been comprehensively surveyed more than 40 years ago, prior to large-scale impoundment of this system. Hierarchical cluster analysis, nonmetric multidimensional scaling, and fuzzy set ordination were performed to compare assemblage structure from the 1975 survey to that of a recent survey in 2016 at similar sampling locations.
3. Comparing sites based on the presence–absence of mussel species, we found no significant differences between the number of taxa and species present; however, we did find significant filtering of mussel life history strategies. Specifically, prior to impoundment, we found that mussel assemblages were filtered based on longitudinal patterns in life history strategy from taxa that are adapted to disturbed habitats to those favoured in more stable habitats with low environmental variation.
4. However, following large-scale impoundment after 1975, we saw a shift in the hydrologic regime towards consistent, homogenised flows and a shift in assemblage structure towards equilibrium species. This shift appears to represent a discontinuity, wherein river impoundment alters physical parameters of the hydrologic regime and these changes in turn modify biotic patterns and processes.
5. Our results provide another example of how large dams can restructure mussel assemblages, highlight the importance of incorporating reference or baseline conditions wherever possible when evaluating the conservation status of aquatic biota, and provide further evidence for the use of life history theory and the serial discontinuity concept in predicting the consequences of flow alteration and river impoundment.

     

Environmental and spatial processes influencing phytoplankton biomass along a reservoirs‐river‐floodplain lakes gradient: A metacommunity approach

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The pairwise approach to analysing species co‐occurrence

The analysis of species co‐occurrence patterns continues to be a main pursuit of ecologists, primarily because the coexistence of species is fundamentally important in evaluating various theories, principles and concepts. Examples include community assembly, equilibrium versus non‐equilibrium organization of communities, resource partitioning and ecological character displacement, the local–regional species diversity relationship, and the metacommunity concept. Traditionally, co‐occurrence has been measured and tested at the level of an entire species presence–absence matrix wherein various algorithms are used to randomize matrices and produce statistical null distributions of metrics that quantify structure in the matrix. This approach implicitly recognizes a presence–absence matrix as having some real ecological identity (e.g. a set of species exhibiting nestedness among a set of islands) in addition to being a unit of statistical analysis. An emerging alternative is to test for non‐random co‐occurrence between paired species. The pairwise approach does not analyse matrix‐level structure and thus views a species pair as the fundamental unit of co‐occurrence. Inferring process from pattern is very difficult in analyses of co‐occurrence; however, the pairwise approach may make this task easier by simplifying the analysis and resulting inferences to associations between paired species.     

Overdispersion of body size in Australian desert lizard communities at local scales only: no evidence for the Narcissus effect

Both local and regional processes may contribute to community diversity and structure at local scales. Although many studies have investigated patterns of local or regional community structure, few have addressed the extent to which local community structure influences patterns within regional species pools. Here we investigate the role of body size in community assembly at local and regional scales in Ctenotus lizards from arid Australia. Ctenotus has long been noted for its exceptional species diversity in the Australian arid-zone, and previous studies have attempted to elucidate the processes underlying species coexistence within communities of these lizards. However, no consensus has emerged on the role of interspecific competition in the assembly and maintenance of Ctenotus communities. We studied Ctenotus communities at several hundred sites in the arid interior of Australia to test the hypothesis that body sizes within local and regional Ctenotus assemblages should be overdispersed relative to null models of community assembly, and we explored the relationship between body size dispersion at local and regional scales. Results indicate a striking pattern of community-wide overdispersion of body size at local scales, as measured by the variance in size ratios among co-occurring species. However, we find no evidence for body size overdispersion within regional species pools, suggesting a lack of correspondence between processes influencing the distribution of species phenotypes at local and regional scales. We suggest that size ratio constancy in Ctenotus communities may have resulted from contemporary ecological interactions among species or ecological character displacement, and we discuss alternative explanations for the observed patterns. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Scale,succession and complexity in island biogeography: are we asking the right questions?

• 1 This paper offers a commentary on the development of island ecological theory since the publication of MacArthur & Wilson’s equilibrium theory in the 1960s. I distinguish the simple model at the core of their Equilibrium Theory of Island Biogeography (ETIB) and the broader body of their theory, which embraces evolutionary as well as ecological patterns — all, however, within the overarching framework or assumption of equilibrium.
• 2 The basic problems with the ETIB have long been known, and its status as a ruling paradigm has been the subject of concern for more than two decades. With the development of nonequilibrium ideas in ecology, island biogeographers arguably now have viable theoretical frameworks to set alongside or around the ETIB. Four conditions are highlighted as extremes: i) dynamic equilibrium; ii) dynamic nonequilibrium; iii) ‘static’ equilibrium; and iv) ‘static’ nonequilibrium: together providing a conceptual framework for island ecological analyses.
• 3 The importance of scale is stressed and attention is drawn to Haila’s spatial‐temporal continuum as an organizational device. It is argued that the processes represented within the ETIB (and by extension, other island theories) may be prominent within only a limited portion of this continuum, while elsewhere they are generally subsumed by other dominant processes.
• 4 Colonization and ecosystem development of near‐shore islands constitute just a special case of ecological succession, and thus the development of theories of island assembly may benefit accordingly from efforts to incorporate ideas from the ecological succession literature.
• 5 The desirability of specifying answerable questions is stressed, as is the need to build a greater degree of complexity into the development of island ecological models. Notwithstanding which, it is also recognized that key advances are often brought about by simple, but bold models, of the form exemplified elsewhere in this issue.

     

Linking community assembly and structure across scales in a wild mouse parasite community

Understanding what processes drive community structure is fundamental to ecology. Many wild animals are simultaneously infected by multiple parasite species, so host–parasite communities can be valuable tools for investigating connections between community structures at multiple scales, as each host can be considered a replicate parasite community. Like free‐living communities, within‐host–parasite communities are hierarchical; ecological interactions between hosts and parasites can occur at multiple scales (e.g., host community, host population, parasite community within the host), therefore, both extrinsic and intrinsic processes can determine parasite community structure. We combine analyses of community structure and assembly at both the host population and individual scales using extensive datasets on wild wood mice (Apodemus sylvaticus) and their parasite community. An analysis of parasite community nestedness at the host population scale provided predictions about the order of infection at the individual scale, which were then tested using parasite community assembly data from individual hosts from the same populations. Nestedness analyses revealed parasite communities were significantly more structured than random. However, observed nestedness did not differ from null models in which parasite species abundance was kept constant. We did not find consistency between observed community structure at the host population scale and within‐host order of infection. Multi‐state Markov models of parasite community assembly showed that a host's likelihood of infection with one parasite did not consistently follow previous infection by a different parasite species, suggesting there is not a deterministic order of infection among the species we investigated in wild wood mice. Our results demonstrate that patterns at one scale (i.e., host population) do not reliably predict processes at another scale (i.e., individual host), and that neutral or stochastic processes may be driving the patterns of nestedness observed in these communities. We suggest that experimental approaches that manipulate parasite communities are needed to better link processes at multiple ecological scales.     

Metacommunity structure analysis reveals nested patterns in deconstructed macroinvertebrates assemblages

1. Understanding processes driving patterns of species distribution and diversity is one of the main objectives of community ecology.
2. The aim of our study was to evaluate the spatial variation in assemblage composition of stream-dwelling macroinvertebrates and identify which factors (e.g. water quality, land cover) are the most important drivers.
3. We applied the elements of the metacommunity structure approach on a dataset of 38 communities from the Futaleufú basin in northwestern Patagonia. To better understand assemblage variation, we deconstructed our macroinvertebrate dataset into different taxonomic and trait groups. We then identified the most influential factors driving community composition using random forests.
4. We found that half of our datasets (i.e. macroinvertebrate groups) exhibited a nested structure with clumped species loss, while the other half showed a quasi-nested pattern with either clumped or stochastic species loss.
5. Overall, water quality was the most important driver of community variation, although climate, geography, and land cover were more or less relevant in particular cases. We found differences in the relative importance of the selected explanatory variables among datasets. This would suggest that different components of the macroinvertebrate community respond differently to environmental factors.
6. Our findings could be of value for conservation planning, as they suggest that preserving the most species-rich streams would, to some extent, guarantee the conservation of the entire species pool.

     

Communities in high definition: Spatial and environmental factors shape the micro-distribution of aquatic invertebrates

1. According to metacommunity theories, the structure of natural communities is the result of both environmental filtering and spatial processes, with their relative importance depending on factors including local habitat characteristics, functional features of organisms, and the spatial scale considered. However, few studies have explored environmental and spatial processes in riverine systems at local scales, explicitly incorporating spatial coordinates into multi-taxa distribution models. To address this gap, we conducted a small-scale study to discriminate between abiotic and biotic factors affecting the distribution of aquatic macroinvertebrates, applying metacommunity concepts.
2. We studied a mountain section in each of three perennial streams within the Po River Basin (northern Italy). We sampled macroinvertebrates both in summer and winter, using specific in situ 50-point random sampling grids. Environmental factors, including benthic organic matter (BOM), flow velocity, water depth, and substrate were recorded together with spatial coordinates for each sampling point. The relationships between community metrics (taxon richness, abundance, biomass, biomass–abundance ratio, and functional feeding groups) and explanatory variables (environmental and spatial) were assessed using generalised additive models. The influence of the explanatory variables on community structure was analysed with joint species distribution models.
3. Environmental variables—primarily BOM—were the main drivers affecting community metrics, whereas the effects of spatial variables varied among metrics, streams, and seasons. During summer, community structure was strongly affected by BOM and spatial position within the riverbed, the latter probably being a proxy for mass effects mediated by biotic and stochastic processes. In contrast, community structure was mainly shaped by hydraulic variables in winter.
4. Using macroinvertebrate communities as a model group, our results demonstrate that metacommunity concepts can explain small-scale variability in community structure. We found that both environmental filtering and biotic processes shape local communities, with the strength of these drivers depending on the season. These insights provide baseline knowledge that informs our understanding of ecological responses to environmental variability in contexts including restoration ecology, habitat suitability modelling, and biomonitoring.

     

Effects of wind‐driven spatial structure and environmental heterogeneity on high‐altitude wetland macroinvertebrate assemblages with contrasting dispersal modes

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An experimental analysis of species sorting and mass effects in freshwater bacterioplankton

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