Testing multiple assembly rule models in avian communities on islands of an inundated lake,Zhejiang Province,China

Aim A fundamental question in community ecology is whether general assembly rules determine the structure of natural communities. Although many types of assembly rules have been described, including Diamond’s assembly rules, constant body‐size ratios, favoured states, and nestedness, few studies have tested multiple assembly rule models simultaneously. Therefore, little is known about the relative importance of potential underlying factors such as interspecific competition, inter‐guild competition, selective extinction and habitat nestedness in structuring community composition. Here, we test the above four assembly rule models and examine the causal basis for the observed patterns using bird data collected on islands of an inundated lake. Location Thousand Island Lake, China. Methods  We collected data on presence–absence matrices, body size and functional groups for bird assemblages on 42 islands from 2007 to 2009. To test the above four assembly rule models, we used null model analyses to compare observed species co‐occurrence patterns, body‐size distributions and functional group distributions with randomly generated assemblages. To ensure that the results were not biased by the inclusion of species with extremely different ecologies, we conducted separate analyses for the entire assemblage and for various subset matrices classified according to foraging guilds. Results The bird assemblages did not support predictions by several competitively structured assembly rule models, including Diamond’s assembly rules, constant body‐size ratios, and favoured states. In contrast, bird assemblages were highly significantly nested and were apparently shaped by extinction processes mediated through area effects and habitat nestedness. The nestedness of bird assemblages was not a result of passive sampling or selective colonization. These results were very consistent, regardless of whether the entire assemblage or the subset matrices were analysed. Main conclusions Our results suggest that bird assemblages were shaped by extinction processes mediated through area effects and habitat nestedness, rather than by interspecific or inter‐guild competition. From a conservation point of view, our results indicate that we should protect both the largest islands with the most species‐rich communities and habitat‐rich islands in order to maximize the number of species preserved.     

Oribatid mites reveal that competition for resources and trophic structure combine to regulate the assembly of diverse soil animal communities

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Community assembly in Lake Tanganyika cichlid fish: quantifying the contributions of both niche‐based and neutral processes

The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche‐based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche‐based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche‐based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche‐based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche‐based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche‐based or neutral‐based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns.     

Habitat fragmentation and extinction rates within freshwater fish communities: a faunal relaxation approach

Aim To estimate population extinction rates within freshwater fish communities since the fragmentation of palaeo‐rivers due to sea level rise at the end of the Pleistocene; to combine this information with rates estimated by other approaches (population surveys, fossil records); and to build an empirical extinction–area relationship. Location Temperate rivers from the Northern Hemisphere, with a special focus on rivers discharging into the English Channel, in north‐western France. Methods (1) French rivers. We used a faunal relaxation approach to estimate extinction rates in coastal rivers after they became isolated by the sea level rise. Tributaries within the Seine were used to build a species–area relationship for a non‐fragmented river system to predict species richness in coastal rivers before their fragmentation. (2) Other rivers. Extinction rates obtained for four other Holarctic river systems fragmented at the end of the Pleistocene, the fragmented populations of one salmonid species (Japan) and the fossil records from the Mississippi Basin were included in the study. Results (1) French rivers. Within strictly freshwater fish species, rare and/or habitat specialist species were the most affected by fragmentation. In contrast, euryhaline species were not affected. A negative relationship between extinction rate and river basin size was observed. (2) Other rivers. Our study established a common scaling relationship for freshwater fish population extinction rates that spans seven orders of magnitude in river basin size. Main conclusions This study strongly suggests that extinctions of fish populations occurred within French coastal rivers after they became isolated 8000 years ago. The patterns observed at regional and inter‐continental scales are consistent with the expectation that large populations are less prone to extinction than small ones, resulting in a strong extinction–area relationship coherent over a large spatio‐temporal scale. Our study is the first multi‐scale quantitative assessment of background extinction patterns for freshwater fishes.     

The loss of indirect interactions leads to cascading extinctions of carnivores

Species extinctions are biased towards higher trophic levels, and primary extinctions are often followed by unexpected secondary extinctions. Currently, predictions on the vulnerability of ecological communities to extinction cascades are based on models that focus on bottom‐up effects, which cannot capture the effects of extinctions at higher trophic levels. We show, in experimental insect communities, that harvesting of single carnivorous parasitoid species led to a significant increase in extinction rate of other parasitoid species, separated by four trophic links. Harvesting resulted in the release of prey from top‐down control, leading to increased interspecific competition at the herbivore trophic level. This resulted in increased extinction rates of non‐harvested parasitoid species when their host had become rare relative to other herbivores. The results demonstrate a mechanism for horizontal extinction cascades, and illustrate that altering the relationship between a predator and its prey can cause wide‐ranging ripple effects through ecosystems, including unexpected extinctions.     

A new dynamic null model for phylogenetic community structure

Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion – often attributed to negative biotic interactions – are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure.     

Biogeographical patterns of freshwater micro‐ and macroorganisms: a comparison between phytoplankton,zooplankton and fish in the eastern Mediterranean

Aim We investigated the biogeographical patterns of phytoplankton, zooplankton and fish in freshwater ecosystems. We tested whether spatial distance or environmental heterogeneity act as potential factors controlling community composition. Location Northern and central Greece, eastern Mediterranean. Method Data on 310 phytoplankton, 72 zooplankton and 37 fish species were collected from seven freshwater systems. Species occurrence data were used to generate similarity matrices describing community composition. We performed Mantel tests to compare spatial patterns in community composition of phytoplankton, zooplankton and fish. Next, we examined the correlation between geographical distance and the degree of similarity in community composition. The analysis was repeated for different taxonomic, trophic and size‐based groups of the microorganisms studied. We assessed different environmental variables (topographic and limnological) as predictors of community composition. Results Phytoplankton community composition showed a strong positive correlation with environmental heterogeneity but was not correlated with the geographical distance between systems. Zooplankton community composition was unrelated to geographical distance and was only weakly correlated with environmental variables. In contrast, fish community similarity decayed significantly with distance. We found no relationship along all pairwise comparisons of the compositional matrices of the three groups. The pairwise comparisons of the different taxonomic, trophic and size‐based groups of the microorganism communities studied were in accordance with the results for the entire microorganism community. Main conclusions Our results support the proposition that the biogeography of microorganisms does not demonstrate a distance–decay pattern and further suggest that, in reality, the drivers of distribution depend on the specific community examined. In contrast, the biogeography of macroorganisms was affected by geographical distance. These differences reflect the dispersal abilities of the different organisms. The microorganisms exhibit passive dispersal through the air, with local environmental conditions structuring their community composition. On the other hand, for macroorganisms such as fish, the terrestrial environment could pose barriers to their dispersal; with fish structuring distinctive communities over greater distances. Overall, we suggest that the biogeography of freshwater phytoplankton and zooplankton reflects contemporary environmental conditions, while the biogeographical patterns for fish inhabiting the same systems are related to factors affecting their dispersal ability.     

Biogeography of the livebearing fish Poecilia gillii in Costa Rica: are phylogeographical breaks congruent with fish community boundaries?

One of the original goals of phylogeography was to use genetic data to identify historical events that might contribute to breaks among communities. In this study, we examine the phylogeography of a common livebearing fish ( Poecilia gillii ) from Costa Rica. Our goal was to determine if phylogeographical breaks in this species were congruent with previously defined boundaries among four fish community provinces. We hypothesized that if abiotic factors influence both community boundaries and genetic structuring in P. gillii then we might find four clades within our focal species that were geographically separated along community boundary lines. Similarly, we expected to find most of the genetic variation in P. gillii partitioned among these four geographical regions. We generated DNA sequence data (mitochondrial cytochrome b and nuclear S7 small ribosomal subunit) for 260 individuals from 42 populations distributed across Costa Rica. We analysed these data using phylogenetic (parsimony and likelihood) and coalescent approaches to estimate phylogenetic relationships among haplotypes, patterns of gene flow and effective population size . Contrary to our expectations, we did not find four monophyletic groups that mapped cleanly to our geographical community provinces. However, one of our clades was restricted to a single province, suggesting that common earth history events could be responsible for both genetic structuring in P. gillii and fish community composition in this area. However, our results show a complex pattern of gene flow throughout other regions in Costa Rica where genetic structuring is not predicted by community province boundaries.     

Competition from sea to mountain: Interactions and aggregation in low‐diversity monogenean and endohelminth communities in twospot livebearer Pseudoxiphophorus bimaculatus (Teleostei: Poeciliidae) populations in a neotropical river

1. The role of interspecific interactions in structuring low‐diversity helminth communities is a controversial topic in parasite ecology research. Most parasitic communities of fish are species‐poor; thus, interspecific interactions are believed to be unimportant in structuring these communities.
2. We explored the factors that might contribute to the richness and coexistence of helminth parasites of a poeciliid fish in a neotropical river.
3. Repeatability of community structure was examined in parasitic communities among 11 populations of twospot livebearer Pseudoxiphophorus bimaculatus in the La Antigua River basin, Veracruz, Mexico. We examined the species saturation of parasitic communities and explored the patterns of species co‐occurrence. We also quantified the associations between parasitic species pairs and analyzed the correlations between helminth species abundance to look for repeated patterns among the study populations.
4. Our results suggest that interspecific competition could occur in species‐poor communities, aggregation plays a role in determining local richness, and intraspecific aggregation allows the coexistence of species by reducing the overall intensity of interspecific competition.

     

Distinguishing the signatures of local environmental filtering and regional trait range limits in the study of trait–environment relationships

Understanding the imprint of environmental filtering on community assembly along environmental gradients is a key objective of trait‐gradient analyses. Depending on local constraints, this filtering generally entails that species departing from an optimum trait value have lower abundances in the community. The community‐weighted mean (CWM) and variance (CWV) of trait values are then expected to depict the optimum and intensity of filtering, respectively. However, the trait distribution within the regional species pool and its limits can also affect local CWM and CWV values apart from the effect of environmental filtering. The regional trait range limits are more likely to be reached in communities at the extremes of environmental gradients. Analogous to the mid‐domain effect in biogeography, decreasing CWV values in extreme environments can then represent the influence of regional trait range limits rather than stronger filtering in the local environment. We name this effect the ‘trait‐gradient boundary effect’ (TGBE). First, we use a community assembly framework to build simulated communities along a gradient from a species pool and environmental filtering with either constant or varying intensity while accounting for immigration processes. We demonstrate the significant influence of TGBE, in parallel to environmental filtering, on CWM and CWV at the extremes of the environmental gradient. We provide a statistical tool based on Approximate Bayesian Computation to decipher the respective influence of local environmental filtering and regional trait range limits. Second, as a case study, we reanalyze the functional composition of alpine plant communities distributed along a gradient of snow cover duration. We show that leaf trait convergence found in communities at the extremes of the gradient reflect an influence of trait range limits rather than stronger environmental filtering. These findings challenge correlative trait–environment relationships and call for more explicitly identifying the mechanisms responsible of trait convergence/divergence along environmental gradients.     

Fish predation regimes modify benthic diatom community structures: Experimental evidence from an in situ mesocosm study

Diatoms are important primary producers in shallow water environments. Few studies have assessed the importance of biological interactions in structuring these communities. In the present study, benthic diatom community structure in relation to manipulated food webs was assessed using in situ mesocosms, whereby predator‐free environments and environments comprising two different fish species were assessed. Zooplankton abundance, settled algal biomass and the diatom community were monitored over a 12‐day period across each of the three trophic scenarios. Differences among treatments over time were observed in zooplankton abundances, particularly copepods. Similarly, the benthic diatom community structure changed significantly over time across the three trophic treatments. However, no differences in total algal biomass were found among treatments. This was likely the result of non‐diatom phytoplankton contributions. We propose that the benthic diatom community structure within the mesocosms was influenced by trophic cascades and potentially through direct consumption by the fish. The study highlights that not only are organisms at the base of the food web affected by predators at the top of the food web, but that predator identity is potentially an important consideration for predator–prey interaction outcomes with consequences for multiple trophic levels.     

Hierarchical spatial structure of stream fish colonization and extinction

Spatial variation in extinction and colonization is expected to influence community composition over time. In stream fish communities, local species richness (alpha diversity) and species turnover (beta diversity) are thought to be regulated by high extinction rates in headwater streams and high colonization rates in downstream areas. We evaluated the spatiotemporal structure of fish communities in streams originally surveyed by Burton and Odum 1945 (Ecology 26: 182–194) in Virginia, USA and explored the effects of species traits on extinction and colonization dynamics. We documented dramatic changes in fish community structure at both the site and stream scales. Of the 34 fish species observed, 20 (59%) were present in both time periods, but 11 (32%) colonized the study area and three (9%) were extirpated over time. Within streams, alpha diversity increased in two of three streams but beta diversity decreased dramatically in all streams due to fish community homogenization caused by colonization of common species and extirpation of rare species. Among streams, however, fish communities differentiated over time. Regression trees indicated that reproductive life‐history traits such as spawning mound construction, associations with mound‐building species, and high fecundity were important predictors of species persistence or colonization. Conversely, native fishes not associated with mound‐building exhibited the highest rates of extirpation from streams. Our results demonstrate that stream fish colonization and extinction dynamics exhibit hierarchical spatial structure and suggest that mound‐building fishes serve as keystone species for colonization of headwater streams.     

Species loss leads to community closure

Global extinction of a species is sadly irreversible. At a local scale, however, extinctions may be followed by re-invasion. We here show that this is not necessarily the case and that an ecological community may close its doors for re-invasion of species lost from it. Previous studies of how communities are assembled have shown that there may be rules for that process and that limitations are set to the order by which species are introduced and put together. Instead of focusing on the assembly process we randomly generated simple competitive model communities that were stable and allowed for two to 10 coexisting species. When a randomly selected single species was removed from the community, the cascading species loss was recorded and frequently the resulting community was more than halved. Cascading extinctions have previously been recorded, but we here show that the relative magnitude of the cascade is dependent on community size (and not only trophic structure) and that the reintroduction of the original species lost often is impossible. Hence, species loss does not simply leave a void potentially refilled, but permanently alters the entire community structure and consequently the adaptive landscape for potential re-invaders.     

Cascading effects of mass mortality events in Arctic marine communities

Mass mortality events caused by pulse anthropogenic or environmental perturbations (e.g., extreme weather, toxic spills or epizootics) severely reduce the abundance of a population in a short time. The frequency and impact of these events are likely to increase across the globe. Studies on how such events may affect ecological communities of interacting species are scarce. By combining a multispecies Gompertz model with a Bayesian state‐space framework, we quantify community‐level effects of a mass mortality event in a single species. We present a case study on a community of fish and zooplankton in the Barents Sea to illustrate how a mass mortality event of different intensities affecting the lower trophic level (krill) may propagate to higher trophic levels (capelin and cod). This approach is especially valuable for assessing community‐level effects of potential anthropogenic‐driven mass mortality events, owing to the ability to account for uncertainty in the assessed impact due to uncertainty about the ecological dynamics. We hence quantify how the assessed impact of a mass mortality event depends on the degree of precaution considered. We suggest that this approach can be useful for assessing the possible detrimental outcomes of toxic spills, for example oil spills, in relatively simple communities such as often found in the Arctic, a region under increasing influence of human activities due to increased land and sea use.     

Fungal infection alters the selection,dispersal and drift processes structuring the amphibian skin microbiome

Symbiotic microbial communities are important for host health, but the processes shaping these communities are poorly understood. Understanding how community assembly processes jointly affect microbial community composition is limited because inflexible community models rely on rejecting dispersal and drift before considering selection. We developed a flexible community assembly model based on neutral theory to ask: How do dispersal, drift and selection concurrently affect the microbiome across environmental gradients? We applied this approach to examine how a fungal pathogen affected the assembly processes structuring the amphibian skin microbiome. We found that the rejection of neutrality for the amphibian microbiome across a fungal gradient was not strictly due to selection processes, but was also a result of species‐specific changes in dispersal and drift. Our modelling framework brings the qualitative recognition that niche and neutral processes jointly structure microbiomes into quantitative focus, allowing for improved predictions of microbial community turnover across environmental gradients.     

Stable isotope analyses reveal dense trophic species packing and clear niche differentiation in a malagasy primate community

Understanding the mechanisms maintaining local species richness is a major topic in tropical ecology. In ecological communities of Madagascar, primates represent a major part of mammalian diversity and, thus, are a suitable taxon to study these mechanisms. Previous research suggested that ecological niche differentiation facilitates the coexistence of lemurs. However, detailed data on all species making up diverse local primate assemblages is rarely available, hampering community‐wide tests of niche differentiation among Malagasy mammals. Here, we took an indirect approach and used stable isotopes as long‐term indicators of individuals' diets to answer the question of whether trophic patterns and food‐related mechanisms stabilize coexistence in a species‐rich lemur community. We analyzed stable carbon and nitrogen isotopes in hair collected from eight syntopic lemurs in Kirindy Forest. We found that lemur species were well separated into trophic niches and ranged over two trophic levels. Furthermore, species were densely packed in isotopic space suggesting that past competitive interactions between species are a major structuring force of this dry forest lemur community. Results of other comparative studies on primates and our findings underline that—in contrast to communities worldwide—the structure and composition of lemur communities follow predictions of ecological niche theory. Patterns of competitive interactions might be more clearly revealed in Malagasy primate communities than elsewhere because lemurs represent a large fraction of ecologically interacting species in these communities. The pronounced trophic niche differentiation among lemurs is most likely due to intense competition in the past as is characteristic for adaptive radiations. Am J Phys Anthropol 153:249–259, 2014. © 2013 Wiley Periodicals, Inc.     

Predator decline leads to decreased stability in a coastal fish community

Fisheries exploitation has caused widespread declines in marine predators. Theory predicts that predator depletion will destabilise lower trophic levels, making natural communities more vulnerable to environmental perturbations. However, empirical evidence has been limited. Using a community matrix model, we empirically assessed trends in the stability of a multispecies coastal fish community over the course of predator depletion. Three indices of community stability (resistance, resilience and reactivity) revealed significantly decreasing stability concurrent with declining predator abundance. The trophically downgraded community exhibited weaker top‐down control, leading to predator‐release processes in lower trophic levels and increased susceptibility to perturbation. At the community level, our results suggest that high predator abundance acts as a stabilising force to the naturally stochastic and highly autocorrelated dynamics in low trophic species. These findings have important implications for the conservation and management of predators in marine ecosystems and provide empirical support for the theory of predatory control.     

Response of marine communities to local temperature changes

As global climate change and variability drive shifts in species’ distributions, ecological communities are being reorganized. One approach to understand community change in response to climate change has been to characterize communities by a collective thermal preference, or community temperature index (CTI), and then to compare changes in CTI with changes in temperature. However, important questions remain about whether and how responsive communities are to changes in their local thermal environments. We used CTI to analyze changes in 160 marine assemblages (fish and invertebrates) across the rapidly‐changing Northeast U.S. Continental Shelf Large Marine Ecosystem and calculated expected community change based on historical relationships between species presence and temperature from a separate training dataset. We then compared interannual and long‐term temperature changes with expected community responses and observed community responses over both temporal scales. For these marine communities, we found that community composition as well as composition changes through time could be explained by species associations with bottom temperature. Individual species had non‐linear responses to changes in temperature, and these nonlinearities scaled up to a nonlinear relationship between CTI and temperature. On average, CTI increased by 0.36°C (95% CI: 0.34–0.38°C) for every 1°C increase in bottom temperature, but the relationship between CTI and temperature also depended on community composition. In addition, communities responded more strongly to interannual variation than to long‐term trends in temperature. We recommend that future research into climate‐driven community change accounts for nonlinear responses and examines ecological responses across a range of temporal and geographical scales.     

Advancing the metabolic theory of biodiversity

A component of metabolic scaling theory has worked towards understanding the influence of metabolism over the generation and maintenance of biodiversity. Specific models within this ‘metabolic theory of biodiversity’ (MTB) have addressed temperature gradients in speciation rate and species richness, but the scope of MTB has been questioned because of empirical departures from model predictions. In this study, we first show that a generalized MTB is not inconsistent with empirical patterns and subsequently implement an eco‐evolutionary MTB which has thus far only been discussed qualitatively. More specifically, we combine a functional trait (body mass) approach and an environmental gradient (temperature) with a dynamic eco‐evolutionary model that builds on the current MTB. Our approach uniquely accounts for feedbacks between ecological interactions (size‐dependent competition and predation) and evolutionary rates (speciation and extinction). We investigate a simple example in which temperature influences mutation rate, and show that this single effect leads to dynamic temperature gradients in macroevolutionary rates and community structure. Early in community evolution, temperature strongly influences speciation and both speciation and extinction strongly influence species richness. Through time, niche structure evolves, speciation and extinction rates fall, and species richness becomes increasingly independent of temperature. However, significant temperature‐richness gradients may persist within emergent functional (trophic) groups, especially when niche breadths are wide. Thus, there is a strong signal of both history and ecological interactions on patterns of species richness across temperature gradients. More generally, the successful implementation of an eco‐evolutionary MTB opens the perspective that a process‐based MTB can continue to emerge through further development of metabolic models that are explicit in terms of functional traits and environmental gradients.     

Convergence of fish communities from the littoral zone of reservoirs

1. Understanding factors that regulate the assembly of communities is a main focus of ecology. Human‐engineered habitats, such as reservoirs, may provide insight into these assembly processes because they represent novel habitats that are subjected to colonization by fishes from the surrounding river basin or transported by humans. By contrasting community similarity within and among reservoirs from different drainage basins to nearby stream communities, we can test the relative constraints of reservoir habitats and regional species pools in determining species composition of reservoirs. 2. We used a large spatial database that included intensive collections from 143 stream and 28 reservoir sites within three major river basins in the Great Plains, U.S.A., to compare patterns of species diversity and community structure between streams and reservoirs and to characterize variation in fish community structure within and among major drainage basins. We expected reservoir fish faunas to reflect the regional species pool, but would be more homogeneous that stream communities because similar species are stocked and thrive in reservoirs (e.g. planktivores and piscivores), and they lack obligate stream organisms that are not shared among regional species pools. 3. We found that fish communities from reservoirs were a subset of fishes collected from streams and dominant taxa had ecological traits that would be favoured in lentic environments. Although there were regional differences in reservoir fish communities, species richness, patterns of rank abundance and community structure in reservoir communities were more homogonous across three major drainage basins than for stream communities. 4. The general pattern of convergence of reservoir fish community structure suggests their assembly is constrained by local factors such as habitat and biotic interactions, and facilitated by the introduction of species among basins. Because there is a reciprocal transfer of biota between reservoirs and streams, understanding factors structuring both habitats is necessary to evaluate the long‐term dynamics of impounded river networks.