MPowering ecologists: community assembly tools for community assembly rules

Null model tests of presence–absence data (‘NMTPAs’) provide important tools for inferring effects of competition, facilitation, habitat filtering, and other ecological processes from observational data. Many NMTPAs have been developed, but they often yield conflicting conclusions when applied to the same data. Type I and II error rates, size, power, robustness and bias provide important criteria for assessing which tests are valid, but these criteria need to be evaluated contingent on the sample size, null hypothesis of interest, and assumptions that are appropriate for the data set that is being analyzed. In this paper, we confirm that this is the case using the software MPower, evaluating the validity of NMTPAs contingent on the null hypothesis being tested, assumptions that can be made, and sample size. Evaluating the validity of NMTPAs contingent on these factors is important towards ensuring that reliable inferences are drawn from observational data about the processes controlling community assembly.     

Priming the productivity pump: flood pulse driven trends in suspended algal biomass distribution across a restored floodplain

1. Chlorophyll a (Chl a) distribution across a 0.36 km² restored floodplain (Cosumnes River, California) was analysed throughout the winter and spring flood season from January to June 2005. In addition, high temporal‐resolution Chl a measurements were made in situ with field fluorometers in the floodplain and adjacent channel. 2. The primary objectives were to characterise suspended algal biomass distribution across the floodplain at various degrees of connection with the channel and to correlate Chl a concentration and distribution with physical and chemical gradients across the floodplain. 3. Our analysis indicates that periodic connection and disconnection of the floodplain with the channel is vital to the functioning of the floodplain as a source of concentrated suspended algal biomass for downstream aquatic ecosystems. 4. Peak Chl a levels on the floodplain occurred during disconnection, reaching levels as high as 25 μg L^?1. Chl a distribution across the floodplain was controlled by residence time and local physical/biological conditions, the latter of which were primarily a function of water depth. 5. During connection, the primary pond on the floodplain exhibited low Chl a (mean = 3.4 μg L^?1) and the shallow littoral zones had elevated concentrations (mean = 4.6 μg L^?1); during disconnection, shallow zone Chl a increased (mean = 12.4 μg L^?1), but the pond experienced the greatest algal growth (mean = 14.7 μg L^?1). 6. Storm‐induced floodwaters entering the floodplain not only displaced antecedent floodplain waters, but also redistributed floodplain resources, creating complex mixing dynamics between parcels of water with distinct chemistries. Incomplete replacement of antecedent floodplain waters led to localised hypoxia in non‐flushed areas. 7. The degree of complexity revealed in this analysis makes clear the need for high‐resolution spatial and temporal studies such as this to begin to understand the functioning of dynamic and heterogeneous floodplain ecosystems.     

Variant restoration trajectories for wetland plant communities on a channelized floodplain

Restoration efforts are typically based on an assumption that reestablishment of altered determinants of ecological structure and function will lead to a predictable reestablishment of populations and reassembly of communities. Dechannelization and reestablishment of natural hydrologic regimes provide the basis for the ongoing restoration of the Kissimmee River in Central Florida, United States. The expected reestablishment of historically dominant broadleaf marsh (BLM) and buttonbush shrub (BB) communities was evaluated over a 10‐year period following implementation of the first phase of the restoration project. Plant species composition and cover were assessed during dry (spring) and wet (summer) season sampling periods at five sites on the restored floodplain, and four “control” sites on the channelized floodplain. Mean daily stage data from nearby gauges indicated hydroperiods and depths on the reflooded floodplain were within the range of historic hydrologic conditions that selected for BLM and BB communities on the pre‐channelization floodplain. After reflooding, pasture grass and upland shrub communities rapidly transitioned to a fluid mix of obligate and facultative wetland species. Although signature BLM and BB species, Sagittaria lancifolia (bulltongue arrowhead), Pontederia cordata (pickerel weed), and Cephalanthus occidentalis (buttonbush), recolonized all study sites, the expected reestablishment of dominant cover of these species did not occur. Results indicate that restoration of BLM and BB communities has been impeded by deep flood pulse disturbances, establishment of invasive wetland grasses, and mineralized soil characteristics of the drained floodplain.     

Aquatic metabolism short-term response to the flood pulse in a Mediterranean floodplain

The pulsing of river discharge affects biodiversity and productivity of whole river–floodplain ecosystems, triggering the transport, storage and processing of carbon. In this study we investigate the short-term changes in water chemistry and net pelagic metabolism (NEP) in two floodplain lakes in response to a flood pulse. The two oxbow lakes investigated in the floodplain of the Mediterranean Ebro River (NE Spain) showed a clear temporal shift in their metabolic balance, controlled by the river discharge and associated changes in water physical and chemical characteristics. Water chemistry (turbidity, water organic matter, chlorophyll a and nutrients concentration) returned to pre-flood values after 4 days, highlighting the resilience of the ecosystem to flood pulses. Lake NEP was depressed before and during floods to a minimum of −34 mg O₂ m⁻³ h⁻¹, and increased after the flood pulse to a maximum of +463 mg O₂ m⁻³ h⁻¹. The phytoplankton assemblage showed before and after floods a replacement of autotrophic species (e.g. Chlorophyceans) by mixotrophic organisms (e.g. Cryptophyceans, Euglenoids). A linear mixed effects model identified abiotic factors, particularly temperature and river discharge, as significant predictors of the net aquatic metabolism and community respiration during flood conditions. Our results suggest that the role of the Ebro floodplain lakes as sources or sinks of C is complex and relative to the time scale investigated, depending strongly on the river discharge dynamics and the transport of limiting nutrients (phosphorus).     

Echoes of a flood pulse: short-term effects of record flooding of the Illinois River on floodplain lakes under ecological restoration

Until recently, only one native and three apparently introduced Daphnia species were known from New Zealand. We demonstrate that (1) Daphnia in subalpine habitats in southern New Zealand differ morphologically and genetically from the native taxon previously labelled Daphnia carinata to merit species nova status and (2) the name of the latter should revert to D. thomsoni, used by Sars (1894) for Daphnia described from New Zealand mud. We compare some key characteristics and cytochrome c oxidase subunit 1 (CO1) sequences of the New Zealand native and other morphologically similar species. Distinctive characteristics of subalpine populations, described as Daphnia tewaipounamu sp. nov., are a wide cephalic shield with lateral flanges curving dorsally via rounded fornices, dorsal cervical depression variably expressed as a ‘step’ in the cephalic shield exuviae and retention of ephippia within shed carapace exoskeletons long after ecdysis. CO1 sequences revealed that D. tewaipounamu sp. nov. belongs to the D. carinata complex but is highly divergent (>14%) from other known members of this complex. New Zealand D. thomsoni is divergent (>15%) from D. carinata s.s. However, it is not endemic to New Zealand, as we confirmed its presence in Tasmania, and some Australian populations are closely related to it.     

Genetic assembly rules and community phenotypes

We present a conceptual construct for a genetic based community assembly rule where the genetic composition of a host plant, or resource, affects the structure of the dependent community. This is related to a genetic similarity rule that states that host plants with similar genetic compositions are hosts to similar arthropod communities. We present preliminary data from the Populus system to support this concept. We review the recent literature to evaluate the current state of the assembly rule concept and interpret a set of previous studies in the context of a genetic assembly rule. We suggest that by incorporating this concept into community ecology we can begin to bring an evolutionary perspective to this discipline.     

Responses of the fish community to the flood pulse and siltation in a floodplain lake of the Trombetas River,Brazil

The distributions of the fish species were examined in relation to environmental variables, to evaluate the effects of environmental degradation on the fish community of Batata Lake, a typical Amazonian clearwater lake. From 1979 to 1989, tailings composed of water and clay, extracted from bauxite by water jets, were discharged into Batata Lake. The tailings spread into about 30% of the lake’s area, where the level of the lake bottom rose and turbidity increased. In the present study, multivariate analyses were performed on data for environmental parameters and fish density and biomass. Fish were collected with gillnets during the annual hydrological cycle (filling, flood, drawdown and dry periods), in the silted area, the partly silted area (intermediate) and the natural area. Values of the Shannon index, density and biomass were compared among areas and periods to evaluate the effects of the tailings on community structure. Sediment resuspension, which reduces transparency, is accentuated in shallow water, and was the main factor regulating differences in the community structure between the natural and silted areas. The decrease in transparency occurs mainly during the filling period in the silted area and during the low-water period in the silted and intermediate areas, when sediment resuspension increases concentrations of nutrients and chlorophyll-a. The strong influence of migratory and piscivore species in low-transparency waters is likely associated with the greater bacterioplankton productivity and turnover rate observed by other authors in the silted area, increasing the importance of the heterotrophic food chain in Batata Lake. Reduction of transparency in the silted area was a selective factor for fish species. The death of part of the flooded forest vegetation was decisive in lowering densities of the igapó-associated species in the silted area. The unconsolidated substrate, the death of part of the igapó forest and the negative effects of low transparency – inhibiting resident visually oriented species in the affected areas – are the main factors causing the low diversity in the silted area as a whole. The correlations between CPUEs, conductivity and nutrients and chlorophyll-a concentrations do not appear to reflect cause–effect relationships, indicating that these environmental parameters are poor predictors of fish density in Batata Lake.     

Impacts of hydrological restoration on lowland river floodplain plant communities

Many lowland floodplain habitats have been disconnected from their rivers by flood defence banks. Removing or lowering these banks can reinstate regular flooding and thus restore these important wetland plant communities. In this study we analyse changes in wetland hydrology and plant community composition following the lowering of flood defence banks at a floodplain of the River Don in the United Kingdom (UK). The aim of the restoration project was to improve the quality of “floodplain grazing marsh” habitat, which is a group of wetland communities that are of conservation interest in the UK. We analyse changes in species richness and community composition over a period of 6 years, and compare the presence of indicator species from the target floodplain grazing marsh plant communities. The lowering of the flood banks increased the frequency of flood events, from an estimated average of 1.7 floods per year to 571 floods per year. The increased flooding significantly increased the proportion of time that the wetland was submerged, and the heterogeneity in hydrological conditions within the floodplain. There were significant differences in composition between the pre-restoration and restored plant communities. Plants with traits for moisture tolerance became more abundant, although the communities did not contain significantly more ‘target’ floodplain grazing marsh species at the end of the study period than prior to restoration. Colonisation by floodplain grazing marsh species may have been limited because environmental conditions were not yet suitable, or because of a shortage of colonising propagules. While the desired target plant community has not been achieved after 5 years, it is encouraging that the community has changed dynamically as a result of hydrological changes, and that moisture-tolerant species have increased in occurrence. Over the next few decades, the restored flood regime may cause further environmental change or colonisation events, thus helping increase the occurrence of desired floodplain grazing marsh indicator species.

     

From simple rules to cycling in community assembly

Simulation studies of community assembly have frequently observed two related phenomena: (1) the humpty dumpty effect in which communities can not be reconstructed by "sequential" invasions (i.e. single species invasions separated by long intervals of time) and (2) cycling between sub-communities. To better understand the mechanisms underlying these phenomena, we analyze a system consisting of two predators and two prey competing for a shared resource. We show how simple dominance rules (i.e. R^* and P^* rules) lead to cycling between sub-communities consisting of predator–prey pairs; predator and prey invasions alternatively lead to prey displacement via apparent competition and predator displacement via exploitative competition. We also show that these cycles are often dynamically unstable in the population phase space. More specifically, while for too slow invasion rates (i.e. "sequential" invasions) the system cycles indefinitely, faster invasion rates lead to coexistence of all species. In the later case, the assembly dynamics exhibit transient cycling between predator-prey subcommunities and the length of these transients decreases with the invasion rate and increases with habitat productivity.     

Ecological assembly rules on arthropod community inhabiting mistletoes

1. The colonisation of a new habitat by a community is led by deterministic and stochastic processes at different spatio-temporal scales. Parasitic plants, such as mistletoe, represent a new habitat within forest canopy that is free to be colonised by many organisms. 2. This study investigates how ecological factors operating at forest and plant scales drive changes in both specialist (mistletoe-dwelling) and tourist (transient visitors) arthropod communities inhabiting European mistletoe, Viscum album subsp. austriacum, in a Mediterranean pine forest. The influence of elevation along a broad elevational gradient was tested by sampling arthropod communities dwelling in mistletoe plants and host pine branches and the effects of mistletoe plant size, distances to other mistletoes, and temporal variation in arthropod assemblages inhabiting mistletoes. 3. The diversity of the specialist community remained constant along the elevational gradient and over the summer period, while the tourist and pine-dwelling arthropod communities showed species turnover. Larger mistletoes were occupied by more species and individuals, whereas more isolated mistletoes presented the same equilibrium point as the more aggregated ones. Thus, mistletoe size is key to the composition of the arthropod community. 4. In conclusion, this study's findings indicate contrasting assembly rules for specialised and tourist arthropod communities associated with mistletoe. The specialist community was highly stable and followed a deterministic trophic sequence of colonisation as the assemblage rule: first, colonisation by the main specialist herbivore, Cacopsylla visci, and, second, by its predator Anthocoris visci. Meanwhile, the tourist community, being a subset of the arthropod assemblage of the pine, acts independent of mistletoe presence.     

Periodic inundations drive community assembly of amphibious plants in floodplain lakes

Hydrobiologia - Understanding the effects of disturbance regimes on community assembly is an essential issue in community ecology. Yet, little is known about how water regimes drive community...     

Avian community assembly rules: The foliage-gleaning guild

Summary The theory of animal community organization has been dominated by general models based on the Lotka-Volterra equations. The predictions of these models are difficult to test in particular situations. Moreover, a great deal of ecological information is incommensurate with the data requirements of these models. A different approach to community organization addresses the ecosystem assembly problem. This problem is defined to be that of constructing an algorithm which assembles a subset of a species pool in a specified environment.A model of ecosystem assembly, based on generative grammars as used in theoretical linguistics, is described. It was constructed from and validated with data collected by D.H. Morse on a guild of foliage-gleaning birds inhabiting spruce forests on islands off the coast of Maine. The data were divided into two groups. One group, from the years 1967–1970, was used for model construction; the second group, from 1971–1975, was used to validate the model.The model has two major components. One component inserts species onto islands according to the microhabitat used by each species and the resources available on each island. A second component deletes those inserted species from islands on which they were not observed to occur during 1967–1970. This component is composed of deletion rules that remove species depending on (a) their sizes and resource requirements, (b) the sizes and resource requirements of other species present in the ecosystem, and (c) the structure of the vegetation on the islands. Model validation was performed by comparing the predicted distributions of species against observed distributions not used in model construction. Model accuracy for the later data (1971–1975) was slightly higher than for the earlier data (1967–1970), approximately 88% and 84%, respectively.The behavior of the model was investigated with several simulations. These included the effects of the removal of certain deletion rules and the effects of the application of the rules without regard to their order. Other simulations demonstrated the application of the model to the prediction of the effects of habitat manipulation and the removal of particular species from the species pool.     

Experimental restoration of a fen plant community after peat mining

Question: Which restoration measures (introduction of donor diaspore material, application of straw mulch, alteration of residual peat depths) contribute to the establishment of a fen plant community on minerotrophic surfaces after peat mining? Location: Rivière‐du‐Loup peatland, southern Québec, Canada at 100 m a.s.1. Methods: The effectiveness of introducing fen plants with the application of donor diaspore material was tested. The donor diaspore material, containing seeds, rhizomes, moss fragments, and other plant propagules, was collected from two different types of natural fens. We tested whether the application of straw mulch would increase fen species cover and biodiversity compared to control plots without straw mulch. Terrace levels of different peat depths (15 cm, 40 cm, and 56 cm) were created to test the effects of different environmental site conditions on the success of re‐vegetation. Results: Applying donor seed bank from natural fens was found to significantly increase fen plant cover and richness after the two growing seasons. Straw mulch proved to significantly increase fen plant richness. The intermediate terrace level (40 cm) had the highest fen plant establishment. Compared to reference sites, the low terrace level (15 cm) was richer in base cations, whereas the high terrace level (56 cm) was much drier. Conclusions: The application of donor diaspore material was demonstrated as an effective technique for establishing vascular fen plants. Further re wetting measures are considered necessary at the restoration site to create a fen ecosystem rather than simply restoring some fen species.     

Non-native earthworms alter the assembly of a meadow plant community

Non-native earthworms can alter ecosystems by modifying soil structure, depredating seeds and seedlings, and consuming soil organic matter, yet the initial responses of plant communities to earthworm invasions remain poorly understood. We assessed the effect of non-native earthworms on seedling survival during germination and after establishment using six native and six non-native plant species grown from seed in single- and multi-species experimental mesocosms. We examined the extent to which earthworms (1) influenced seedling survival, (2) selectively depredated native versus non-native plants, (3) impacted establishment based on seed size and/or root morphology, and (4) shaped community assembly. The effect of earthworms on seedling survival varied temporally and among species but inconsistently with respect to species origin. Differences in seed/seedling survival translated to changes in community assembly. Earthworms tended to reduce species abundance, richness, evenness, and diversity in multi-species mesocosms and led to the divergence of communities by treatment. In general, species with large seeds and fibrous roots dominated communities with earthworms present, whereas species with small seeds and taproots only persisted in multi-species mesocosms without earthworms. Our findings suggest that earthworms act as ecological filters in the early stages of invasion to shape community composition based on plant morphological traits.

     

A niche-based modeling approach to phytoplankton community assembly rules

Six niche-based models proposed by Tokeshi, based on different assumptions of resource allocation by species, were fitted on phytoplankton relative abundance distributions, and potential environmental and biotic factors supporting the applicability of the fitted models were discussed. Overall 16 assemblages corresponding to different sampling times, various environmental conditions, and resource regimes within a year were fitted to the models. Phytoplankton biovolume was used as a measure of abundance, and a randomization test was applied to compare the model fit to the field data. The majority of the phytoplankton assemblages (11 of 16) were successfully described by the Random Fraction model, which is based on the theoretical assumption that resource is apportioned by the species in a random way. Only a few assemblages (three of 16), characterized by extremes in resource availability or disturbance, were not fitted by any of the models. The Random Fraction model in particular was rejected due to a steep slope during the first ranks, while the rest of the distribution remained relatively even, providing further evidence of resilience in phytoplankton communities. Although larger cells seem to have the potential to develop higher biomass, it seems that other factors, including the surface-to-volume ratio, counterbalance this advantage, resulting in a random-like behaviour in resource acquisition by phytoplankton, irrespective of cell size or species identity.     

Flood pulse regulation of bacterioplankton community composition in an Amazonian floodplain lake

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Post-fire restoration of Mediterranean forests: Testing assembly rules mediated by facilitation

In view of the importance of facilitative interactions between plants, nurse-based planting has been proposed as a restoration technique for Mediterranean vegetation. However, facilitation efficiency is known to depend on the environmental context and the particular pair of interacting species. Understanding these context- and pair-specific dependences is fundamental to understanding Mediterranean vegetation dynamics and to improving the use of nurse-based plantation for restoration. We assessed the effectiveness of nurse-based plantation and the significance for post-fire restoration of some assembly rules mediated by facilitation. In two nearby areas of different burning ages, we compared seedling establishment of 13 tall shrubs and trees planted in open ground and under nurses. Nurses and planted seedlings were selected from different life-forms. Tests of the assembly rules were provided by the partitioning of the statistical interaction effect between nurse and planted seedling life-forms in a two-factor design. Nurse-based plantation increased seedling survival 2–9 times compared to plantation in open ground, depending on the year. The higher efficiency of nurse-based plantation was consistent for the two burned areas and occurred in many species even in years with contrasting rainfall. We detected pair-specific differences in the efficiency of facilitation. This pair-specificity was partly explained by the dependence between life-forms of nurse and guest species, suggesting the existence of assembly rules. Our results confirm that nurse-based plantation would be an appropriate post-fire restoration technique in Mediterranean mountains under dry-subhumid climate, but suggest that attention to the life-form assemblage rules is needed for an efficient implementation of such technique.