scholarly journals Community trait overdispersion due to trophic interactions: concerns for assembly process inference

2016 ◽  
Vol 283 (1840) ◽  
pp. 20161729 ◽  
Author(s):  
Mikael Pontarp ◽  
Owen L. Petchey
Keyword(s):  
Trophic Interactions ◽  
Community Assembly ◽  
Competitive Exclusion ◽  
Ecological Model ◽  
Model Parameters ◽  
Theoretical Studies ◽  
Assembly Process ◽  
Habitat Filtering ◽  
Secondary Consumers ◽  
Trait Space

The expected link between competitive exclusion and community trait overdispersion has been used to infer competition in local communities, and trait clustering has been interpreted as habitat filtering. Such community assembly process inference has received criticism for ignoring trophic interactions, as competition and trophic interactions might create similar trait patterns. While other theoretical studies have generally demonstrated the importance of predation for coexistence, ours provides the first quantitative demonstration of such effects on assembly process inference, using a trait-based ecological model to simulate the assembly of a competitive primary consumer community with and without the influence of trophic interactions. We quantified and contrasted trait dispersion/clustering of the competitive communities with the absence and presence of secondary consumers. Trophic interactions most often decreased trait clustering (i.e. increased dispersion) in the competitive communities due to evenly distributed invasions of secondary consumers and subsequent competitor extinctions over trait space. Furthermore, effects of trophic interactions were somewhat dependent on model parameters and clustering metric. These effects create considerable problems for process inference from trait distributions; one potential solution is to use more process-based and inclusive models in inference.

scholarly journals Phylogenetic community structure metrics and null models: a review with new methods and software

2015 ◽  
Author(s):  
Eliot T Miller ◽  
Damien R Farine ◽  
Christopher H Trisos
Keyword(s):  
Community Structure ◽  
Community Assembly ◽  
Competitive Exclusion ◽  
Null Model ◽  
Error Rates ◽  
Null Models ◽  
Type I ◽  
Habitat Filtering ◽  
Phylogenetic Community Structure ◽  
Structure Metrics

Competitive exclusion and habitat filtering are believed to have an important influence on the assembly of ecological communities, but ecologists and evolutionary biologists have not reached a consensus on how to quantify patterns that would reveal the action of these processes. No fewer than 22 phylogenetic community structure metrics and nine null models can be combined, providing 198 approaches to test for such patterns. Choosing statistically appropriate approaches is currently a daunting task. First, given random community assembly, we assessed similarities among metrics and among null models in their behavior across communities varying in species richness. Second, we developed spatially explicit, individual-based simulations where communities were assembled either at random, by competitive exclusion or by habitat filtering. Third, we quantified the performance (type I and II error rates) of all 198 approaches against each of the three assembly processes. Many metrics and null models are functionally equivalent, more than halving the number of unique approaches. Moreover, an even smaller subset of metric and null model combinations is suitable for testing community assembly patterns. Metrics like mean pairwise phylogenetic distance and phylogenetic diversity were better able to detect simulated community assembly patterns than metrics like phylogenetic abundance evenness. A null model that simulates regional dispersal pressure on the community of interest outperformed all others. We introduce a flexible new R package, metricTester, to facilitate robust analyses of method performance. The package is programmed in parallel to readily accommodate integration of new row-wise matrix calculations (metrics) and matrix-wise randomizations (null models) to generate expectations and quantify error rates of proposed methods.

scholarly journals Emergent Simplicity in Microbial Community Assembly

2017 ◽  
Author(s):  
Joshua E. Goldford ◽  
Nanxi Lu ◽  
Djordje Bajic ◽  
Sylvie Estrela ◽  
Mikhail Tikhonov ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Community Assembly ◽  
Competitive Exclusion ◽  
Ex Situ ◽  
Coarse Grained ◽  
Natural Environments ◽  
Complex Dynamic ◽  
Microbial Community Assembly ◽  
Consumer Resource

AbstractMicrobes assemble into complex, dynamic, and species-rich communities that play critical roles in human health and in the environment. The complexity of natural environments and the large number of niches present in most habitats are often invoked to explain the maintenance of microbial diversity in the presence of competitive exclusion. Here we show that soil and plant-associated microbiota, cultivated ex situ in minimal synthetic environments with a single supplied source of carbon, universally re-assemble into large and dynamically stable communities with strikingly predictable coarse-grained taxonomic and functional compositions. We find that generic, non-specific metabolic cross-feeding leads to the assembly of dense facilitation networks that enable the coexistence of multiple competitors for the supplied carbon source. The inclusion of universal and non-specific cross-feeding in ecological consumer-resource models is sufficient to explain our observations, and predicts a simple determinism in community structure, a property reflected in our experiments.

Bryophyte community assembly on young land uplift islands – Dispersal and habitat filtering assessed using species traits

2019 ◽  
Vol 46 (10) ◽  
pp. 2188-2202 ◽  
Author(s):  
Andreas Karlsson Tiselius ◽  
Sofi Lundbäck ◽  
Niklas Lönnell ◽  
Roland Jansson ◽  
Mats Dynesius
Keyword(s):  
Community Assembly ◽  
Species Traits ◽  
Habitat Filtering ◽  
Land Uplift

scholarly journals A phylogenetic approach to disentangling the role of competition and habitat filtering in community assembly of Neotropical forest birds

2010 ◽  
Vol 79 (6) ◽  
pp. 1181-1192 ◽  
Author(s):  
Juan Pablo Gómez ◽  
Gustavo A. Bravo ◽  
Robb T. Brumfield ◽  
José G. Tello ◽  
Carlos Daniel Cadena
Keyword(s):  
Community Assembly ◽  
Forest Birds ◽  
Habitat Filtering ◽  
Neotropical Forest

Trait contributions to fish community assembly emerge from trophic interactions in an individual-based model

2013 ◽  
Vol 251 ◽  
pp. 32-43 ◽  
Author(s):  
Henrique C. Giacomini ◽  
Donald L. DeAngelis ◽  
Joel C. Trexler ◽  
Miguel Petrere
Keyword(s):  
Trophic Interactions ◽  
Community Assembly ◽  
Fish Community ◽  
Individual Based Model

scholarly journals Four fundamental processes of community assembly

2017 ◽  
Author(s):  
Joshua Ladau ◽  
Steven J. Schwager
Keyword(s):  
Community Assembly ◽  
Interspecific Interactions ◽  
A Priori ◽  
Ecological Models ◽  
Habitat Filtering ◽  
Stochastic Sampling ◽  
Sampling Process ◽  
Ecological Mechanisms

A central aim of ecology is understanding the mechanisms of community assembly. To address this problem, community assembly is often modeled as a sampling process, in which species are selected from a pool of available species, possibly with effects of interspecific interactions, habitat filtering, and other ecological mechanisms. However, the fundamental stochastic sampling process by which species are selected from the pool remains unexplored. Here we demonstrate the distinctness of four canonical sampling processes, the Bernoulli, Plackett-Luce, multinomial, and fractional multinomial processes. Each process can be affected by ecological mechanisms or it can occur in their absence. Although all four of the processes are a priori plausible and the first two are widely used in ecological models, we show that the multinomial and fractional multinomial processes broadly underlie community assembly.

scholarly journals A new dispersal-informed null model for community ecology shows strong performance

2016 ◽  
Author(s):  
Eliot Miller
Keyword(s):  
Community Structure ◽  
Competitive Exclusion ◽  
Null Model ◽  
Error Rates ◽  
Null Models ◽  
Type I ◽  
Habitat Filtering ◽  
Exclusion Processes ◽  
Phylogenetic Community Structure ◽  
Structure Metrics

AbstractNull models in ecology have been developed that, by maintaining some aspects of observed communities and repeatedly randomizing others, allow researchers to test for the action of community assembly processes like habitat filtering and competitive exclusion. Such processes are often detected using phylogenetic community structure metrics. When biologically significant elements, such as the number of species per assemblage, break down during randomizations, it can lead to high error rates. Realistic dispersal probabilities are often neglected during randomization, and existing models make the oftentimes empirically unreasonable assumption that all species are equally probable of dispersing to a given site. When this assumption is unwarranted, null models need to incorporate dispersal probabilities. I do so here, and present a dispersal null model (DNM) that strictly maintains species richness, and approximately maintains species occurrence frequencies and total abundance. I tested its statistical performance when used with a wide breadth of phylogenetic community structure metrics across 3,000 simulated communities assembled according to neutral, habitat filtering, and competitive exclusion processes. The DNM performed well, exhibiting low error rates (both type I and II). I also implemented it in a re-analysis of a large empirical dataset, an abundance matrix of 696 sites and 75 species of Australian Meliphagidae. Although the overall signal from that study remained unchanged, it showed that statistically significant phylogenetic clustering could have been an artifact of dispersal limitations.

scholarly journals The ‘filtering’ metaphor revisited: competition and environment jointly structure invasibility and coexistence

2018 ◽  
Vol 14 (8) ◽  
pp. 20180460 ◽  
Author(s):  
Rachel M. Germain ◽  
Margaret M. Mayfield ◽  
Benjamin Gilbert
Keyword(s):  
Community Assembly ◽  
Environmental Conditions ◽  
Competitive Exclusion ◽  
Environmental Filtering ◽  
Competitive Environment ◽  
Species Persistence ◽  
Competitive Coexistence ◽  
Small Scales ◽  
Demographic Approach ◽  
Shallow Roots

‘Filtering’, or the reduction in species diversity that occurs because not all species can persist in all locations, is thought to unfold hierarchically, controlled by the environment at large scales and competition at small scales. However, the ecological effects of competition and the environment are not independent, and observational approaches preclude investigation into their interplay. We use a demographic approach with 30 plant species to experimentally test: (i) the effect of competition on species persistence in two soil moisture environments, and (ii) the effect of environmental conditions on mechanisms underlying competitive coexistence. We find that competitors cause differential species persistence across environments even when effects are lacking in the absence of competition, and that the traits which determine persistence depend on the competitive environment. If our study had been observational and trait-based, we would have erroneously concluded that the environment filters species with low biomass, shallow roots and small seeds. Changing environmental conditions generated idiosyncratic effects on coexistence outcomes, increasing competitive exclusion of some species while promoting coexistence of others. Our results highlight the importance of considering environmental filtering in the light of, rather than in isolation from, competition, and challenge community assembly models and approaches to projecting future species distributions.

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