Stochastic processes dominate community assembly in cichlid communities in Lake Tanganyika

ABSTRACTThe African Great Lakes are characterized by an extraordinary diversity of endemic cichlid fish species. The cause of this diversity is still largely unknown. Most studies have tried to solve this question by focusing on macro-evolutionary processes, such as speciation. However, the ecological processes determining local cichlid diversity have so far been understudied, even though knowledge on these might be crucial for understanding larger scale biodiversity patterns.Using trait, environmental and abundance data of cichlid fishes along 36 transects, we have studied how differences in local environmental conditions influence cichlid community assembly in the littoral of Lake Tanganyika, Zambia. We investigated changes in average trait values and in trait-based community assembly processes along three key environmental gradients.Species diversity and local abundance decreased with increasing sand cover and diet-associated traits changed with depth. Analyses on within-community trait diversity patterns indicated that cichlid community assembly was mainly driven by stochastic processes, to a smaller extent by processes that limit the similarity among co-existing species and least by filtering processes that limit the range of species traits occurring in an environment. Despite, the low impact of habitat filtering processes, we find community dissimilarity to increase with increasing environmental difference.Our results suggest that local environmental conditions determine cichlid abundance, while the predominance of stochastic community assembly across all environments explains why the communities with the highest abundances contain most species.

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Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests

10.7287/peerj.preprints.27223v1 ◽

2018 ◽

Author(s):

Pengyu Zhao ◽

Jiabing Bao ◽

Xue Wang ◽

Yi Liu ◽

Cui Li ◽

...

Keyword(s):

Microbial Community ◽

Stochastic Processes ◽

Community Assembly ◽

Soil Microbial Community ◽

Analytical Methods ◽

Community Dynamics ◽

Coniferous Forests ◽

Ecological Processes ◽

Soil Microbial ◽

Microbial Community Assembly

The mechanisms underlying community dynamics, which govern the complicated biogeographical patterns of microbes, have long been a research hotspot in community ecology. However, the mixing of multiple ecological processes and the one-sidedness of analytical methods make it difficult to draw inferences about the community assembly mechanisms. In this study, we investigated the driving forces of the soil microbial community in subalpine coniferous forests of the Loess Plateau in Shanxi, China, by integrating multiple analytical methods. The results of the null model demonstrated that deterministic processes (especially interspecific relationships) were the main driving force of the soil microbial community assembly in this study area, relative to stochastic processes. Based on the results of the net relatedness index (NRI) and nearest taxon index (NTI), we inferred that historical and evolutionary factors, such as climate change and local diversification, may have similar effects on microbial community structure based on the climatic niche conservatism. Based on the results of a functional traits analysis, we found that the effects of ongoing ecological processes on the microbial community assembly varied among sites. Therefore, the functional structures seemed to be more related to ongoing ecological processes, whereas the phylogenetic structures seemed to be more related to historical and evolutionary factors, as well as the tradeoff between deterministic and stochastic processes. The functional and phylogenetic structures were mainly shaped by different ecological processes. By integrating multiple ecological processes, our results provide more details of the mechanisms driving the community assembly

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Community Assembly and Co-occurrence Patterns Underlying the Core and Satellite Bacterial Sub-communities in the Tibetan Lakes

Frontiers in Microbiology ◽

10.3389/fmicb.2021.695465 ◽

2021 ◽

Vol 12 ◽

Author(s):

Qi Yan ◽

Jianming Deng ◽

Feng Wang ◽

Yongqin Liu ◽

Keshao Liu

Keyword(s):

Community Assembly ◽

454 Sequencing ◽

Species Traits ◽

Rrna Gene ◽

Natural Environments ◽

Ecological Processes ◽

The Core ◽

Core Species ◽

Occurrence Patterns ◽

Satellite Species

Microbial communities normally comprise a few core species and large numbers of satellite species. These two sub-communities have different ecological and functional roles in natural environments, but knowledge on the assembly processes and co-occurrence patterns of the core and satellite species in Tibetan lakes is still sparse. Here, we investigated the ecological processes and co-occurrence relationships of the core and satellite bacterial sub-communities in the Tibetan lakes via 454 sequencing of 16S rRNA gene. Our studies indicated that the core and satellite bacterial sub-communities have similar dominant phyla (Proteobacteria, Bacteroidetes, and Actinobacteria). But the core sub-communities were less diverse and exhibited a stronger distance-decay relationship than the satellite sub-communities. In addition, topological properties of nodes in the network demonstrated that the core sub-communities had more complex and stable co-occurrence associations and were primarily driven by stochastic processes (58.19%). By contrast, the satellite sub-communities were mainly governed by deterministic processes (62.17%). Overall, this study demonstrated the differences in the core and satellite sub-community assembly and network stability, suggesting the importance of considering species traits to understand the biogeographic distribution of bacterial communities in high-altitude lakes.

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Can functional traits explain phylogenetic signal in the composition of a plant community?

10.1101/032938 ◽

2015 ◽

Author(s):

Daijiang Li ◽

Anthoy R Ives ◽

Donald M Waller

Keyword(s):

Functional Traits ◽

Community Assembly ◽

Phylogenetic Signal ◽

Species Traits ◽

Functional Trait ◽

Phylogenetic Information ◽

Ecological Processes ◽

Forest Sites ◽

Species Abundances ◽

Understory Plant

Phylogeny-based and functional trait-based analyses are two principle ways to study community assembly and underlying ecological processes. In principle, knowing all information about species traits would make phylogenetic information redundant, at least that component of phylogenetic signal in the distribution of species among communities that is caused by phylogenetically related species sharing similar traits. In reality, phylogenies may contain more information than a set of singular, discretely measured traits because we cannot measure all species traits and may misjudge which are most important. The extent to which functional trait information makes phylogenetic information redundant, however, has not been explicitly studied with empirical data in community ecology. Here, we use phylogenetic linear mixed models to analyze community assembly of 55 understory plant species in 30 forest sites in central Wisconsin. These communities show strong phylogenetic attraction, yet variation among sites in 20 environmental variables could not account for this pattern. Most of the 15 functional traits we measured had strong phylogenetic signal, but only three varied strongly among sites in ways that affected species' abundances. These three traits explained only 19% of variation in phylogenetic patterns of species co-occurrence. Thus, phylogenies appear to provide considerably more information about community assembly than the functional traits measured in this study, demonstrating the value of phylogeny in studying of community assembly processes even with abundant functional traits.

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

Ecology and Evolution ◽

10.1002/ece3.2689 ◽

2017 ◽

Vol 7 (4) ◽

pp. 1057-1067 ◽

Cited By ~ 6

Author(s):

Thijs Janzen ◽

Adriana Alzate ◽

Moritz Muschick ◽

Martine E. Maan ◽

Fons van der Plas ◽

...

Keyword(s):

Community Assembly ◽

Lake Tanganyika ◽

Cichlid Fish ◽

Neutral Processes

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A common framework for identifying linkage rules across different types of interactions

10.1101/024315 ◽

2015 ◽

Cited By ~ 2

Author(s):

Ignasi Bartomeus ◽

Dominique Gravel ◽

Jason Tylianakis ◽

Marcelo Aizen ◽

Ian Dickie ◽

...

Keyword(s):

Ecosystem Functioning ◽

Species Interactions ◽

Community Dynamics ◽

Developmental Stages ◽

Environmental Gradients ◽

Interspecific Interactions ◽

General Structure ◽

Species Traits ◽

Ecological Processes ◽

Wrong Reason

Species interactions, ranging from antagonisms to mutualisms, form the architecture of biodiversity and determine ecosystem functioning. Understanding the rules responsible for who interacts with whom, as well as the functional consequences of these interspecific interactions, is central to predicting community dynamics and stability. Species traitssensu latomay affect different ecological processes determining species interactions through a two-step process. First, ecological and life-history traits govern species distributions and abundance, and hence determine species co-occurrence, which is a prerequisite for them to interact. Second, morphological traits between co-occurring potential interaction partners should match for the realization of an interaction. Moreover, inferring functioning from a network of interactions may require the incorporation of interaction efficiency. This efficiency may be also trait-mediated, and can depend on the extent of matching, or on morphological, physiological or behavioural traits. It has been shown that both neutral and trait-based models can predict the general structure of networks, but they rarely accurately predict individual interactions, suggesting that these models may be predicting the right structure for the wrong reason. We propose to move away from testing null models with a framework that explicitly models the probability of interaction among individuals given their traits. The proposed models integrate both neutral and trait-matching constraints while using only information about known interactions, thereby overcoming problems originating from under-sampling of rare interactions (i.e. missing links). They can easily accommodate qualitative or quantitative data, and can incorporate trait variation within species, such as values that vary along developmental stages or environmental gradients. We use three case studies to show that they can detect strong trait matching (e.g. predator-prey system), relaxed trait matching (e.g. herbivore-plant system) and barrier trait matching (e.g. plant-pollinator systems). Only by elucidating which species traits are important in each process, i.e. in determining interaction establishment, frequency, and efficiency, can we advance in explaining how species interact and the consequences for ecosystem functioning.

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Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests

10.7287/peerj.preprints.27223 ◽

2018 ◽

Author(s):

Pengyu Zhao ◽

Jiabing Bao ◽

Xue Wang ◽

Yi Liu ◽

Cui Li ◽

...

Keyword(s):

Microbial Community ◽

Stochastic Processes ◽

Community Assembly ◽

Soil Microbial Community ◽

Analytical Methods ◽

Community Dynamics ◽

Coniferous Forests ◽

Ecological Processes ◽

Soil Microbial ◽

Microbial Community Assembly

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Environment affects specialisation of plants and pollinators

10.1101/866772 ◽

2019 ◽

Author(s):

E. Fernando Cagua ◽

Audrey Lustig ◽

Jason M. Tylianakis ◽

Daniel B. Stouffer

Keyword(s):

Environmental Stress ◽

Community Composition ◽

Environmental Conditions ◽

Species Interactions ◽

Evolutionary History ◽

Environmental Gradients ◽

Species Traits ◽

Environmental Variable ◽

Species Level ◽

Plant Pollinator

AbstractWhat determines whether or not a species is a generalist or a specialist? Evidence that the environment can influence species interactions is rapidly accumulating. However, a systematic link between environment and the number of partners a species interacts with has been elusive so far. Presumably, because environmental gradients appear to have contrasting effects on species depending on the environmental variable. Here, we test for a relationship between the stresses imposed by the environment, instead of environmental gradients directly, and species specialisation using a global dataset of plant-pollinator interactions. We found that the environment can play a significant effect on specialisation, even when accounting for community composition, likely by interacting with species’ traits and evolutionary history. Species that have a large number of interactions are more likely to focus on a smaller number of, presumably higher-quality, interactions under stressful environmental conditions. Contrastingly, the specialists present in multiple locations are more likely to broaden their niche, presumably engaging in opportunistic interactions to cope with increased environmental stress. Indeed, many apparent specialists effectively behave as facultative generalists. Overall, many of the species we analysed are not inherently generalist or specialist. Instead, species’ level of specialisation should be considered on a relative scale depending on where they are found and the environmental conditions at that location.

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Beta Diversity of Antarctic and Sub-Antarctic Benthic Communities Reveals a Major Role of Stochastic Assembly Processes

Frontiers in Marine Science ◽

10.3389/fmars.2021.780268 ◽

2021 ◽

Vol 8 ◽

Author(s):

Nelson Valdivia ◽

José Garcés-Vargas ◽

Ignacio Garrido ◽

Iván Gómez ◽

Pirjo Huovinen ◽

...

Keyword(s):

Stochastic Processes ◽

Spatial Variation ◽

Community Assembly ◽

Beta Diversity ◽

Seawater Temperature ◽

Environmental Filtering ◽

Ecological Processes ◽

Mean Values ◽

Sampling Protocols ◽

Strait Of Magellan

Community assembly is the result of both, deterministic and stochastic processes. The former encompasses niche-based local-scale mechanisms such as environmental filtering and biotic interactions; the latter includes ecological drift, probabilistic colonisation, and random extinctions. Using standardised sampling protocols, we show that the spatial variation in species composition (beta diversity) of shallow subtidal macrobenthic communities of sub-Antarctic (Strait of Magellan and Yendegaia Fjord [Beagle Channel]) and Antarctic (Fildes Bay [King George Island, West Antarctic Peninsula]) localities reflects a high contribution of stochastic processes to community assembly. Null model analyses indicated that random sampling from species pools of different sizes drove the observed among-locality differences in incidence- and abundance-based beta diversity. We analysed a normalised stochasticity ratio (NST), which delimits between more deterministic (<50%) and more stochastic (>50%) assembly. NST was notably larger than 50%, with mean values of 69.5% (95% CI = 69.2–69.8%), 62.5% (62.1–62.9%), and 72.8% (72.5–73.2%) in Strait of Magellan, Yendegaia Fjord, and Fildes Bay, respectively. Accordingly, environmental factors, such as depth, seawater temperature, salinity, and underwater light penetration, accounted for a small fraction of the spatial variation in community composition across the three localities. In this region, therefore, stochastic processes could have stronger effects on community assembly than deterministic niche-based factors. As anthropogenic biotic homogenisation continues apace, our study can give useful insights into the major ecological processes in Southern Ocean’ coastal marine communities.

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A novel framework for modeling the evolution of cross-scale ecological assembly

10.1101/2020.03.17.994319 ◽

2020 ◽

Author(s):

Amanda S. Gallinat ◽

William D. Pearse

Keyword(s):

Community Assembly ◽

Evolutionary Dynamics ◽

Environmental Gradients ◽

Spatial Scales ◽

Regional Scale ◽

Species Traits ◽

Temporal And Spatial ◽

Environmental Responses ◽

Conceptual Overview ◽

Species Assembly

AbstractCommunity assembly can be driven by species’ responses to environmental gradients, and interactions within (e.g., competition) and across (e.g., herbivory) clades. These ecological dynamics are mediated by species’ traits, which are in turn shaped by past evolution. As such, identifying the drivers of species assembly is made difficult by the differing temporal and spatial scales of ecological and evolutionary dynamics. Two recent advances have emerged to address the cross-scale challenge of modeling species assembly: phylogenetic generalized linear mixed modeling (PGLMM) and earth observation networks (EONs). PGLMM integrates through time by modeling the evolution of trait-based community assembly, while EONs synthesize across space by placing standardized site-level species occurrence data within their regional context. Here we describe a framework for combining these tools to investigate the drivers of species assembly, and so address three outstanding questions: (1) Does evolution adapt or constrain regional-scale environmental responses? (2) Do evolved responses to past competition minimize or enhance present-day competition? (3) Are species’ cross-clade associations evolutionarily constrained? We provide a conceptual overview of how PGLMM and EONs can be synthesized to answer these questions, and provide exemplar Bayesian PGLMM code. Finally, we describe the capacity of these tools to aid in conservation and natural resource management, including predicting future colonization by rare and invasive species, vulnerable mutualisms, and pest and pathogen outbreaks.

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High dispersal levels and lake warming are emergent drivers of cyanobacterial community assembly over the Anthropocene in peri-Alpine lakes

10.1101/419762 ◽

2018 ◽

Cited By ~ 1

Author(s):

Marie-Eve Monchamp ◽

Piet Spaak ◽

Francesco Pomati

Keyword(s):

Stochastic Processes ◽

Climate Warming ◽

Community Assembly ◽

Sequence Data ◽

Environmental Gradients ◽

Spatial Scales ◽

Alpine Lakes ◽

Cyanobacterial Community ◽

Water Column Stability ◽

High Dispersal

Disentangling the relative importance of deterministic and stochastic processes in shaping natural communities is central to ecology. Studies on community assembly over broad temporal and spatial scales in aquatic microorganisms are scarce. Here, we used 16S rDNA sequence data from lake sediments to test for community assembly patterns in cyanobacterial phylogenies across ten European peri-Alpine lakes and over a century of eutrophication and climate warming. We studied phylogenetic similarity in cyanobacterial assemblages over spatial and temporal distance, and environmental gradients, comparing detected patterns with theoretical expectations from deterministic and stochastic processes. We found limited evidence for deviation of lake communities from a random assembly model and no significant effects of geographic distance on phylogenetic similarity, suggesting no dispersal limitation and high levels of stochastic assembly. We did not detect a significant effect of phosphorus and nitrogen levels on deviation of community phylogenies from random. We found however a significant decay of phylogenetic similarity for non-random communities over a gradient of air temperature and water column stability. We show how phylogenetic data from sedimentary archives can improve our understanding of microbial community assembly processes, and support previous evidence that climate warming has been the strongest environmental driver of cyanobacterial community assembly over the Anthropocene.

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