scholarly journals Individual-based models of community assembly: Neighbourhood competition drives phylogenetic community structure

2018 ◽  
Vol 107 (2) ◽  
pp. 735-746 ◽  
Author(s):  
Shinichi Tatsumi ◽  
Marc W. Cadotte ◽  
Akira S. Mori
Keyword(s):  
Community Structure ◽  
Community Assembly ◽  
Phylogenetic Community Structure ◽  
Individual Based Models

scholarly journals Deep-Sea Nematodes of the Mozambique Channel: Evidence of Random Community Assembly Dynamics in Seep Sediments

2021 ◽  
Vol 8 ◽  
Author(s):  
Lara Macheriotou ◽  
Annelien Rigaux ◽  
Karine Olu ◽  
Daniela Zeppilli ◽  
Sofie Derycke ◽  
...  
Keyword(s):  
Community Structure ◽  
Community Assembly ◽  
Deep Sea ◽  
Cold Seeps ◽  
Reference Area ◽  
Successional Stage ◽  
Stochastic Sampling ◽  
Phylogenetic Community Structure ◽  
Mozambique Channel ◽  
Occurrence Patterns

Cold seeps occur globally in areas where gases escape from the seafloor, occasionally resulting in the formation of topographic depressions (pockmarks), characterised by unique physicochemical conditions such as anoxic and sulphuric sediments. Free-living marine nematodes tend to dominate the meiofaunal component in such environments, often occurring at extremely high densities and low richness; the mechanisms defining community assembly in areas of fluid seepage, however, have received little attention. Here we focus on a low-activity pockmark at 789 m in the Mozambique Channel (MC). We assessed the diversity, co-occurrence patterns and phylogenetic community structure of nematodes at this bathyal site to that of a nearby reference area as well as abyssal sediments using metabarcoding. In addition, we compared our molecularly-derived diversity estimates to replicate samples identified morphologically. Overall, nematode Amplicon Sequence Variants (ASVs) and generic richness were similar between Pockmark and Abyssal sediments, but lower compared to the Reference area. Although more than half the genera were shared, over 80% of ASVs were unique within each area and even within each replicate core. Even though both methodologies differentiated the Pockmark from the Reference and Abyssal sites, there was little overlap between the molecularly and morphologically identified taxa, highlighting the deficit of reference sequences for deep-sea nematodes in public databases. Phylogenetic community structure at higher taxonomic levels was clustered and did not differ between the three areas yet analysis within three shared and dominant genera (Acantholaimus, Desmoscolex, Halalaimus), revealed randomness with respect to phylogeny as well as co-occurrence which was exclusive to the Pockmark area. These patterns point to the influence of neutral dynamics at this locality resulting from the stochastic sampling of early colonizing taxa, the successional stage at sampling and/or the functional redundancy within the investigated genera.

scholarly journals Phylogenetic turnover during subtropical forest succession across environmental and phylogenetic scales

2017 ◽  
Author(s):  
Oliver Purschke ◽  
Stefan G. Michalski ◽  
Helge Bruelheide ◽  
Walter Durka
Keyword(s):  
Community Structure ◽  
Community Assembly ◽  
Deterministic Model ◽  
Species Turnover ◽  
Subtropical Forest ◽  
List Type ◽  
Spatial And Temporal Patterns ◽  
Species Sorting ◽  
Phylogenetic Community Structure ◽  
Successional Stages

SummaryAlthough spatial and temporal patterns of phylogenetic community structure during succession are inherently interlinked and assembly processes vary with environmental and phylogenetic scale, successional studies of community assembly have yet to integrate spatial and temporal components of community structure, while accounting for scaling issues. To gain insight into the processes that generate biodiversity after disturbance, we combine analyses of spatial and temporal phylogenetic turnover across phylogenetic scales, accounting for covariation with environmental differences.We compared phylogenetic turnover, at the species-and individual-level, within and between five successional stages, representing woody plant communities in a subtropical forest chronosequence. We decomposed turnover at different phylogenetic depths and assessed its covariation with between-plot abiotic differences.Phylogenetic turnover between stages was low relative to species turnover and was not explained by abiotic differences. However, within the late successional stages, there was high presence/absence-based turnover (clustering) that occurred deep in the phylogeny and covaried with environmental differentiation.Our results support a deterministic model of community assembly where (i) phylogenetic composition is constrained through successional time, but (ii) towards late succession, species sorting into preferred habitats according to niche traits that are conserved deep in phylogeny, becomes increasingly important.

Relationships between climate and phylogenetic community structure of fossil pollen assemblages are not constant during the last deglaciation

2020 ◽  
Author(s):  
Kavya Pradhan ◽  
Diego Nieto-Lugilde ◽  
Matthew C. Fitzpatrick
Keyword(s):  
Community Structure ◽  
Community Assembly ◽  
Environmental Drivers ◽  
Fossil Pollen ◽  
Climate Variables ◽  
Last Deglaciation ◽  
Phylogenetic Community Structure ◽  
Significant Relationships ◽  
Long Time ◽  
The Last Deglaciation

AbstractDisentangling the influence of environmental drivers on community assembly is important to understand how multiple processes influence biodiversity patterns and can inform understanding of ecological responses to climate change. Phylogenetic Community Structure (PCS) is increasingly used in community assembly studies to incorporate evolutionary perspectives and as a proxy for trait (dis)similarity within communities. Studies often assume a stationary relationship between PCS and climate, though few if any studies have tested this assumption over long time periods with concurrent community data. We estimated Nearest Taxon Index (NTI) and Net Relatedness index (NRI), two PCS metrics, of fossil pollen assemblages of angiosperms in eastern North America data over the last 21 ka BP at 1ka intervals. We analyzed spatiotemporal relationships between PCS and seven climate variables, evaluated the potential impact of deglaciation on PCS, and tested for the stability of climate-PCS relationships. The broad scale patterns of PCS, with overdispersion increasing towards the southern and eastern parts of the study area, remained largely stable across time. Most importantly, we found that significant relationships between climate variables and PCS (slope) were unstable as climate changed during the last deglaciation and new ice-free regions were colonized. We also found weak, but significant, relationships between both PCS metrics (i.e., NTI and NRI) and climate and time-since-deglaciation, which were stable even though the baselines (intercepts) changed through time. Overall, our results suggest that (1) PCS of fossil Angiosperm assemblages during the last 21ka BP have had predictable spatial patterns, but (2) the instability in the relationships between PCS and climate brings into question their usefulness in predictive modeling of community assembly.

scholarly journals Relationships between climate and phylogenetic community structure of fossil pollen assemblages are not constant during the last deglaciation

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0240957
Author(s):  
Kavya Pradhan ◽  
Diego Nieto-Lugilde ◽  
Matthew C. Fitzpatrick
Keyword(s):  
Community Structure ◽  
Community Assembly ◽  
Environmental Drivers ◽  
Fossil Pollen ◽  
Climate Variables ◽  
Last Deglaciation ◽  
Phylogenetic Community Structure ◽  
Significant Relationships ◽  
Long Time ◽  
The Last Deglaciation

Disentangling the influence of environmental drivers on community assembly is important to understand how multiple processes influence biodiversity patterns and can inform understanding of ecological responses to climate change. Phylogenetic Community Structure (PCS) is increasingly used in community assembly studies to incorporate evolutionary perspectives and as a proxy for trait (dis)similarity within communities. Studies often assume a stationary relationship between PCS and climate, though few studies have tested this assumption over long time periods with concurrent community data. We estimated two PCS metrics—Nearest Taxon Index (NTI) and Net Relatedness index (NRI)—of fossil pollen assemblages of Angiosperms in eastern North America over the last 21 ka BP at 1 ka intervals. We analyzed spatiotemporal relationships between PCS and seven climate variables, evaluated the potential impact of deglaciation on PCS, and tested for the stability of climate-PCS relationships through time. The broad scale geographic patterns of PCS remained largely stable across time, with overdispersion tending to be most prominent in the central and southern portion of the study area and clustering dominating at the longitudinal extremes. Most importantly, we found that significant relationships between climate variables and PCS (slope) were not constant as climate changed during the last deglaciation and new ice-free regions were colonized. We also found weak, but significant relationships between both PCS metrics (i.e., NTI and NRI) and climate and time-since-deglaciation that also varied through time. Overall, our results suggest that (1) PCS of fossil Angiosperm assemblages during the last 21ka BP have had largely constant spatial patterns, but (2) temporal variability in the relationships between PCS and climate brings into question their usefulness in predictive modeling of community assembly.

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 The capacity of wastewater treatment plants drives bacterial community structure and its assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Young Kyung Kim ◽  
Keunje Yoo ◽  
Min Sung Kim ◽  
Il Han ◽  
Minjoo Lee ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
High Capacity ◽  
Operating Conditions ◽  
Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

scholarly journals Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Jizhong Zhou ◽  
Wenzong Liu ◽  
Ye Deng ◽  
Yi-Huei Jiang ◽  
Kai Xue ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Community Assembly ◽  
Ecosystem Functioning ◽  
Dominant Role ◽  
Microbial Biodiversity ◽  
Stochastic Assembly

ABSTRACTThe processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.IMPORTANCEMicroorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.

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