cati: an R package using functional traits to detect and quantify multi-level community assembly processes

Ecography ◽  
2015 ◽  
Vol 39 (7) ◽  
pp. 699-708 ◽  
Author(s):  
Adrien Taudiere ◽  
Cyrille Violle
Keyword(s):  
Functional Traits ◽  
Community Assembly ◽  
R Package ◽  
Multi Level

scholarly journals Phylogenetic and Functional Traits Verify the Combined Effect of Deterministic and Stochastic Processes in the Community Assembly of Temperate Forests along an Elevational Gradient

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 591
Author(s):  
Wensong Zhou ◽  
Yuxin Zhang ◽  
Shuang Zhang ◽  
Basil N. Yakimov ◽  
Keming Ma
Keyword(s):  
Stochastic Processes ◽  
Functional Traits ◽  
Community Assembly ◽  
Woody Plants ◽  
Elevational Gradient ◽  
Combined Effect ◽  
Abiotic Environment ◽  
Spatial Factors ◽  
Assembly Mechanism ◽  
Deterministic Processes

Explaining community assembly mechanisms along elevational gradients dominated by deterministic processes or stochastic processes is a pressing challenge. Many studies suggest that phylogenetic and functional diversity are significant indicators of the process. In this study, we analyzed the structure and beta diversity of phylogenetic and functional traits along an elevational gradient and discussed the effects of environmental and spatial factors. We found that the phylogenetic and functional traits showed inconsistent changes, and their variations were closely related to the abiotic environment. The results suggested that the community assembly of woody plants was obviously affected by the combined effect of deterministic processes and the stochastic hypothesis (primarily by the latter). Phylogenetic and functional traits had a certain relationship but changed according to different rules. These results enhance our understanding of the assembly mechanism of forest communities by considering both phylogenetic and functional traits.

scholarly journals hilldiv: an R package for the integral analysis of diversity based on Hill numbers

2019 ◽  
Author(s):  
Antton Alberdi ◽  
M Thomas P Gilbert
Keyword(s):  
Phylogenetic Trees ◽  
R Package ◽  
Diversity Partitioning ◽  
Diet Reconstruction ◽  
Functional Correlation ◽  
Community Profiling ◽  
High Throughput Dna Sequencing ◽  
Multi Level ◽  
Diversity Profile ◽  
Hill Numbers

AbstractHill numbers provide a powerful framework for measuring, comparing and partitioning the diversity of biological systems as characterised using high throughput DNA sequencing approaches. In order to facilitate the implementation of Hill numbers into such analyses, whether focusing on diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses, we present a new R package. ‘Hilldiv’ provides a set of functions to assist analysis of diversity based on Hill numbers, using count tables (e.g. OTU, ASV) and associated phylogenetic trees as inputs. Multiple functionalities of the library are introduced, including diversity measurement, diversity profile plotting, diversity comparison between samples and groups, multi-level diversity partitioning and (dis)similarity measurement. All of these are grounded in abundance-based and incidence-based Hill numbers, and can accommodate phylogenetic or functional correlation among OTUs or ASVs. The package can be installed from CRAN or Github, and tutorials and example scripts can be found in the package’s page (https://github.com/anttonalberdi/hilldiv).

Community assembly and species traits

2019 ◽  
pp. 231-246
Author(s):  
Gary G. Mittelbach ◽  
Brian J. McGill
Keyword(s):  
Functional Traits ◽  
Community Assembly ◽  
Species Traits ◽  
Fundamental Question ◽  
Species Pool ◽  
Environmental Filters ◽  
Abiotic Environment ◽  
Local Site ◽  
Powerful Approach ◽  
Regional Species Pool

There is perhaps no more fundamental question in ecology than what determines the number and kinds of species found in a community and their relative abundances. This chapter lays out a powerful approach to answering this question, based on the concepts of a regional species pool and environmental filters. The species pool is the set of species that could potentially colonize a local site or community. Of these potential colonists, some species are limited in their ability to disperse to site, some are limited by their ability to survive the abiotic environment, and some are limited by their interactions with other species. These “filters” act individually or in concert, and the functional traits of species determine their success in passing through these filters to colonize a local site. There is growing empirical evidence that both abiotic and biotic processes select for specific functional traits. Focusing on the functional traits of species may lead to rules of community assembly that are general and help unify a variety of more specific theories.

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

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.

scholarly journals Maximum entropy models elucidate the contribution of metabolic traits to patterns of community assembly

2019 ◽  
Author(s):  
Jason Bertram ◽  
Erica A Newman ◽  
Roderick Dewar
Keyword(s):  
Community Structure ◽  
Maximum Entropy ◽  
Functional Traits ◽  
Community Assembly ◽  
Species Abundance ◽  
Metabolic Rates ◽  
Species Identity ◽  
Metabolic Traits ◽  
Abundance Patterns ◽  
Species Specific

Aim: Maximum entropy (MaxEnt) models promise a novel approach for understanding community assembly and species abundance patterns. One of these models, the "Maximum Entropy Theory of Ecology" (METE) reproduces many observed species abundance patterns, but is based on an aggregated representation of community structure that does not resolve species identity or explicitly represent species-specific functional traits. In this paper, METE is compared to "Very Entropic Growth" (VEG), a MaxEnt model with a less aggregated representation of community structure that represents species (more correctly, functional types) in terms of their per capita metabolic rates. We examine the contribution of metabolic traits to the patterns of community assembly predicted by VEG and, through aggregation, compare the results with METE predictions in order to gain insight into the biological factors underlying observed patterns of community assembly. Innovation: We formally compare two MaxEnt-based community models, METE and VEG, that differ as to whether or not they represent species-specific functional traits. We empirically test and compare the metabolic predictions of both models, thereby elucidating the role of metabolic traits in patterns of community assembly. Main Conclusions: Our analysis reveals that a key determinant of community metabolic patterns is the "density of species" distribution, defined as the intrinsic number of species with metabolic rates in a given range that are available to a community prior to filtering by environmental constraints. Our analysis suggests that appropriate choice of of the density of species in VEG may lead to more realistic predictions than METE, for which this distribution is not defined, and thus opens up new ways to understanding the link between functional traits and patterns of community assembly.

scholarly journals Revealing the functional traits linked to hidden environmental factors in community assembly

2021 ◽  
Author(s):  
Valério D. Pillar ◽  
Francesco Maria Sabatini ◽  
Ute Jandt ◽  
Sergio Camiz ◽  
Helge Bruelheide
Keyword(s):  
Environmental Factors ◽  
Functional Traits ◽  
Community Assembly

scholarly journals Accurate annotation of protein coding sequences with IDTAXA

2021 ◽  
Vol 3 (3) ◽  
Author(s):  
Nicholas P Cooley ◽  
Erik S Wright
Keyword(s):  
Antibiotic Resistance ◽  
R Package ◽  
Protein Coding ◽  
Common Error ◽  
New Approach ◽  
Coding Sequences ◽  
Microbial Genomes ◽  
Prokaryotic Genomes ◽  
Multi Level ◽  
Novel Associations

Abstract The observed diversity of protein coding sequences continues to increase far more rapidly than knowledge of their functions, making classification algorithms essential for assigning a function to proteins using only their sequence. Most pipelines for annotating proteins rely on searches for homologous sequences in databases of previously annotated proteins using BLAST or HMMER. Here, we develop a new approach for classifying proteins into a taxonomy of functions and demonstrate its utility for genome annotation. Our algorithm, IDTAXA, was more accurate than BLAST or HMMER at assigning sequences to KEGG ortholog groups. Moreover, IDTAXA correctly avoided classifying sequences with novel functions to existing groups, which is a common error mode for classification approaches that rely on E-values as a proxy for confidence. We demonstrate IDTAXA’s utility for annotating eukaryotic and prokaryotic genomes by assigning functions to proteins within a multi-level ontology and applied IDTAXA to detect genome contamination in eukaryotic genomes. Finally, we re-annotated 8604 microbial genomes with known antibiotic resistance phenotypes to discover two novel associations between proteins and antibiotic resistance. IDTAXA is available as a web tool (http://DECIPHER.codes/Classification.html) or as part of the open source DECIPHER R package from Bioconductor.

Functional traits of individual trees reveal ecological constraints on community assembly in tropical rain forests

Oikos ◽  
2011 ◽  
Vol 120 (5) ◽  
pp. 720-727 ◽  
Author(s):  
C. E. Timothy Paine ◽  
Christopher Baraloto ◽  
Jérôme Chave ◽  
Bruno Hérault
Keyword(s):  
Functional Traits ◽  
Community Assembly ◽  
Tropical Rain Forests ◽  
Rain Forests ◽  
Ecological Constraints ◽  
Individual Trees
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