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

Ecography ◽  
2016 ◽  
Vol 40 (4) ◽  
pp. 461-477 ◽  
Author(s):  
Eliot T. Miller ◽  
Damien R. Farine ◽  
Christopher H. Trisos
Keyword(s):  
Community Structure ◽  
Null Models ◽  
Phylogenetic Community Structure ◽  
New Methods ◽  
Structure Metrics

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 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 discovery of population differences in network community structure: New methods and applications to brain functional networks in schizophrenia

NeuroImage ◽  
2012 ◽  
Vol 59 (4) ◽  
pp. 3889-3900 ◽  
Author(s):  
Aaron Alexander-Bloch ◽  
Renaud Lambiotte ◽  
Ben Roberts ◽  
Jay Giedd ◽  
Nitin Gogtay ◽  
...  
Keyword(s):  
Community Structure ◽  
Functional Networks ◽  
Population Differences ◽  
Network Community ◽  
New Methods ◽  
Brain Functional Networks

scholarly journals Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)

PLoS ONE ◽  
2017 ◽  
Vol 12 (10) ◽  
pp. e0185861 ◽  
Author(s):  
Jacqueline Heckenhauer ◽  
Kamariah Abu Salim ◽  
Mark W. Chase ◽  
Kyle G. Dexter ◽  
R. Toby Pennington ◽  
...  
Keyword(s):  
Community Structure ◽  
Dna Barcodes ◽  
Dipterocarp Forest ◽  
Plant Dna ◽  
Phylogenetic Community Structure ◽  
Brunei Darussalam ◽  
Mixed Dipterocarp Forest

scholarly journals Spatial analysis of phylogenetic community structure: New version of a classical method

2015 ◽  
Author(s):  
Carlo Ricotta ◽  
Eszter EA Ari ◽  
Giuliano Bonanomi ◽  
Francesco Giannino ◽  
Duncan Heathfield ◽  
...  
Keyword(s):  
Community Structure ◽  
Spatial Scales ◽  
Point Pattern ◽  
Maximum Deviation ◽  
Individual Plant ◽  
Phylogenetic Distance ◽  
Phylogenetic Structure ◽  
Phylogenetic Community Structure ◽  
Point Patterns ◽  
Wide Range

The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylogenetic patterns, the spatial aspects of phylogenetic community structure have received far less attention. Accordingly, the question for this study is: can point pattern analysis be used for revealing the phylogenetic structure of multi-species assemblages? We introduce a new individual-centered procedure for analyzing the scale-dependent phylogenetic structure of multi-species point patterns based on digitized field data. The method uses nested circular plots with increasing radii drawn around each individual plant and calculates the mean phylogenetic distance between the focal individual and all individuals located in the circular ring delimited by two successive radii. This scale-dependent value is then averaged over all individuals of the same species and the observed mean is compared to a null expectation with permutation procedures. The method detects particular radius values at which the point pattern of a single species exhibits maximum deviation from the expectation towards either phylogenetic aggregation or segregation. Its performance is illustrated using data from a grassland community in Hungary and simulated point patterns. The proposed method can be extended to virtually any distance function for species pairs, such as functional distances.

scholarly journals Disturbance macroecology: a comparative study of community structure metrics in a high‐severity disturbance regime

Ecosphere ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Erica A. Newman ◽  
Mark Q. Wilber ◽  
Karen E. Kopper ◽  
Max A. Moritz ◽  
Donald A. Falk ◽  
...  
Keyword(s):  
Community Structure ◽  
Comparative Study ◽  
Disturbance Regime ◽  
High Severity ◽  
Structure Metrics
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