Data and code from: Mechanisms of community assembly through the lens of phylogenetic diversity: A critical reappraisal

Darwin was one of the first to hypothesize a connection between niche differentiation and competition and species relatedness, offering an appealing framework to disentangle the processes involved in community assembly based on their phylogenetic structure. Community assembly is, however, the result of several processes, including potentially confounding factors associated with dispersal limitations and spatial effects, casting doubt about the application of phylogenetic diversity metrics to infer community assembly processes. We implemented a spatially-explicit model involving limited dispersal, drift, trait-based selection, and competition to simulate community composition under competing assembly processes in a landscape with contrasted habitat connectivity. Our results formalize the idea that habitat selection and limiting similarity leave a significant signature in the phylogenetic structure of communities. We identify the phylogenetic diversity metrics that best per..., This dataset was simulated. , , The coMet pipeline (standing for **COM**munity **MET**rics) is a pipeline developed to create communities following assembly rules and compute phylogenetic diversity metrics based on these communities.
It is written mainly in R (the community simulator is written in C) and operated by command line. It is, by nature, designed to be launched on remote machines in slurm environment to create numerous replicates.
However, it is possible to operate it completely on local machines.

All \"tar.gz\" files are the simulated datasets of all scenarios used in the manuscript.

TO USE IT:

The first step is the modification of the default configuration file \"Foo.R\" following the user's needs. This configuration file will be used to pilot the pipeline.

The second step is to launch the pipeline using this command line: ./Bash_coMet_Pipeline.sh Foo.R \"Foo\"
The first argument is the name of the configuration file, and the second argument is the name of the Scenario.

NOTES:

* Script 1 and 6 are designed...,