Data and code from: Mechanisms of community assembly through the lens of phylogenetic diversity: A critical reappraisal
Data files
Oct 06, 2025 version files 110.02 GB
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coMet_ComSim_Outputs.zip
33.85 MB
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Equa50Stab50_Sig2.tar.gz
10.79 GB
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Equa50Stab50_Sig5.tar.gz
13.85 GB
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Equalizing100_Sig2_SF1.tar.gz
16.33 GB
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Equalizing100_Sig2_SF2.tar.gz
12.68 GB
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Equalizing100_Sig2.tar.gz
8.62 GB
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Equalizing100_Sig5.tar.gz
18.10 GB
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README.md
1.40 KB
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Stabilizing100_Sig5.tar.gz
11.61 GB
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Stochastic100_Sig5.tar.gz
18.02 GB
Abstract
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 perform to retrieve community assembly processes, but raise caution regarding their interpretation, which can be misleading due to spatial effects.
The coMet pipeline (standing for COMmunity METrics) 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 to be used on a -slurm- remote machine to allow the creation of multiple replicates. However, you can still launch these two script for one replicate at a time on your local machine.
- More details on the parameters and the pipeline usage directly in the "Foo.R" and "Bash_coMet_Pipeline.sh" scripts.
DATA: The data "coMet_ComSim_Outputs.zip" represent standard outputs for all the procedure.
This dataset was simulated.