Data and code from: Effects of phylogeny on coexistence in model communities

This repository contains code and data needed for the analyses presented in the paper 'Effects of phylogeny on coexistence in model communities'. In that contribution, by coupling a simple model of trait evolution on a phylogenetic tree with Lotka-Volterra community dynamics, allows us to derive properties of a community of coexisting species as a function of the number of traits, tree topology and the size of the species pool. Our analysis highlights how phylogenies, through traits, affect the coexistence of a set of species. Together, these results provide much-needed baseline expectations for the ways in which evolutionary history, summarized by phylogeny, is reflected in the size and structure of ecological communities. Here we provide de code needed to compute analytic expectations, to simulate community dynamics, as well as the dataset (Biodiversity II experiments, Tilman et al., Science 2001) used to test model predictions., Raw data was taken from Biodiversity II experiments (Tilman et al., Science 2001). That biodversity dataset was filtered by Lemos-Costa et al. (https://onlinelibrary.wiley.com/doi/10.1111/ele.14490, 2024). Only datasets satisfying three conditions were taken into account by Lemos-Costa et al.: a) only species that appear in multiple plots are considered to be part of the pool; b) unidentified biomass or non-target species do not dominate the plots; c) there is sufficient replication or diversity of assemblages to confidently fit the model. In the raw dataset, aside from the original target pool of eighteen species, many other species are found in the plots, along with a substantial amount of litter or unidentified biomass. Therefore, a larger number of species was included in the “species pool” , and also plots in which the total biomass for species not in the pool surpassed 10% of the total biomass were excluded. In this way, Lemos-Costa et al. extracted nine data sets (for distinct ye..., , # Data and code from: Effects of phylogeny on coexistence in model communities

[https://doi.org/10.5061/dryad.cvdncjtck](https://doi.org/10.5061/dryad.cvdncjtck)

## Description of the data and file structure

This repository contains code and data needed for the analyses presented in the paper 'Effects of phylogeny on coexistence in model communities'.

### Files and variables

#### File: Data-Code.zip

**Description:** The compressed file contains several files and folders described below.

The folder **Data** contains the datasets: a sub-folder BiodivII contains Biodiversity II data, and the file Senna.MCC.nex is the Senna tree in nexus format.

The folder **Data/BiodivII** contains:

* Raw data in the sub-folder **Data/BiodivII/RawData**, listing (for each year the experiment was conducted) the associated plots, together with the species present in them as well as their biomass at the end of the experiment. We refer the reader to the original reference (Tilman et al., Science 2001)...,