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)...,本仓库包含论文《系统发育对模型群落共存的影响》（Effects of phylogeny on coexistence in model communities）中各项分析所需的代码与数据。在该项研究中，我们将系统发育树（phylogenetic tree）上的简单性状进化模型与洛特卡-沃尔泰拉（Lotka-Volterra）群落动力学模型相结合，得以推导共存物种种群的群落属性，该属性可表示为性状数量、树拓扑结构（tree topology）以及物种种库（species pool）规模的函数。本研究分析揭示了系统发育如何通过性状调控物种种群的共存模式。综上，本研究结果为以系统发育概括的进化历史如何反映在生态群落的规模与结构中这一问题，提供了亟需的基准预期。 本仓库提供了用于计算解析预期、模拟群落动力学的代码，以及用于验证模型预测的数据集（生物多样性II实验，Tilman等人，《科学》2001年）。原始数据取自生物多样性II实验（Tilman等人，《科学》2001年）。该生物多样性数据集已由Lemos-Costa等人进行筛选（https://onlinelibrary.wiley.com/doi/10.1111/ele.14490, 2024）。Lemos-Costa等人仅纳入满足以下三项条件的数据集：a) 仅将在多个样地中出现的物种纳入物种种库；b) 未识别生物量或非目标物种不得在样地中占主导地位；c) 样地组合需具备足够的重复次数或多样性，以确保模型拟合结果可靠。在原始数据集中，除了最初设定的18个目标物种种库外，样地中还存在大量其他物种，以及相当数量的枯落物或未识别生物量。因此，筛选后的物种种库纳入了更多物种，同时排除了非种库物种总生物量占比超过总生物量10%的样地。通过上述步骤，Lemos-Costa等人共提取得到9组数据集（针对不同的酵母……）。 # 数据与代码来源：《系统发育对模型群落共存的影响》 DOI：10.5061/dryad.cvdncjtck ## 数据与文件结构说明 本仓库包含论文《系统发育对模型群落共存的影响》中各项分析所需的代码与数据。 ### 文件与变量说明 #### 文件：Data-Code.zip **描述：** 该压缩文件包含以下若干文件与文件夹。 **Data** 文件夹包含各类数据集：其中子文件夹BiodivII存放生物多样性II实验数据，文件Senna.MCC.nex为Nexus格式的Senna系统发育树。 **Data/BiodivII** 文件夹包含以下内容： * 原始数据存放在子文件夹**Data/BiodivII/RawData**中，该文件夹按实验开展的年份记录了对应的样地、样地内出现的物种以及实验结束时各物种的生物量。详细信息请参阅原始文献（Tilman et al., Science 2001）……