The spatial signature of introgression after a biological invasion with hybridization

<strong>Simulated Data and Custom Scripts</strong> This repository contains data for performing simulations with SPLATCHE3 and the custom R scripts used in the following manuscript: Quilodrán CS, Tsoupas A and M Currat. 2020. The spatial signature of introgression after a biological invasion with hybridization. Frontiers in Ecology and Evolution. There are three main folders (.zip files): Settings: the setting files of SPLATCHE3 used in all explored scenarios. The example folder for each scenario (01_newset) contains the setting file and setting folder needed to run SPLATCHE3. This example folder contains a single simulation of the interbreeding rate (MigrRate_P1_to_P2 and MigrRate_P2_to_P1) that generates an output of 10,000 simulated loci. The folder also contains a public version of SPLATCHE3 for Linux. The software version for other platforms (Mac OS X and Windows) can be obtained from “http://www.splatche.com/splatche3". Results: all results obtained in the different scenarios. The three simulations in a square world are presented for the invasive (NC files) and local organisms (NCbis). The neanderthal scenario presents the simulated proportion of introgression in modern humans sampled in France and China. Rcustom: custom R functions and files used for plotting the results. There are also four R scripts for plotting all main figures in the manuscript. <strong>Acknowledgments </strong><br> This study was financed by grants from the Swiss National Science Foundation n° 31003A_182577 to MC and P400PB_183930 to CSQ. All computations were performed using the High-Performance Computing (HPC) cluster at baobab.unige.ch<strong>模拟数据与定制脚本</strong> 本仓库收录用于配合SPLATCHE3开展模拟实验的数据，以及发表于以下论文的定制R脚本：Quilodrán CS、Tsoupas A与M Currat，2020年，《生物入侵伴杂交后的渐渗空间特征》，刊载于《生态学与进化前沿》（Frontiers in Ecology and Evolution）。本仓库包含三个主要的压缩文件夹（.zip格式）： 1. **配置文件夹（Settings）**：涵盖所有探索场景中使用的SPLATCHE3配置文件。每个场景的示例文件夹（如01_newset）包含运行SPLATCHE3所需的配置文件与配置目录。该示例文件夹针对一次杂交速率（MigrRate_P1_to_P2与MigrRate_P2_to_P1）开展单次模拟，可生成包含10000个模拟位点的输出结果。文件夹内还提供了适用于Linux系统的SPLATCHE3公开版本，其他平台（Mac OS X与Windows）的软件版本可从「http://www.splatche.com/splatche3」获取。 2. **结果文件夹（Results）**：收录所有不同模拟场景下的计算结果。其中展示了方形世界场景下的三组模拟结果，分别对应入侵物种（NC文件）与本地物种（NCbis文件）。尼安德特人渐渗场景则呈现了在法国与中国采样的现代人类群体中，模拟得到的渐渗比例。 3. **定制R脚本文件夹（Rcustom）**：包含用于结果可视化的定制R函数与相关文件，同时附带四份可复现论文中所有核心图表的R脚本。 <strong>致谢</strong><br>本研究由瑞士国家科学基金会资助，资助项目编号分别为MC的31003A_182577与CSQ的P400PB_183930。所有计算任务均通过baobab.unige.ch的高性能计算（High-Performance Computing, HPC）集群完成。