The spatial signature of introgression after a biological invasion with hybridization

Simulated Data and Custom Scripts

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. 

Acknowledgments 
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