This repository contains the data and describe the scripts used to run the analysis included in the paper "Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties." https://doi.org/10.1073/pnas.1817664116 ### Prerequisites VCFtools 0.1.15 PLINK v1.9 R version 3.6.1 Admixture 1.3 FastTree angsd version: 0.921-9-ga30d0b4 custom scripts available at the github repository: - https://github.com/owensgl/reformat - https://github.com/owensgl/pop_gen R packages: ggplot2 SNPRelate permute lattice vegan RColorBrewer ### Directories The repository is divided in the figures included in the paper "Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties" 1) SNP_Calling This directory contains the scripts to perform the sequence alignment and varian calling 2) data/ bam: This directory contains the bam files (.bam, .bai) to run the gene flow analysis and to compute Tajima's D and the genetic diversity estimators: Theta and Pi. vcf/Zea_mays.AGPv4.2x_0.8_0.01.NewID.Rojas2019.recode.vcf: The vcf used to compute Fst between samples collected at different periods. plink/ PCA_Rojas_Romay_CMLs_LRs_MVs: The plink binary files used to perform the PCAs with the Romay et al., 2013 data set.It includes, the landraces and modern varieties genotypes in B73_AGPv2. 3) ancestry_analysis Contains the command description used to run admixture. 4) gene_flow Contains the command description used to run gene flow models, and examples of metadata files. All the meta data files can be generated with the information available at meta/metadata_385_taxa_Rojas_etal_2019.txt 5) fst_genome-wide Contains the executable files to compute Fst per site and window, and one markdown file with examples to run the analysis 6) PCA Contains the html files thath show how to perform the PCA analysis with the files saved at data directory 7) nucleotide_diversity Contains a text file that explains the steps to compute pi, theta and Tajima's D with the bam files provided. 8) meta Contains the metadata information for the 385 taxa included in the paper i.e.: Accession ID, coordinates, Population Sorting, etc. ### Contact Idalia Rojas icrojasb@gmail.com icrojasb@iecologia.unam.mx