Scripts for analyses and plotsContent: 'admixtureplot.R' to plot admixture analyses, 'maices_estimatingpopgenstats_wrapall.R' R code for estimating He, Ho, and Fst, 'maices_PCAs_plots.html' and 'maices_PCAs_plots.Rmd' show a Rmarkdown document used to plot the PCA, NJ trees and maps. 'runadmixture.sh' code used to run admixture. These scripts need the data and metada available at the DataandMetadata.zip section of this repositorybin.zipAdmixture outputContains the log, .Q, .P and se files of the admixture analyses. For command line used and code for plotting see the Scripts section of this repo.admixture.zipData and Meta'data/SNPs' contains SNP data provided in plink and gds format along with a README of how each file was produced. 'data/spatial' contains the shapefiles used for the maps. Please uncompress each one before use. 'meta/maizteocintle_SNP50k_meta_extended.txt' is a text file containing sampling locality, lat, long, and other metadata of each of the samples. Columns correspond to the data collected as part of the Global Maize Proyect and are further detailed at http://www.biodiversidad.gob.mx/genes/pdf/proyecto/Anexo13_Base %20de%20datos/Contenido%20y%20observaciones%20de%20la%20BdeD.pdfDataandMeta.zip

The present dataset comprises 36,931 SNPs genotyped in 46 maize landraces native to Mexico as well as the teosinte subspecies Zea maiz ssp. Parviglumis and ssp. Mexicana. These landraces were collected directly from farmers mostly between 2006 and 2010. We accompany these data with a short description of the variation within each landrace, as well as maps, principal component analyses and neighbor joining trees showing the distribution of the genetic diversity relative to landrace, geographical features and maize biogeography. High levels of genetic variation were detected for the maize landraces (HE = 0.234 to 0.318 (mean 0.311), while slightly lower levels were detected in Zea m. mexicana and Zea m. parviglumis (HE = 0.262 and 0.234, respectively). The distribution of genetic variation was better explained by environmental variables given by the interaction of altitude and latitude than by landrace identity. This dataset is a following up product of the Global Native Maize Project, an initiative to update the data on Mexican maize landraces and their wild relatives, and to generate information that is necessary for implementing the Mexican Biosafety Law.