Scripts for analyses and plots

Content: '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 repositor

Data 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.pd

SNPdata_Aguirre_Liguori_etal_SNPdata

The SNPdata_Aguirre_Liguori_etal.txt file contains the genotypes exported from GenomeStudio. SNPs were genotyped using the Illumina MaizeSNP50 Genotyping BeadChip. Loci are in rows and individuals are in columns. Each column is named as the population and individual separated by “_”. For example “Mochitlan_Mochitlan_9” indicates that the individual comes from the site Mochitlan in the Mochitlan “Municipio” and corresponds to the 9th individual. Sample information (Population, coordinates and the subspecies) is found in the sample_information_Aguirre_Liguori_etal.txt file and in the manuscript. Genotypes downloaded from Pyhäjärvi et al. (2013) can be found in the following link http://datadryad.org/resource/doi:10.5061/dryad.8m648/

Sample information of teosintes

The sample_information_Aguirre_Liguori_etal.txt file contains the geographic coordinates and the subspecies information of each of the populations sampled

Data_Sheet_1.PDF

<p>Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (H_E = 0.428 in sororia, and H_E = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (F_ST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene flow among populations at a regional scale (<0.01), except for the Yucatan Peninsula, and the northern portion of the Pacific Coast. Our analyses suggested that the Isthmus of Tehuantepec is an effective barrier isolating southern populations. Our SDM results indicate that environmental characteristics in the Balsas-Jalisco region, a potential center of domestication, were suitable for the presence of sororia during the Holocene.</p