Olotillo Genetic Diversity

This repository contains the data, scripts, and analyses associated with the article: “Diversity and genetic structure within a Mexican maize race reveal consistent biocultural processes across geographic scales.”

Repository structure

The following zip files correspond to the Repository structure below:

• 01_data_general_SNPs.zip: General genomic dataset
• 02_meta_general.zip: General metadata
• 03_figure_1_2_maps.zip: Geographic and environmental maps
• 04_figure_3_PCA.zip: Principal Component Analysis (PCA) data and scripts
• 05_figure_4_admixture.zip: Admixture and ancestry analyses
• 06_tables_diversity_and_supple.zip: Supplementary diversity tables and scripts

  Olotillo-genetic-diversity/
  ├── 01_data_general_SNPs/                     # General genomic SNP dataset
  │   ├── data_general_README.md                # Description of the genomic data source and file format
  │   └── mixplates_filtered_2x.vcf.gz          # Filtered VCF file containing SNP genotype data
  │
  ├── 02_meta_general/                          # General project metadata
  │   └── meta_Olotillo.xlsx                    # Metadata describing samples, accessions, localities, and traits
  │
  ├── 03_figure_1_2_maps/                       # Scripts and input files for Figures 1 and 2
  │   ├── Readme.md                             # Documentation for maps and environmental-condition analyses
  │   ├── map_&_environmental_conditions.Rproj  # RStudio project file for map and environmental analyses
  │   ├── bin/                                  # R Markdown scripts for spatial and environmental analyses
  │   │   ├── .Rprofile                         # R project startup configuration file
  │   │   ├── map_olotillo.Rmd                  # R Markdown script for generating Olotillo distribution maps
  │   │   └── olotillo_weather.Rmd              # R Markdown script for environmental and weather analyses
  │   ├── meta/                                 # Metadata used for mapping and environmental analyses
  │   │   ├── README.md                         # Description of metadata files in this folder
  │   │   ├── olotillo_PGMN_siagro.csv          # Occurrence and passport data from PGMN/SIAGRO sources
  │   │   ├── olotillo_points_meta_clean.csv    # Cleaned geographic point metadata for mapping
  │   │   ├── olotillo_weather.csv              # Weather and environmental metadata for Olotillo localities
  │   │   ├── pca_meta_mixplate.csv             # Sequencing plate and sample metadata used across analyses
  │   │   └── plate1_fullmeta.txt               # Full metadata table for sequencing plate 1
  │   └── shape/                                # Spatial vector layers used for map generation
  │       ├── destdv1gw/                        # Shapefile layer and auxiliary files for environmental/geographic mapping
  │       └── oloti_7cgw/                       # Shapefile layer and auxiliary files for Olotillo geographic mapping
  │
  ├── 04_figure_3_PCA/                          # Files associated with Principal Component Analysis (PCA)
  │   ├── bin/                                  # R scripts for PCA computation and visualization
  │   ├── data/                                 # PCA output files and related datasets
  │   └── meta/                                 # Metadata used to annotate samples and groups in PCA plots
  │
  ├── 05_figure_4_admixture/                    # Files associated with ADMIXTURE and ancestry analyses
  │   ├── bin/                                  # R and bash scripts for ADMIXTURE runs and visualization
  │   ├── data/                                 # ADMIXTURE output files, including Q matrices and related results
  │   └── meta/                                 # Sample and population metadata used for ADMIXTURE plots
  │
  ├── 06_tables_diversity_and_supple/           # Genetic diversity and supplementary table files
  │   ├── bash/                                 # Bash scripts for diversity metrics calculated with VCFtools
  │   ├── bin/                                  # R scripts for processing and summarizing diversity analyses
  │   ├── data/                                 # Genetic diversity output tables and supplementary data
  │   └── meta/                                 # Metadata and diversity-related tables used in downstream analyses
  │
  ├── .gitignore                                # Git ignore rules for files that should not be tracked
  └── README.md                                 # Main project overview and repository documentation

Project Overview

This project explores the genetic diversity and population structure of the Olotillo maize race, a traditional landrace cultivated in southern Mexico.
Analyses combine genomic, environmental, and geographic information to investigate how biocultural processes influence genetic variation at local and regional scales.

Contents

• Genomic Data: Filtered VCF datasets and associated metadata.
• Scripts: R and bash scripts for data processing, analysis, and visualization.
• Figures: Scripts and inputs for reproducing Figures 1–4 of the article.
• Supplementary Tables: Diversity and population structure results supporting the main text.

Requirements

Main analyses were conducted using R (>= 4.3) and the following key packages:

• dplyr, ggplot2, sf, raster, cowplot, pophelper, adegenet, vcfR

Some analyses require bash and ADMIXTURE to reproduce population structure results.

Contact

For questions or collaboration inquiries, please contact: Duhyadi Oliva-García duhyadi.oliva@st.ib.unam.mx