diff --git a/README.md b/README.md
index 9580ab772b055e5b9aa0416bd9f5302395d1493d..41b91bf342397e9e758873cb8bbbb5390e4e3473 100644
--- a/README.md
+++ b/README.md
@@ -1,18 +1,12 @@
-# TEOSINTE Project: Comparative Genomics of Maize's Wild Relatives (Teosinte)
+# Comparative Genomics of Maize's Wild Relatives (Teosinte)
-## Description
-
-> **Project Start:** 01.10.2021
-
-> **Project Status:** Active
+This documentation supports the manuscript _From Habitat to Genotype: The Complex Interplay of Climate, Phenotypes, and Taxonomy in Teosinte_.
-> **Responsible Investigator:** Joseph Atemia
+The manuscript explores the genetic and ecological diversity of **teosinte**, the wild relatives of maize, using a **Genome-Wide Association Studies (GWAS)** approach. This integrative research examines the relationships between **habitats, genetic adaptations, and phenotypic traits**, highlighting the evolutionary processes that have shaped teosinte populations.
-> **Supervisor:** Asis Hallab
-
-> **Project Partners:** Alicia Mastretta-Yanes (Instituto de Ecologia, UNAM, Mexico), Ana Wegier (JardÃn Botánico, Instituto de Biologia, UNAM, México)
+## Description
-Crop wild relatives represent important sources of genetic variation that could be of great aid to breeding programs, especially regarding adaptation to extreme environmental conditions [ISBN:978-1-78064-197-3]. Maize close wild relatives are teosintes, which have a wide ecogeographic distribution in Mexico spanning extreme ranges of precipitation and temperatures [doi:10.1371/journal.pone.0192676]. The identification of the genetic variants associated with adaptation to such conditions is a necessary step in order to better monitor, conserve and use such diversity in applied projects. As part of preliminary research, the Mexican partners performed an extensive teosinte sampling, including ca. 4000 individuals of 276 populations of all the 7 teosinte species and subspecies distributed in Mexico. These samples were phenotyped in a greenhouse common garden, and genotyping by sequencing (GBS) was applied yielding ca. 60,000 SNPs. Ecogeographical analyses were also performed [doi:10.1371/journal.pone.0192676]. This dataset encompasses probably the most complete teosinte sampling done so far providing genomic data at a population level. However, teosinte genomes have proved to be incredibly diverse and complex, and during the course of domestication the differences among maize and its parental teosintes (​Zea mays ssp. ​ parviglumis and ssp. ​ mexicana) not only included re-shuffling allele-frequencies,but also structural and expression changes [doi:10.1038/ng.2309]. Therefore, fully exploring the variation associated to teosinte adaptation to diverse environments requires new approaches. Here, we aim to identify the genetic variants associated with teosinte adaptation to different environmental conditions, in the context of the genomic changes associated with domestication.
+Teosintes, wild relatives of maize, exhibit significant ecological and genetic diversity across Mexico and Central America, adapting to diverse climates. A study of 3,455 individuals from 276 populations (excluding Zea vespertillio) analyzed 33,929 SNPs, revealing genetic structure, ecological adaptations, and candidate genes tied to climate and traits. Genome-wide association studies (GWAS) identified SNPs linked to morphological and environmental factors, highlighting both shared and unique genetic variants compared to maize. Functional analysis of loci revealed diverse adaptive strategies even within similar environments. These findings emphasize teosinte’s genetic diversity, its role in gene flow with maize, and its conservation under global frameworks, addressing risks like transgenic flow and weed emergence.
---
@@ -24,16 +18,17 @@ This project is funded by the German Ministry for Science and Education (BMBF 03
## Data and Code Availability
-- **Genotyping-by-sequencing (GBS) Data**: The GBS data used in this study was obtained from publicly available sources and is detailed in the following published papers:
- - [Ecogeography of Teosinte](https://doi.org/10.1371/journal.pone.0192676)
- - [Genomic Diversity and Population Structure of Teosinte (Zea spp.) and Its Conservation Implications](https://doi.org/10.1371/journal.pone.0291944)
+- **Genotyping-by-sequencing (GBS) Data**: The GBS data used in this study was obtained from publicly available sources and is detailed in the following published papers:
+
+ - [Ecogeography of Teosinte](https://doi.org/10.1371/journal.pone.0192676)
+ - [Genomic Diversity and Population Structure of Teosinte (Zea spp.) and Its Conservation Implications](https://doi.org/10.1371/journal.pone.0291944)
- **Repository**:
All code, scripts, and associated files used for the Genome-Wide Association Study (GWAS) are hosted in this repository.
-- **Data and File Tracking**:
- - Large datasets and other outputs generated during the study are stored and version-controlled using **Git LFS** (Large File Storage) for efficient tracking of changes and sharing of substantial files within the repository.
- - The specific data and outputs related to this GWAS study are included and organized in the repository for direct access.
+- **Data and File Tracking**:
+ - Large datasets and other outputs generated during the study are stored and version-controlled using **Git LFS** (Large File Storage) for efficient tracking of changes and sharing of substantial files within the repository.
+ - The specific data and outputs related to this GWAS study are included and organized in the repository for direct access.
## Directory Structure
@@ -69,9 +64,9 @@ This project is funded by the German Ministry for Science and Education (BMBF 03
## Steps in Analysis
-The sections that follow outlines the key steps taken to explore and analyze the relationships described in the manuscript *From Habitat to Genotype: The Complex Interplay of Climate, Phenotypes, and Taxonomy in Teosinte*. Each step is detailed to ensure reproducibility and transparency in the analysis.
+The sections that follow outlines the key steps taken to explore and analyze the relationships described in the manuscript _From Habitat to Genotype: The Complex Interplay of Climate, Phenotypes, and Taxonomy in Teosinte_. Each step is detailed to ensure reproducibility and transparency in the analysis.
-*Caution: Please note that some of the directory paths in the scripts may need to be modified to match your local environment in order to ensure proper reproducibility.*
+_Caution: Please note that some of the directory paths in the scripts may need to be modified to match your local environment in order to ensure proper reproducibility._
---
diff --git a/studies/README.md b/studies/README.md
new file mode 100644
index 0000000000000000000000000000000000000000..273800a2a81d64f5908c37b27407205945294aad
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+++ b/studies/README.md
@@ -0,0 +1,26 @@
+# GWAS Data for Teosinte Taxa
+
+This repository contains resources for conducting **Genome-Wide Association Studies (GWAS)** on **3,455 teosinte individuals**, spanning all seven teosinte taxa. The data integrates **climatic, morphological, and genetic datasets**, enabling both comprehensive and taxa-specific analyses.
+
+## Directory Structure
+
+- **[`initial_data/`](./initial_data)**
+ Contains the raw, unprocessed data files.
+
+- **[`processed_genotype_phenotype_teosinte_data/`](./processed_genotype_phenotype_teosinte_data)**
+ Finalized, GWAS-ready datasets and resources. This directory includes:
+ - **Comprehensive dataset** for all 3,455 individuals.
+ - **Subsetted datasets** tailored for each of the seven teosinte taxa:
+ - _Zea mays ssp. parviglumis_
+ - _Zea mays ssp. mexicana_
+ - _Zea diploperennis_
+ - _Zea mays ssp. huehuetenangensis_
+ - _Zea luxurians_
+ - _Zea nicaraguensis_
+ - _Zea perennis_
+
+---
+
+The dataset supports targeted analyses of teosinte’s genetic diversity, population structure, and adaptation. It was curated for GWAS analyses.
+
+---
diff --git a/studies/initial_data/README.md b/studies/initial_data/README.md
index c5b4f9fb9e1cac73a50cfc8406929112890b69f6..527238699f981cd536ee779161a5895b9a541a0b 100644
--- a/studies/initial_data/README.md
+++ b/studies/initial_data/README.md
@@ -1,3 +1,3 @@
# Contents
-Data and scripts provided by Alicia Mastretta-Yanes to the German team in December 2021. The data includes metadata, SNP data, and admixture output for teosinte. See the [resources]('./resources') directory for further details.
+Data and scripts provided by Alicia Mastretta-Yanes to the German team in December 2021. The data includes metadata, SNP data, and admixture output for teosinte. See the [resources](./resources) directory for further details.
diff --git a/studies/processed_genotype_phenotype_teosinte_data/README.md b/studies/processed_genotype_phenotype_teosinte_data/README.md
index 14f99526b78cd8da8230211408bec08c03ea7f5f..a861ed4372aee0c32cf60fdb5eb2aac6cabcaa02 100644
--- a/studies/processed_genotype_phenotype_teosinte_data/README.md
+++ b/studies/processed_genotype_phenotype_teosinte_data/README.md
@@ -5,7 +5,7 @@ The dataset includes climate, morphological, and genetic data, and is subsetted
## Directory Structure
-## [Resources](`resources/gwas_data_3455_accessions`)
+## [Resources](resources/gwas_data_3455_accessions)
### Key Files