Fig-SSR: Diffuse and Regionally Structured Domestication of the Common Fig

This repository contains all the code used to reproduce analyses for the work:

Diffuse and regionally structured domestication of the common fig (Ficus carica L.) in the Mediterranean Basin

Repository layout

├─ env/ # Conda environment + R extras + external tool notes └─ scripts/ # Analysis scripts, one folder per module

Scripts structure

scripts/ ├─ ADZE/ # AR / AP diversity calculations ├─ eems/ # Effective migration surfaces ├─ geocoding/ # Site geocoding utilities ├─ max_membership/ # STRUCTURE membership coefficient analyses ├─ pca/ # PCA scripts and notebooks ├─ pophelper/ # STRUCTURE admixture plots ├─ STRUCTURE/ # Job submission and STRUCTURE runs ├─ structure_harvester/ # Evanno’s ΔK (Structure Harvester or R equivalents) ├─ tess3r/ # tess3r clustering analyses └─ willcoxon_comparison/ # Wilcoxon tests for AR / AP

Each subfolder includes a README.md describing:

• Purpose
• Key files
• How to run
• Inputs / outputs

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Environment setup

Create and activate the conda environment:

mamba env create -f env/environment.yml mamba activate fig-ssr

Then install extra R packages (from CRAN / GitHub): Rscript env/R-packages.R See env/README.md for full details, including external tools like STRUCTURE, SPAGeDI, and EEMS.

Usage 1. Set up the environment (env/). 2. Navigate to the relevant folder under scripts/. 3. Follow that folder’s README.md for how to run the script(s).

Outputs will be written to the locations defined inside each script’s instructions.