Population genomics of Nigerian goat breeds and neighbouring populations in the West Africa–Cameroon transboundary livestock corridor

Abstract

This Zenodo deposit accompanies the manuscript by providing the analysis scripts and the derived outputs needed to reproduce the figures/tables from the processed genotype dataset (not included here). The `script/` directory contains the R scripts used for each analysis step: preprocessing/admixture, PCA, FST, TreeMix, ALDER-based admixture timing, LD-based Ne (SNeP), ROH, phasing/DCMS scans, DCMS annotation, and GO analysis. The `results/` directory contains the corresponding final exported outputs (manuscript-ready figures and supplementary tables), organized by analysis module. What is excluded: this deposit does not include genotype data, large intermediate files (e.g., PLINK binaries, per-chromosome VCFs, phased haplotypes, temporary log files), or any materials that could be restricted by data-sharing agreements. External executables and third-party tools used to run parts of the pipeline (e.g., PLINK, ADMIXTURE, ALDER, SNeP, selscan, Beagle, bcftools/tabix/bgzip, and helper Python scripts). Users should install those dependencies separately and follow their original licenses/citation requirements.