Data and Analysis Materials for "Genome-Wide Population Structure Reveals Distinct Genomic Differentiation of Sumatran Buffalo Across the Sunda–Wallacea Biogeographic Context"

This dataset supports the research article entitled “Genome-Wide Population Structure Reveals Distinct Genomic Differentiation of Sumatran Buffalo Across the Sunda–Wallacea Biogeographic Context.” The study integrates whole-genome sequencing data from 28 Sumatran water buffaloes, comprising 14 river buffaloes and 14 swamp buffaloes, with publicly available Asian buffalo genomes. The dataset contains sample metadata, accession mappings, variant-quality-control summaries, processed and linkage-disequilibrium-pruned genotype data, and input and output files supporting principal component analysis, ADMIXTURE, pairwise FST analysis, population-tree reconstruction, and TreeMix analysis. Source data for the tables and figures and the analysis commands/scripts are also provided. Raw sequencing reads generated in this study are deposited in the European Nucleotide Archive under project accession PRJEB116015. Comparative public datasets were obtained under accessions SRP478364, PRJNA1057008, and PRJNA1135737. The water buffalo reference genome used for read alignment was NDDB_SH_1, accession GCF_019923935.1. Detailed descriptions of the files, variables, analytical inputs, software versions, and relationships between files and manuscript figures are provided in the README.