A curated genome-scale nucleotide diversity panel of non-human primates

Primates constitute one of the most phylogenetically and ecologically diverse eutherian mammalian orders and have a central role in advancing our knowledge of human evolution, speciation processes, and conservation biology. Although thousands of whole-genome sequences are available across many primate taxa, discrepancies in data processing—particularly the lack of ploidy-aware variant calling in sex-linked regions—have limited the utility of existing datasets for large-scale comparative analyses. Here, we use publicly available short-read sequencing data from non-human primates, recently published primate genome assemblies, and a ploidy-aware variant calling procedure to generate a genome-scale nucleotide diversity panel comprising 3,240 individuals from 269 species and 71 genera. To further facilitate cross-species comparisons, we generate a multiple-genome alignment of the primate assemblies used for variant calling. This curated resource of non-human primate diversity provides a foundation for future research in primate evolutionary biology, speciation, and sex chromosome evolution.