Primate Genome Diversity
Primates constitute one of the most phylogenetically and ecologically diverse mammalian orders, with a central role in advancing our knowledge of human evolution, speciation processes and conservation biology. While thousands of whole-genome sequences have been generated across a multitude of 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 utilized publicly available short-read sequencing data of non-human primates - together with 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 generated a multiple-genome alignment of the 48 primate assemblies used for variant calling. This publicly available resource provides a foundation for future research in primate evolutionary biology, speciation, and sex chromosome evolution.