Patterns of transposable element variations in the human pangenome reference consortium v1 dataset

The Human Pangenome Reference Consortium dataset (HPRC), phase 1, composed of 47 genetically diverse phased genomes, provides an unprecedented opportunity to investigate the dynamics of Transposable Elements (TEs) variation. We established the first comprehensive analysis of presence/absence variants of TEs in the HPRC v1 and computed their frequencies and divergence-based ages. The TE patterns were consistent with the known human population history (African vs. non-African). Most TE variants were recent and located in low-recombination and intergenic regions, yet some were present in exons. Selection scans highlight 154 TE loci potentially evolving under positive selection. Our study illustrates the power of pangenomics to uncover the intricacies of TE evolution.