Fig. 2: Divergent regions and repeats.
a, The number of lineage-specific SDRs detected on two haplotypes (H1 and H2) and classified by different genomic content. QH region, heterochromatic q-banded satellite-containing region. b, Ape phylogeny with speciation times in millions of years (black) and effective population size (Ne) in thousands (red) for terminal and ancestral nodes. For Ne, values in inner branches refer to TRAILS estimates, whereas that of terminal nodes is predicted using MSMC2 considering the harmonic mean of the Ne after the last inferred split. c, Left, species-specific Alu, SVA and L1 mobile element insertion (MEI) counts normalized by millions of years (using speciation times from b). Right, species-specific full-length (FL) L1 ORF status. The inner number in each circle represents the absolute count of species-specific FL L1 elements. d, Species-specific ERV retrotransposons depict PtERV1 and HERV-K elements (inner ring) and long terminal repeats (LTRs) and potential protein-coding domains (outer ring). TSD, target-site duplication.
