Fig. 3: Hyper-divergent haplotypes are widespread in the H. bakeri genome.

Distribution of heterozygosity in the genomes of (a) H. polygyrus ngHelPoly1 and (b) H. bakeri nxHelBake1. Points represent the density of biallelic SNPs in 10 kb windows. nxHelBake1 was male and therefore had a hemizygous X chromosome; the SNP density peaks on the X chromosome are therefore erroneous and are derived from mismapped PacBio HiFi reads. ngHelPoly1 was female. SNPs called in repeat-containing regions were filtered out and SNP density was calculated as the number of non-repetitive SNPs per non-repetitive base. Blue lines represent LOESS smoothing functions fitted to the data. c H. bakeri nxHelBake1 PacBio HiFi read alignments to the nxHelBake1.1 reference genome in a 143 kb region on chromosome V (87.7 − 87.9 Mb) that contains a 56 kb hyper-divergent haplotype. The top panel shows the coverage and the bottom panel shows aligned PacBio HiFi reads. The coloured vertical lines indicate mismatched bases at that position. An alignment between the two assembled haplotypes in this region is shown in Supplementary Fig. 10. Source data this figure can be found in the GitHub repository.