Extended Data Fig. 8. Young XY system in P. exspectatus.

a, Coverage analysis of the X chromosome between sexes of P. exspectatus. Coverage depth of each 100 kb sliding window was normalized by average coverage and log₂-transformed. Each lines indicates the values of sliding windows of a single individual. b, Increasing Y-derived alternative SNPs around the fusion breakpoint. Definitions of male heterozygous SNPs, X-derived alternative SNPs and Y-derived alternative SNPs are found in Materials and Methods and Supplementary Fig. 22. The proportion of SNPs in 100 kb sliding windows are shown. c, Diagram of the XY system of P. exspectatus. d, Evolutionary model of sex chromosome evolution in nematodes, consistent with the ref. ⁸⁷. First, chromosome fusions of an X chromosome and an autosome in a XO system results in an XY system containing neo-X and neo-Y chromosome regions. Second, inversions occur between the neo-X and ancestral-X chromosomes. Restricted recombination between neo-X and neo-Y chromosomes results in the gradual degeneration of the neo-Y chromosome. Third, additional inversions accumulate in the X chromosome and the Y chromosome becomes smaller by further degeneration. Finally, the X chromosome has mixed fractions of ancestral-X and neo-X chromosomes (see Extended Data Fig. 4c), and the Y chromosome is completely lost. This final step results in the reoccurrence of the XO system. Note that the chromosome fusions of P. exspectatus and C. elegans happened independently and their sex chromosomes represent different stages in nematode sex chromosome evolution.