Fig. 2: Germline positive selection.

a–c, Genes with significant dN/dS ratios from exome-wide and restricted hypothesis tests. a, Mutation count split by mutation class. b, Enrichment over expectation of mutation classes. c, Mutation type driving dN/dS enrichment, COSMIC cancer gene tier, developmental disorder (DD) gene status in DDG2P and potential germline selection gene set. d,e, Observed sperm mutations across the cohort for CUL3 and SMAD4. The height of each lollipop represents the number of biologically independent samples with a mutation at that position, and the colour indicates mutation type. Mutations are labelled with their amino acid consequence or, for insertions (ins) and deletions (del), as in-frame (IF) or frameshift (FS). A ‘P’ indicates pathogenic/likely pathogenic classification in ClinVar. Exons are shown as purple rectangles and the blue background shows the total duplex coverage across the cohort. Lines below the gene indicate somatic mutations in cancer from COSMIC. f,g, dN/dS ratios for sperm SNVs across sets of individuals or genes, where the dotted black line indicates neutrality and the dotted orange line represents the cohort average across all genes. f, Exome-wide dN/dS ratios for younger, middle and older age groups of n = 11, n = 9 and n = 18 biologically independent sperm samples, respectively. g, Expression levels as log₂ of unique molecular identifier (UMI) counts and cell-type clusters from single-cell sequencing of germ cells²⁹. Germ-cell types include undifferentiated and differentiated spermatogonial stem cells (SSCs), spermatocytes, round spermatids (spermatid 1) and elongating spermatids (spermatid 2). Data are from mutations detected in n = 38 biologically independent sperm samples. h, Observed/expected mutation rates in sperm for variant recurrence bins (data from COSMIC and DDD databases) using mutations from n = 38 biologically independent sperm samples. Data in f–h show ratio point estimates, error bars indicate 95% CIs.