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Figure S1. Proportion of functional genes on the Y chromosome (out of 10) with a deleterious mutation fixed after T = 105 generations, as a function of selection coefficient s (log10 scale) and for different values of dominance h.

Figure S2. Time to turnover for different c values (mating-success cost) as a function of hs (log10 scale).

Figure S3. Proportion of functional genes on the Y chromosome (out of 10) with a deleterious mutation fixed at turnover time, as a function of hs (log10 scale), for different mating-success costs (black: c = 0; red: c = 0.005; blue: c = 0.02; Ne fixed to 103).

Figure S4. Outcome of one simulation with parameter values s = 0.01, h = 0.25, Ne = 103, and c = 0.02, 10 loci on the nonrecombining segment.

Figure S5. Proportion of functional genes on the Y chromosome (out of 10) with a fixed deleterious mutation at turnover time, as a function of hs (log10 scale), for different population sizes Ne (102 in black, 103 in red, 104 in blue).

Figure S6. Turnover probability as a function of hs (log10 scale) for different population sizes and lengths of nonrecombining segment.

Figure S7. Time to turnover as a function of hs (log10 scale) for different population sizes and lengths of nonrecombining segment.

Figure S8. Turnover probability as a function of hs (log10 scale) for different male recombination rates.

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