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Fig. S1 Results of management for a population size of 20 individuals on observed heterozygosity and mean fitness, scaled with their values at t = 0, plotted against management generations using genealogical, molecular coancestry or with segment-based coancestry (ROH) with different minimum segment lengths, under the CGD and Mukai scenarios.

Fig. S2 Results of management for a population size of 100 individuals on observed heterozygosity and mean fitness, scaled with their values at t = 0, against management generations, with contributions calculated using genealogical, molecular or segment-based coancestry or at random.

Fig. S3 Results of management for a population size of 100 individuals on observed heterozygosity and mean fitness, scaled with their values at t = 0, against management generations, with contributions calculated using genealogical, molecular or segment-based coancestry or at random.

Fig. S4 Results of management for a population size of 100 individuals on observed heterozygosity and mean fitness, scaled with their values at t = 0, against management generations, with contributions calculated using genealogical or molecular coancestry or at random.

Table S1 r2 between adjacent marker, selected and neutral loci in the base populations, measured in positions which are not fixed.

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