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Table. S1 Species and references used in our meta-analysis. The Overfished column indicates whether any populations of the species were known to be overfished.

Table. S2 Summary of sample size (in total number of species and in number of overfished species), allelic richness (A), and expected heterozygosity (H) for loci that are not cross-species amplifications. Data are reported separately for overfished populations (AOF and HOF) and for those that were not overfished (ANO and HNO).

Fig. S1 Simulated bottlenecks of 50% in a species with discrete generations (a, c) or with overlapping generations (b, d). Contour lines indicate proportion of allelic richness lost in a sample of 50 individuals (a, b) or proportion of heterozygosity lost (c, d). Initial effective population size (Ne) is indicated along the y-axis, and generations postbottleneck are indicated along the x-axis.

Fig. S2 Expected loss of allelic richness in the entire population. Graphs show simulated bottlenecks of 50% in a species with discrete generations (a) or overlapping generations (b). See legend of Fig. S1 for other notes.

Fig. S3 Simulations for populations linked by immigration rates of 0.1% (a, d), 1% (b, e) or 10% (c, f). All populations experienced a bottleneck of 90%. Contour lines indicate proportion of allelic richness lost in a sample of 50 individuals (a, b, c) or proportion of heterozygosity lost (d, e, f). Initial effective population size (Ne) is indicated along the y-axis, and generations postbottleneck are indicated along the x-axis.

Fig. S4 Simulations for populations linked by immigration rates of 0.1% (a, d), 1% (b, e) or 10% (c, f). Only the focal population experienced a bottleneck of 90%. Contour lines indicate proportion of allelic richness lost in a sample of 50 individuals (a, b, c) or proportion of heterozygosity lost (d, e, f). Initial effective population size (Ne) is indicated along the y-axis, and generations postbottleneck are indicated along the x-axis.

Fig. S5 Simulations initialized with mutation rates of 1 × 10−3. Simulated bottlenecks of 50% (a,c) or 90% (b, d) in a species with discrete generations. Contour lines indicate proportion of allelic richness lost in a sample of 50 individuals (a, b) or proportion of heterozygosity lost (c, d). Initial effective population size (Ne) is indicated along the y-axis, and generations postbottleneck are indicated along the x-axis.

Fig. S6 Simulations initialized with mutation rates of 1 × 10−4. Simulated bottlenecks of 50% (a,c) or 90% (b, d) in a species with discrete generations. Contour lines indicate proportion of allelic richness lost in a sample of 50 individuals (a, b) or proportion of heterozygosity lost (c, d). Initial effective population size (Ne) is indicated along the y-axis, and generations postbottleneck are indicated along the x-axis.

Fig. S7 Statistical power to detect declines in a) allelic richness or b) heterozygosity with samples taken before and after a 90% decline in population size. Parameter sets for the simulations were a pre-bottleneck Ne of 1000 and samples taken three generations postbottleneck (solid line); Ne of 3162 and five generations (dashed line); and Ne of 10 000 and 15 generations (dotted). These parameter sets were chosen to produce declines in genetic diversity consistent with our meta-analysis results (i.e., 10% decline in allelic richness, 0–2% decline in heterozygosity).

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