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Fig. S1 True and estimated values of π and θw as a function of the chromosome sampling depth for θ = ρ = 0.01 per bp.

Fig. S2 Mean values of πe (solid red) and θe (solid blue) for loci with different sampling depth cutoffs (i.e. loci that have at least the specified number of sampled chromosomes with intact recognition sequences).

Fig. S3 Chromosome sampling depth proportions for the standard (red) and double digest (blue) RADseq protocols.

Fig. S4 True π (solid lines) and estimated π (dashed lines) vary as a function of chromosome sampling depth for the standard (blue) and double-digest (red) RADseq protocols.

Fig. S5 Mean values of πe (solid red) and θe (solid blue) for loci with different sampling depth cutoffs (CSDC, i.e. loci that have at least the specified number of sampled chromosomes with intact recognition sequences).

Fig. S6 Distribution of estimated FST when all haplotypes are sampled (blue) vs. the true distribution (black), for Nm = 10 (A), Nm = 1 (B), and Nm = 0.1 (C).

Fig. S7 Proportion of estimated π (red), θw (blue), or D (purple) 5% outlier loci that are false positives (solid lines) or false negatives (dashed lines) relative to the true distribution for different chromosome sampling depth cutoffs.

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