Table 1.

Number of SNPs used for LD-based analysis resulting from simulations in simuPop

		Initial variation at t 0			Final variation at t 20
		RAD mutation	10%	50%	RAD mutation	10%	50%
N	λ	# SNPs	# SNPs	# SNPs	# SNPs	# SNPs	# SNPs
250	1.0	3660	3938	4527	3521	3695	4223
500	1.0	3718	4054	4657	3629	3876	4451
1000	1.0	3756	4130	4742	3703	4013	4611
250	0.9	3915	3941	4676	3099	2965	3457
500	0.9	3719	4053	4661	3392	3493	3975
1000	0.9	3756	4128	4739	3570	3773	4327

SNPs were calculated as average across the 100 replicates for each simulated scenario and are presented for the initial generation (t ₀) after the 10-generation equilibrium phase and from the final generation (t ₂₀). SNP levels are broken down across the different initial population sizes (N), population growth rates (λ), and data-filtering methods (LD RAD mutation, 10% missing, and 50% missing data sets).