Table 2.

Number of single nucleotide polymorphisms (SNPs) remaining after minor allele frequency (MAF) pruning, mean polymorphic information content (PIC) and number of remaining individuals across all six datasets produced

	No. of remaining individuals	No. of SNPs remaining after a pruning regime using…
		MAF < 0.05 (1)	MAF < 0.01 (2)	MAF = 0 (3)
de novo approach (SNP set A)	72	1,809 (mean PIC = 0.21)	2,658 (mean PIC = 0.28)	3,459 (mean PIC = 0.26)
ref_map approach (SNP set B)	68	2,909 (mean PIC = 0.26)	3,410 (mean PIC = 0.22)	3,480 (mean PIC = 0.18)