Table 2.

Matrices of SNP data. Filtering setting in Stacks: –p: minimal number of populations required to be scored for each SNP; ‐n: maximum number of SNPs per locus; alleles: maximum number of alleles per locus. In all cases, only the first SNP of each locus is included

Data matrix	Populations included	‐p	‐n	Alleles	Unlinked SNPs	Analysis	Missing data (%)
							Avg	SD	Min	Max
1	6	6	4	8	529	Structure	50	20	21	89
1a	6	6	1	2	151	Descriptive statistics, PCA and IBS	49	20	19	91
2	5	2	3	6	2,888	Structure	66	13	42	89
2a	5	2	1	2	1,319	Descriptive statistics, PCA and IBS	67	13	42	88