Table 2.

Population genetic statistics and PCA results of ddRAD data for the different Stacks settings (b2: m3 M2 N4 n2, b1: m3 M3 N5 n3, and b3: m3 M4 N6 n4). Ho, Hs, and Ht are observed heterozygosity, within‐population gene diversity, and overall gene diversity, respectively. F _ST and F _IS were calculated according to Weir and Cockerham (1984)

Dataset	Stacks setting	n	# Loci	Ho	Hs	Ht	F ST	F IS	Sig. PCA axes	% Variance explained by
										1. axis	2. axis	Other axes
Unfiltered	b2	275	875	0.45	0.28	0.40	0.30	−0.57	27	39.9	8.4	<2.0
Unfiltered	b1	275	1,753	0.54	0.32	0.42	0.24	−0.65	31	36.5	6.2	<1.6
Unfiltered	b3	275	2,319	0.58	0.34	0.43	0.20	−0.69	34	33.2	5.6	<1.7
Filtered	b2	268	1,070	0.42	0.27	0.39	0.32	−0.53	26	40.7	9.3	<2.1
Filtered	b1	267	2,135	0.50	0.31	0.42	0.27	−0.62	30	38.9	6.8	<1.6
Filtered	b3	267	2,838	0.55	0.33	0.43	0.23	−0.66	28	35.7	6.0	<1.6