Table 3.

Basic population genetic statistics of ddRAD data for the different nuclear cluster and respective 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)

Nuclear cluster	Stacks setting	n	# Loci	Ho	Hs	Ht	F ST	F IS
Af Ι	b2	119	970	0.60	0.35	0.39	0.13	−0.70
Af Ι	b1	119	1,824	0.70	0.39	0.43	0.09	−0.76
Af Ι	b3	119	2,414	0.74	0.41	0.44	0.07	−0.78
Af ΙΙ	b2	104	1,060	0.69	0.40	0.44	0.10	−0.75
Af ΙΙ	b1	104	2,065	0.76	0.42	0.45	0.07	−0.80
Af ΙΙ	b3	104	2,705	0.78	0.43	0.46	0.06	−0.81
Af ΙΙΙ	b2	37	766	0.66	0.41	0.42	0.04	−0.60
Af ΙΙΙ	b1	37	1,408	0.75	0.44	0.44	0.02	−0.70
Af ΙΙΙ	b3	37	1,886	0.77	0.45	0.45	0.02	−0.72