Table 2.

RADseq run information per population (Tern, Midway, Torishima or all) for all positions (both variant and fixed), based on data set 1

Populations	All
Total number of 100-bp reads produced by the RADseq run	78 803 224
Number of loci in Stacks catalogue before filtering in populations	115 359
Number of loci retained in Stacks catalogue after filtering in populations	9760
Total number of RAD sites	879 856
Number of detected SNPs (data set completeness: 80.4%)	3455
Number of polymorphic RAD loci with ≥1 SNP	2769

Populations	Tern	Midway	Torishima
Average number of individuals per population across loci	13.9927	7.80374	13.8236
Stack depth of coverage	Mean = 180.9 SD = 150.8	Mean = 120.3 SD = 128.2	Mean = 203.2 SD = 148.3
Total number of RAD sites present in all individuals	873 713	787 400	857 790
Total number of polymorphic RAD sites present in all individuals	2647	1871	2066
Number of variant sites	3426	3154	3385
Observed heterozygosity	0.00063	0.00063	0.00059
Observed homozygosity	0.99937	0.99937	0.99941
Expected heterozygosity	0.00062	0.00060	0.00058
Expected homozygosity	0.99935	0.99936	0.99940
π (nucleotide diversity)	0.00065	0.00064	0.00060

SNP, single nucleotide polymorphism.