Table 1 Distribution of samples through sampling areas, sampling sites, years of sampling and management type

Sampling areas/sites	Management type	Samples 2007	Samples 2008	Total samples	Cyt-b haplotype	F_is	H_e	Allelic richness	Number of private alleles	N_e[95% CI]
Kalø
KC1	C	12	28	40	1-3-4	0.052	0.800	7.25	0.333	2007: 369.6 (83.5–infinite); 2008: NN
KO1	O	19	6	25	1	0.058	0.803	7.11	0.333	2007: 358.9 (141.8–infinite); 2008: NN
KO2	O	26	13	39	1-7	0.067	0.809	7.04	0.467	2007: 162.8 (106–335); 2008: NN
KO3	O	9	0	9	1	0.059	0.733	6.12	0.067	NN
KO4	O	13	0	13	1-8	0.021	0.737	6.72	0.000	NN
KO5	O	0	9	9	1	0.026	0.717	8.21	0.000	NN
KO6	O	0	36	36	1	0.013	0.779	7.42	0.067	2008: 280.9 (147.4–1959.1)
Kalø total	C+O	79	93	172	1-3-4-7-8		0.830		1.600
Fussingø
FC1	C	13	0	13	1-2	0.042	0.671	5.41	0.000	2007: 4.8 (3.2–6.3)
FC2	C	0	39	39	1-2-5	0.048	0.835	8.25	0.467	2008: 759.8 (276.4–infinite)
FC3	C	0	54	54	1-2	0.037	0.829	7.60	0.867	2008: 591.7 (267.9–infinite)
FO1	O	20	14	34	1-2-5	0.070	0.795	7.37	0.333	2007: 30.6 (25.7–37.2); 2008: NN
FO2	O	12	7	19	1-2-6	0.029	0.795	7.20	0.133	2007: NN; 2008: NN
FO3	O	18	9	27	1-2-6	0.033	0.806	7.20	0.333	2007: 86.3 (61.1–142.8); 2008: NN
Fussingø total	C+O	64	123	187	1-2-5-6		0.850		2.867
Tipperne
TO1	O	19	65	84	1-9	0.033	0.799	7.05	0.533	2007: 115.1 (65.1–410.7); 2008: 329.1 (205.2–771.2)
Tipperne total	O	19	65	84	1-9		0.799		0.533

Abbreviations: C, conventional; CI, confidence interval; H_e, expected heterozygosity; N_e, population size; O, organic.
Cyt-b haplotype: haplotypes present for each sampling site/area. Values of F_is had no deviation from Hardy–Weinberg was found). Last column: N_e estimates and their 95% CIs (NN, not possible to retrieve an estimate of N_e). The parameters estimated in the last five columns are all based on microsatellite markers.

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