Table 2 Genetic diversity indices and Neutrality test from mtDNA HVRI, COI and Nuclear AK and ODC sequences.

		HVRI (n = 251, 451 pb)							COI (n = 290, 846 pb)				AK (n = 231, 532 pb)				ODC (n = 277, 701 pb)
Species	Location	H	S	Hd	π	∏	D	Fs	H	S	Hd	π	H	S	Hd	π	H	S	Hd	π
E. schlegeli	MACQ	11	18	1.00	0.013	5.64	−0.37	−6.45***	3	2	0.38	0.0006	14	17	0.96	0.008	5	6	0.69	0.003
White-faced¹	MARI1	2	5	0.67	0.008	3.33	0.00	2.36	1	0	0	0	2	4	0.33	0.002	3	4	0.68	0.003
E. chrysolophus	CROZ	13	25	0.90	0.008	3.73	−1.93	−6.27**	5	4	0.51	0.0006	19	20	0.94	0.007	8	9	0.69	0.003
	MARI	16	34	0.97	0.012	5.20	−1.76	−7.39**	8	7	0.44	0.0005	25	17	0.97	0.006	8	8	0.65	0.003
	KERG	13	36	0.99	0.019	8.25	−1.17	−5.08*	5	4	0.48	0.0006	21	22	0.95	0.008	8	8	0.70	0.003
	BOUV	9	26	0.96	0.021	9.13	0.13	−1.10	3	2	0.44	0.0005	16	15	0.98	0.008	7	8	0.86	0.004
	BIRD	5	24	1.00	0.026	11.60	0.05	−0.14	2	2	0.26	0.0005	12	14	0.95	0.007	9	9	0.76	0.002
	ELEP	9	26	0.98	0.019	8.31	−0.46	−2.09	4	3	0.45	0.0005	14	14	0.97	0.007	8	7	0.82	0.003
E. moseleyi	NIGH	15	19	0.98	0.007	3.14	−1.67	−11.63***	1	0	0	0	9	8	0.81	0.003	3	2	0.10	0.0002
E. moseleyi	AMST	16	29	0.94	0.010	4.63	−1.45	−5.96*	3	2	0.16	0.0002	8	8	0.70	0.001	4	4	0.28	0.0005
E. filholi	CROZ	17	27	0.96	0.015	6.70	−0.32	−6.01*	5	7	0.59	0.0024	13	13	0.88	0.003	7	7	0.57	0.002
	MARI	16	27	0.99	0.018	7.99	−0.00	−8.03**	4	4	0.69	0.0019	7	8	0.79	0.003	9	8	0.65	0.002
	KERG	14	25	0.92	0.013	5.69	−0.70	−3.94	5	8	0.68	0.0026	13	13	0.86	0.003	7	6	0.63	0.001
	MACQ	7	17	1.00	0.014	4.15	−0.68	−2.55	3	5	0.73	0.0029	4	6	0.68	0.003	8	10	0.84	0.004
E. chrysocome	FALK	8	15	0.89	0.007	3.20	−1.53	−2.36	5	6	0.51	0.0010	7	10	0.86	0.007	5	5	0.80	0.003
	SANJ	4	14	0.69	0.008	3.61	−1.19	0.57	3	3	0.60	0.0010	8	13	0.89	0.009	8	8	0.76	0.003
	FRAN	10	25	0.92	0.009	4.07	−1.82	−4.60*	4	4	0.25	0.0004	22	13	0.92	0.008	8	7	0.76	0.003
	TERH	6	15	0.89	0.010	4.57	−1.07	−0.67	2	2	0.29	0.0006	5	9	0.89	0.008	7	7	0.63	0.002

H the number of haplotypes, S the number of polymorphic sites, Hd the haplotype diversity, ∏ the pairwise difference and π the nucleotide diversity. D Tajima’s test (D) and Fs, Fu’s test. ¹White-faced penguin from Marion could be royal or macaroni penguins with white-faces or hybrids. *p < 0.05, **p < 0.01, ***p < 0.001.

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