Table 1. Symbiodinium ITS2 sequences in adults and eggs of Montipora capitata, and ATP synthetase subunit β genotypes for the adult corals sampled at three sites on Moku O Lo’e Island, Kane’ohe Bay, Hawai’i.

Site	Year	Colony ID	Symbiodinium ITS2 sequence/s ADULTS	S	Symbiodinium ITS2 sequences/s EGG	S	PSI	Φ	p	G
BTN	2007	1	C315, C31.22, C212, C171	1	C32.28, C311	1	0.50	0.807	<0.001*	U
		8	D14, D1a4, D1a.12	1	D1a2, C312, C31.41, C21.21,C21.101, C17.21, C31	2	0.22	0.734	<0.001*	H
		10	D1a4, D13, D1a.12	1	C32.16, C312, C17.21	1	0.00	0.934	<0.001*	F
		11	D1a7, D11, D1a.11	1	D1a5, D1a.13, D12	1	0.72	−0.039	0.670	G
		12	D19, D1a4	1	C314, C17.22, D1a1,C211, C31.11, C31.41, C32.11	2	0.10	0.875	<0.001*	I
		18	D13, D1a3, D1a.12, D1a.21	1	C319, C211, C17.21	1	0.00	0.987	<0.001*	M
		19	C313, C213, D1a3, D11,D1a.11	2	C315, C21.112, D1a1,C17.21	2	0.38	0.157	0.072	N
	2008	8	D15, D1a4	1	C213, C31.12, D1a1,C21.31, C21.81, C21.51	2	0.11	0.856	<0.001*	H
		10	D15, D1a5, D1a.11	1	D14, D1a.13, D1a2, C21.111	2	0.69	0.006	0.339	F
		19	C212, C21.22, C21.11, C21.41,C21.71, C21.91, C21.111, C311	1	C213, C21.51, C21.61, C21.81,C21.111, C17.11, C32.21, D1a1	2	0.30	0.007	0.387	N
GL	2007	23	C17.25, C313, C171, C21.111 C3.11	1	C17.23, C313,C17.11, C211, C32.21	1	0.65	−0.045	0.912	T
		29	C318, C211	1	C315, C31.11, C31.21,C3.11	1	0.63	−0.055	0.527	D
		30	C214, C313,C17.22, C21.112	1	C313, C17.23, C171, C21.31, C31.11, C31.31	1	0.45	0.095	0.104	W
		35	D1a6, D13, D1.31,D1a.11	1	D1a5, D14, D1.31	1	0.86	−0.074	0.811	E
		36	C315, C212,C17.11, C31.41, D11	2	C317, C32.12,C31.11	1	0.50	0.004	0.414	P
		37	C17.26, C21.12,C211, C21.101,C31.21	1	C318, C17.21, C31.11	1	0.10	0.500	<0.001*	E
		39	C316, C31.12,C17.11, C211, C31.31	1	C316, C31.22, C31.11, C31.31 C31	1	0.73	−0.028	0.718	G
	2008	23	C17.12, C312,C211, C21.41, C21.81	1	C217, C171, C21.91, C31.21	1	0.14	0.044	0.241	T
		29	C217, C312	1	C219, C311	1	0.88	−0.057	0.578	D
		37	C215, C21.103, C21.21, C21.111,C311	1	C313,C212, C21.82, C21.31, C21.51, C21.111	1	0.38	0.060	0.121	E
PR	2008	B1	C214, C21.62, C21.102, C21.112, C31.41	1	C315, C212, C21.111, C3.11, D11, D1a.21	2	0.27	0.119	0.009	P
		B2	C214, C314, C21.112, C17.21	1	C17.24, C212, C21.41, C21.61,C21.71, C21.111, C311	1	0.45	−0.011	0.403	D
		B5	C213, C313, C21.72,C21.11, C21.111, C17.21	1	C214, C313, C21.21, C21.111,C17.21, D11	2	0.73	−0.018	0.944	B
		B6	C21.93, C312, C21.42, C17.11, C211, C21.101	1	C315, C17.23, C21.51, C171,C32.21	1	0.20	0.126	0.039	B
		B7	C214, C313, C17.11, C17.21, C21.61, C21.111	1	C313, C31.12, C31.22, D1.32, C21.111,C32.21	2	0.36	0.111	0.025	B
		B8	C315, C21.82, C211, C21.11, C21.111, C31.11	1	C216, C17.22, C312,C21.51, C21.91,C21.101	1	0.24	0.099	0.108	D
		P1	C314, C21.12, C21.22, C17.11, C211, C21.111	1	C214, C21.62, C312, C17.22,C21.51	1	0.27	−0.023	0.515	J
		P2	C313, C213, C21.113, C17.21, C21.41	1	C313, C213, C17.21, C21.61, D1a1	2	0.64	−0.003	0.430	L
		P5	C315, C31, C211, C21.71, C21.101, C21.111, C31.21	1	D1a.15, D14, D1a3, D1a.21	1	0.00	0.973	<0.001*	G
		P6	C313, C213, C21.32, C21.112, C21.21	1	C215, C313, C21.41, C21.111, C31	1	0.64	−0.055	0.839	B
		P7	D1a.17, D1a3, C211, C21.81	2	D1a4, D1a.11, D11, C211, C21.81	2	0.54	−0.085	0.641	N
		P9	C216, C21.51, C21.81, C311, C17.21	1	C214, C21.112, C21.21, C21.31,C21.81, C311, D1a.11	2	0.55	−0.002	0.514	A

Site abbreviations: BTN – Bridge to Nowhere, GL – Gilligan’s Lagoon, PR – Point Reef. Column Headings: S - number of clades/sample, PSI – Percent similarity index (between life stages), Φ - genetic differentiation, G – adult genotype. Numerals superscripts indicate the number of times a specific Symbiodinium ITS2 sequence was retrieved.