Table 2 Results of three way ANOVAs for pH_ECM, pH_i (Fig. 1) and calcification, and two way ANOVAs for photosynthesis and respiration (Fig. 2).

Variable	Effect	df	MS	F	P	Post hoc
pH_ECM	pH_SW	3.00	1.56	242.66	<0.0001	8.1 > 7.8, 7.4, 7.2; 7.8 > 7.4, 7.2; 7.4 > 7.2
	L/D	1.00	0.55	85.48	<0.0001	Light > Dark
	Sp	2.00	0.25	38.33	<0.0001	SP > PD, AH
	pH_SW * lightdark	3.00	0.02	2.70	0.05
	pH_SW * species	6.00	0.02	2.48	0.03	See S 1
	lightdark * species	2.00	0.09	13.70	<0.0001	See S 1
	pH_SW * lightdark * species	6.00	0.02	3.34	0.01	See S 1
	Error	96.00	0.01
pH_I	pH_SW	3	0.22	107.86	<0.0001	8.1 > 7.8, 7.4, 7.2; 7.8 > 7.4, 7.2; 7.4 > 7.2
	L/D	1	0.04	18.79	<0.0001	Light > Dark
	Sp	2	0.55	271.63	<0.0001	SP > PD; SP > AH; PD > AH
	pH_SW * lightdark	3	0.00	1.27	0.294
	pH_SW * species	6	0.01	4.94	<0.001	See S 1
	lightdark * species	2	0.00	1.19	0.314
	pH_SW * lightdark * species	6	0.00	0.25	0.955
	Error	48	0.00
Calcification rate	pH_SW	3	8394.50	45.93	<0.0001	8.1 > 7.4, 7.2; 7.8 > 7.4, 7.2; 7.4 > 7.2; 8.1 = 7.8
	Light/Dark	1	57911.62	316.87	<0.0001	Light > Dark
	Species	2	16810.57	91.98	<0.0001	PD > SP; PD > AH; SP > AH
	pH_SW * lightdark	3	297.56	1.63	0.195
	pH_SW * species	6	899.73	4.92	<0.001	See S 1
	lightdark * species	2	1803.86	9.87	<0.0001	See S 1
	pH_SW * lightdark * species	6	831.49	4.55	<0.001	See S 1
	Error	48	182.76
Photosynthetic rate	pH_SW	3	0.16	0.24	0.87
	Species	2	7.49	11.22	<0.0001	AH > SP, PD
	pH_SW * Species	6	2.67	3.99	<0.0001	See results text
	Error	48	0.67
	Total
Respiration rate	pH_SW	3	0.37016	0.649083	0.587392441
	Species	2	6.42856	11.272649	<0.0001	SP > AH, PD
	pH_SW * Species	6	0.38002	0.6663842	0.677041204
	Error	48	0.57028

SP = Stylophora pistillata; PD = Pocillopora damicornis; AH = Acropora hyacinthus.

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