Table 2. Description of Symbiodinium samples, host origin, and GenBank accession numbers of all DNAs used in this study.

Sample#	Cladea	ITS2b	Host origin	Isolate IDc	nr28S	elf2	cp23S	psbA	coI	cob
1	C	C1	Amphisorus hemprichii	2359X [S]	JN558040	JN557869	JN557969	JN557844	JN557891	JN557943
2		C90	Sorites sp.	1355X [S]	JN558045	JN557871	JN557975	JN557846	JN557893	JN557945
3		C91	Sorites sp.	2467X [S]	JN558048	JN557872	JN557978	JN557847	JN557894	JN557946
4		C15	Amphisorus hemprichii	2361X [S]	JN558042	JN557870	JN557972	JN557845	JN557892	JN557944
5	H	H1	Sorites sp.	2382X [S]	JN558051	JN557873	JN557981	JN557848	JN557895	JN557947
6		H1a	Sorites sp.	2350X [S]	JN558053	JN557874	JN557984	JN557849	JN557896	JN557948
7	F2	F2	Sorites sp.	206J [S]	JQ247043	JQ277946	JQ247052	JQ277935	JQ277957	JQ277979
8		F2a	Sorites sp.	215J [S]	JQ247044	JQ277947	JQ247053	JQ277936	JQ277958	JQ277980
9	F3	F3.2	Amphisorus hemprichii	2551X [S]	JQ247046	JQ277949	JQ247055	JQ277938	JQ277960	JQ277982
10		F3.1a	Amphisorus hemprichii	455X [S]	JQ247045	JQ277948	JQ247054	JQ277937	JQ277959	JQ277981
11	F4	F4.1	Sorites sp.	5121X [S]	JQ247047	JQ277950	JQ247056	JQ277939	JQ277961	JQ277983
12		F4.8	Sorites sp.	2692X [S]	JQ247048	JQ277951	JQ247057	JQ277940	JQ277962	JQ277984
13	F5	F5.1	Meandrina meandrites	RT-133 [C]	JN558063	JN557876	JN557996	JN557851	JN557898	JN557950
14		F5.1d	Sinularia sp.	Sin [C]	JN558069	JN557877	JN558000	JN557852	JN557899	JN557951
15		F1	Montipora verrucosa	Mv [C]	JN558066	JN557875	JN557997	JN557850	JN557897	JN557949
16		F5.2g	Montastraea faveolata	Mf [C]	JN558072	JN557878	JN558004	JN557853	JN557900	JN557952
17	B	B1	Plexaura kuna	704 [C]	JN558057	JN557879	JN557991	JN557854	JN557901	JN557953
18		B2	Eunicea flexuosa	Pflex [C]	JN558060	JN557880	JN557993	JN557855	JN557902	JN557954
19		B19a	Plexaura kuna	703 [C]	JN558055	JN557881	JN557987	JN557856	JN557903	JN557955
20	I	I1	Sorites sp.	OHU7 [S]	FN561559	JQ277955	FN561563	JQ277944	JQ277966	JQ277988
21		I2	Sorites sp.	OHU3 [S]	FN561560	JQ277956	FN561564	JQ277945	JQ277967	JQ277989
22	D1	D1	Acropora sp.	A001 [C]	JN558075	JN557882	JN558007	JN557857	JN557904	JN557956
23		D1a	unknown anenome	Ap02 [C]	JN558078	JN557883	JN558010	JN557858	JN557905	JN557957
24	D2	D1.1	Marginopora vertebralis	2485X [S]	JQ247049	JQ277952	JQ247058	JQ277941	JQ277963	JQ277985
25		D1.2	Haliclona koremella	HK [C]	JN558081	JN557884	JN558013	JN557859	JN557906	JN557958
26	G1	G2	Marginopora vertebralis	2479X [S]	JN558089	JN557885	JN558019	JN557860	JN557907	JN557959
27		G2b	Marginopora vertebralis	3590X [S]	JN558088	N/A	JN558017	JN557861	JN557908	JN557960
28	G2	G2.1*	Cliona orientalis	OR2 [S]	JQ247050	JQ277953	JQ247059	JQ277942	JQ277964	JQ277986
29		G2.2*	Cliona orientalis	RN3 [S]	JQ247051	JQ277954	JQ247060	JQ277943	JQ277965	JQ277987
30	E	E1	Anthopleura elegantissima	RT-383 [C]	JN558084	N/A	JN558015	JN557862	JN557909	JN557961
31	A	A2_ 1	Bartholomea annulata	RT-23 [C]	JN558097	JN557887	JN558029	JN557864	JN557911	JN557963
32		A2_ 2	Gorgonia ventallina	RT-89 [C]	JN558100	JN557888	JN558032	JN557865	JN557912	JN557964
33		A3	Pseudoplexaura porosa	725 [C]	JN558091	JN557889	JN558021	JN557866	JN557913	JN557965
34		A13	Plexaura kuna	708 [C]	JN558094	JN557886	JN558027	JN557863	JN557910	JN557962
Outgroup1	G. simplex	N/A	N/A	CCMP419 [C]	JN558103	JN557890	JN558033	JN557867	JN557914	JN557966
Outgroup2	P. beii	N/A	N/A	PB-1 [C]	JN558106	N/A	N/A	N/A	JN557915	JN557967
Outgroup3	P. glacialis	N/A	N/A	CCMP1383 [C]	JN558108	N/A	JN558036	JN557868	JN557916	JN557968

Notes.

^aLetters A to H refer to the Symbiodinium clades, and lineages D1-D2, F2-F5, and G1-G2 are the Symbiodinium sub-clades.

^bAlpha-numeric names correspond to Symbiodinium ITS2 rDNA molecular taxonomy sensu Pochon et al. (2007). Letters correspond to the Symbiodinium clades, and numbers correspond to a specific ITS2 sequence. All samples are genetically distinct, except for Symbiodinium A2, which was found in two distinct cultures and referred here to as A2_ 1 and A2_ 2. Types D1.1 and D1.2 corresponds to the symbionts of the foraminifer M. vertebralis and the sponge Haliclona koremella, respectively (see Pochon et al., 2007 for details), and were previously described as belonging to Symbiodinium sub-clade D1 (Garcia-Cuetos, Pochon & Pawlowski, 2005; Pochon & Pawlowski, 2006), but reclassified here as sub-clade D2. Sub-clade D1 contains Symbiodinium strains that are commonly associated with Scleractinian corals, such as symbiont ITS2 types D1 and D1a (Stat & Gates, 2011). Types G2 and G2b belong to sub-clade G1 as shown in Pochon et al. (2012).

^cSamples ID are followed by [C] if DNA was extracted from a culture, or [S] if extracted from a symbiotic host. All GenBank accession numbers starting with the letters ‘JQ’ were obtained in the present study.

^*Indicates new ITS2 sequences; novel types G2.1 and G2.2 belong to sub-clade G2 following Hill et al. (2011).