Table 3. Taxa and their accession numbers used for the different alignments and phylogenetic analyses.

Taxon	SSU rDNA	LSU rDNA	Hsp90 (Hsp+SSU)	Combined (Hsp+SSU)	Combined (Hsp+SSU+LSU)
Ciliates, apicomplexans & Perkinsus (outgroups)
Blepharisma **	M97909	x	AY390395	x	x
Cryptosporidium parvum	AF093489	AE040725	AY423866	included	included
Eimeria tenella	EF210325	x	AAB97088	included	x
Halteria grandinella	AY00744	x	AY391253	included	x
Paramecium tetraurelia	EF502045	x	AAG00569	included	x
Perkinsus marinus	AF126013	AY876319	AY391259	included	included
Tetrahymena bergeri	AF364039	x	AY391257	included	x
Tetrahymena pyriformis	EF070254	x	AAG00567	included	x
Theileria parva	AF013418	AF218825	AAA30132	included	included
Toxoplasma gondii	M97703	L25635.1	AAQ24837	included	included
Dinoflagellates & Oxyrrhis (ingroup)
Oxyrrhis marina	x	x	AAR27544	x	x
Akashiwo sanguinea	AF276818	AF260396	GU295192	included	included
Alexandrium tamarense	AB088333	AY438021	AM184118	included	included
Alex. tamarense UBC	x	x	GU295210	x	x
Amphidinium carterae	AF274251	AY455669	EU876701	included	included
Amphidinium mootonorum	GU295202	GU295205	GU295199	included	included
Crypthecodinium cohnii	M64245	FJ939575	AAM02974	included	included
Diplopsalis lenticula	x	EF152794	GU295193	x	x
Gymnodinium chlorophorum	AM184122	AF200669	AM184119	included	included
Gymnodinium fuscum	AF022194	AF200676	GU295194	included	included
Gymnodinium simplex	DQ388466	AF060901	GU295211	included	included
Heterocapsa triquetra	AF022198	AF260401	AAR27541	included	included
Karenia brevis	AF172714	AF200677	AM184117	included	included
Karenia mikimotoi	AF022195	AF200682	AM184120	included	included
Karlodinium micrum	AF172712	AF200675	AM184121	included	included
Kryptoperidinium foliaceum	AF274268	EF052684	AAV32830	included	included
Lessardia elongata	AF521100	x	AY391256	included	x
Noctiluca scintillans	AF022200	x	AB297471	included	x
Peridinium willei	AF274272	AF260384	GU295195	included	included
Polarella glacialis	AF099183	AY571373	GU295196	included	included
Prorocentrum micans	M14649	AF260377	AAR27546	included	included
Prorocentrum minimum	AY421791	AF260379	GU295201	included	included
Protoperidinium crassipes	AB261515	EF152846	GU295197	included	included
Protoperidinium steidingerae	x	DQ444231	GU295198	x	x
Protoperidinium sp.	x	x	GU295212	x	x
Scrippsiella trochoidea	AF274277	AF260393	GU295213	included	included
Spiniferodinium galeiformis	GU295203	GU295206	GU295214	included	included
Thecadinium kofoidii	GU295204	GU295207	GU295215	included	included
Thecadinium yashimaense	AY238477	GU295209	GU295200	included	included
Togula britannica UBC	x	GU295208	GU295216	included	included
Togula britannica	AY443010	AY455679	X	included	included

**B. intermedium for Hsp90; B. americanum for SSU rDNA.

Accession numbers indicated in bold denotes sequences generated in this study.