Twenty-two ribosomal proteins were obtained for Perkinsus and various organisms; Maximum Likelihood (ML) trees inferred from the individual sequences gave varied tree topologies (Figures S1, S2, S3, S4). In general, P. marinus, dinoflagellates, apicomplexans, and ciliates formed a monophyletic group, while in several cases the heterokont diatoms, the closest relative of the alveolates, branched with some of the alveolate lineages, but without bootfostrap support. Perkinsus spp. allied with dinoflagellates in some cases (e.g. Figures S1C, 1F, S2E) , and with apicomplexans (e.g. Figure S1D ) or the diatoms (e.g. Figure S2D ) in others, often with weak or no bootstrap support in these cases, indicating an unstable phylogenetic affinity. In contrast, NJ trees based on the 12 conserved protein sequences (actin, b-tubulin, GAPDH, atubulin, centrin, HSP90, EF1-a, ADP ribosylation factor, TIF5A, SmD1, cytochrome C and 14-3-3) produced similar tree topology, with P. marinus clustering with dinoflagellates in most of the cases (Figures S5, S6) . For mt genes, Perkinsus spp. clustered with ciliates in COB tree, while allied with dinoflagellate/apicomplexan cluster in COX1 tree ( Figure 6 ). When the concatenated RP sequence data (3,142 aa) was used, analyses using NJ, ML, and MB produced trees of similar topologies in which P. marinus branched at the base of the dinoflagellate clade (Figure 7) . This was true for the analyses both without ( Figure 7A ) and with ( Figure 7B ) the ancient dinoflagellate lineage Oxyrrhis marina. The only exception was the MB tree in which P. marinus was allied with the clade of apicomplexans ( Figure 7A) . Similarly, when the other 12 protein sequences were concatenated (3,879 aa) the consensus tree inferred from the three algorithms showed the close relationship between P. marinus and dinoflagellates ( Figure 7C ). In most of these concatenated trees, the alliance of P. marinus and dinoflagellates was supported.