Perkinsus is a distinct pre-dinoflagellate taxon As SL trans-splicing occurs in both basal (e.g. Amoebophrya and Oxyrrhis) and advanced (e.g. Alexandrium) lineages of dinoflagellates but not in apicomplexans and ciliates [8] , the two closest relatives of dinoflagellates, the occurrence of this distinct mRNA processing mechanism is considered a defining indicator for dinoflagellates [12] . The presence of SL RNA trans-splicing in Perkinsus spp. indicates its inclusion in or alliance with the phylum of dinoflagellates, in accord with previous molecular phylogenetic studies (e.g. [2] - [4] , [30] ). Likewise, our multi-protein phylogenies consistently show that P. marinus is related to dinoflagellates among other representative eukaryotes with moderate-to-strong bootstrap support. Among the many single-gene phylogenetic trees, the majority is in agreement with the concatenated protein trees. In all trees, P. marinus was positioned as the earliest divergent even when Oxyrrhis, a genus hypothesized to be a pre-dinoflagellate [32] or an ancient lineage [12] , was included. In addition, P. marinus was always placed basal to Amoebophrya, another ancient lineage of dinoflagellates.