Yet some degree of uncertainty exists in the phylogenetic position of Perkinsus. Contrary to the long-held notion that dinoflagellates did not possess nucleosomes and canonical histones, genes of all four major histones have recently been found in dinoflagellates (for review see [21] ); however, dinoflagellate histones usually have unique sequences with insertions/deletions in several places, resulting long branches in the phylogenetic trees (Figures 8, 9 ). Comparing to dinoflagellates, P. marinus histones have typical eukaryotic sequences and group with apicomplexans in the phylogenetic trees. Besides histone trees, some other individual protein trees ( Figures S1D, S2A , 2B, 2C, S3B, S5C) also show an alliance of Perkinsus spp. with apicomplexans, in agreement with earlier morphological and cytological studies [2] . In rare cases, P. marinus is clustered with diatoms, apparently because the protein sequence was too short to provide strong support of any topology.