Effects of sequence alignment on the phylogeny of Sarcocystis deduced from 18S rDNA sequences

The family Sarcocystidae contains a wide variety of parasitic protozoa, some of which are important pathogens of livestock and humans. The taxonomic relationships between two of the genera in this family (Toxoplasma and Sarcocystis) have been debated for a number of years and remain controversial. Recent studies, from comparisons of 18S rDNA-sequence data, have suggested that Sarcocystis is paraphyletic, although a hypothesis supporting monophyly of Sarcocystis could not be rejected. The present study shows that the phylogenetically informative nucleotide positions within the 18S rDNA are primarily located in the regions that make up the helices in the secondary structure of the 18S rRNA. A phylogenetic analysis of 18S rDNA-sequence data aligned by secondary structure constraints, or a subset of the data corresponding to all nucleotides found in the helices, provide unambiguous evidence supporting monophyly of Sarcocystis.