Investigating phylogenetic relationships within the Apicomplexa using sequence data: the search for homology.

Whether stated explicitly or not, all molecular studies that seek to infer "homologies" among sequences or that attempt to determine the "relatedness" of taxa based on sequence comparisons are evolutionary studies. The generation of a reliable evolutionary hypothesis based on molecular sequences is dependent almost exclusively on the ability to align sequences such that bases or amino acids in the same position of two sequences are positionally homologous (i.e., they share the same position in the gene under study). The selection of suitable gene targets (commonly 18S small subunit rRNA gene sequences in the Apicomplexa) and appropriate ingroup and outgroup taxa will affect the ability to align sequences unambiguously. Mathematically derived alignments based on local sequence similarity have been shown to be less reliable than alignments based on conserved secondary structures coupled with an analysis of compensatory base changes. Use of staggered sequence alignments through hypervariable regions of 18S small subunit rRNA gene sequences in which subsets of taxa are aligned independently may permit inclusion of more of the primary sequences with an associated increase in information content in the data set. The use of these highly variable regions is critical for determining the branching order of closely related terminal taxa in the phylum Apicomplexa.