The microsporidia possess several apomorphic (defining) characters that distinguish them as a taxon: (i) the presence, in the spore stage, of a coiled polar filament, (ii) the posterior vacuole, (iii) the anterior polaroplast, and (iv) the diplokaryon (not present in all species). The advent of molecular analysis has radically changed how we classify the microsporidia, resulting in a major revolution in microsporidian taxonomy which includes the reassignment of many genera as well as the erection of new genera.Most modern microsporidian species descriptions include detailed microscopic and ultrastructural images, and many of the more recent descriptions also include a small subunit ribosomal DNA (ssrDNA) sequence analysis. Characters that have traditionally been used for taxonomic purposes include phenotypic, developmental, and ecological characters. While these characters provide a convenient and important means for classifying newly discovered species, the phylogenetic significance of taxonomic groupings based on these characters is not clear.With the advent of modern methods of systematics and, in particular, cladistic analysis (Hennig 1966), attempts were made to develop microsporidian phylogenies, but the significance of the characters commonly used for microsporidian classification remained elusive. The fortunate concurrent development of digital computers and DNA sequencing technology allowed for the analysis of microsporidian relationships using hundreds of characters each with four distinct character states. The use of molecular data for phylogenetic analyses has resulted in new insight into the relationships within and among most taxa, including the microsporidia.We have always thought that the logical way to integrate DNA sequence data and other characters used for microsporidian classification is to create molecular phylogenies of the microsporidia and then to place the nonmolecular data upon the tree (Baker et al. 1994) (Fig. 6.1). A complete analysis will be a monumental effort, but viewing a phylogeny with the nonmolecular characters added would help understand the evolution of the microsporidia, including the loss and gain of alternate hosts, host switching, loss and gain of sexual recombination, use of the pansporoblastic membrane, changes in the numbers of coils in the polar filament versus tissues infected, strategies of generalist versus specialist parasites, and changes in genome size and composition.When we add nonmolecular characters to a molecular phylogeny of the microsporidia, we see a lot of homoplasy (convergence, parallelism, and reversal). It is likely that the limited sizes of microsporidian genomes (Katinka et al. 2001) and the obligate parasitic nature of these organisms contribute to these homoplasies, as character states may be changing 204 Chapter 6 Phylogeny of the Microsporidia back and forth rather rapidly as the microsporidia recycle a limited number of character states in response to changes in host and host ecology.
STRUCTURAL, ULTRASTRUCTURAL, AND ECOLOGICAL CHARACTERS(s...