To examine relationships among spirotrich ciliates using multi-locus sequence analyses and to provide preliminary insights into molecular diversity within species, we sequenced the small subunit rDNA (SSU rDNA), 5.8S rDNA, alpha-tubulin and the internally transcribed spacer regions (ITS1 and ITS2) of the rDNA genes from seven choreotrich (Class: Spirotrichea) and three oligotrich (Class: Spirotrichea) taxa. Genealogies constructed from SSU rDNA and ITS sequences are concordant and broadly support current classifications based on morphology. The one exception is the freshwater oligotrich Halteria grandinella, which, as has been previously noted, falls outside of the clade containing the other oligotrichs. In contrast, analyses of alpha-tubulin sequences are discordant with traditional taxonomy and rDNA genealogies. These analyses also indicate that considerably more genetic variation exists among choreotrich and oligotrich genera than among stichotrich genera. To explore the level of genetic variation among individuals in temporally isolated populations, we collected additional samples of a subset of planktonic choreotrichs and oligotrichs and characterized polymorphisms in ITS1, ITS2 and 5.8S rDNA. Analyses of these data indicate that, at least for some ciliate lineages, DNA polymorphisms vary temporally, and that genetic heterogeneity underlies some very similar morphological types.


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