The biogeography of microbial eukaryotes has long been debated, but few phylogeographic data have been available to assess whether protists tend to have ubiquitous or endemic distributions. We addressed this issue in the ciliate Tetrahymena thermophila, a highly successful model system in cell and molecular biology. We found that this species has a distribution that is restricted to the Eastern United States, with high diversity in the northeast and low diversity across the rest of its distribution. We find high levels of population subdivision, low rates of migration and significant isolation by distance, supporting the moderate endemicity model of protist biogeography. This restricted gene flow may be a result of small population size, which would reduce the probability of migration events, or the inability to establish after migration. This work lays the foundation for T. thermophila to become a valuable model system for studying population biology.

Genome architecture varies greatly among eukaryotes. This diversity may profoundly affect the origin and maintenance of genetic variation within a population. Ciliates are microbial eukaryotes with unusual genome features, such as separation of germline and somatic genomes within a single cell and amotitic division. These features have previously been proposed to increase the rate of molecular evolution in these species. Here, we assessed the fitness effects of genetic variation in the two genomes of natural isolates of the ciliate Tetrahymena thermophila. We find more extensive genetic variation in fitness in the transcriptionally-silent germline genome than in the expressed somatic genome. Surprisingly, this variation is not primarily deleterious, but has both beneficial and deleterious effects. We conclude that Tetrahymena genome architecture allows for the maintenance of genetic variation that would otherwise be eliminated by selection. We consider the impacts of reproductive strategies and the mechanism of sex determination on the structure of this variation.

Background:Introns constitute a large fraction of eukaryotic genomes and were once considered neutrally evolving sequences. Recently, however, some introns have been found to harbor sequences that are involved in a variety of regulatory and other functions and show evidence of purifying selection. Results: We examine the pattern of sequence divergence among ciliates in the genus Tetrahymena. We find that on average introns are more highly conserved than four-fold degenerate sites. Among introns, we find a correlation between conservation strength and both position rank in the gene as well as size of the coding region; the most conserved introns are found closer to the 5' end of the largest genes. Conclusion:Our results indicate that Tetrahymena introns experience selective constraint, possibly due to harboring regulatory sequences. We advocate for further experimental study of possible intron functions in Tetrahymena.