Research

Many unusual genomic and life history features of ciliates have made these microbial eukaryotes instrumental model systems in molecular and cell biology. We are exploiting these features to address questions in molecular evolution, mating system evolution, and population genetics.

Ciliate molecular evolution

Ciliates are defined by an unusual genome structure; two types of nuclei reside in each cell, one with a transcriptionally active somatic genome, the other with a germline genome that gets exchanged during sexual reproduction. During development, the somatic genome undergoes massive reorganization that involves chromosomal fragmentation and rearrangement and specific sequence elimination. These processes are analogous to, albeit more extensive than, DNA reorganization found in other eukaryotes (e.g. DNA elimination during antibody development in humans). Further, the degree of reorganization varies widely among ciliates. We are thus able to use ciliates to study the causes and consequences of developmentally regulated genome rearrangements (Zufall et al. 2005).

We have investigated the relationship between the extent of genome reorganization and rates of molecular evolution and find that ciliates experience faster rates of protein evolution than other eukaryotes, and within ciliates, those with more extensive genome reorganization have the fastest rates of protein evolution (Zufall et al. 2006)

To understand the forces acting on evolution of non-coding sequences, we are currently studying the patterns of molecular evolution in non-coding sequences restricted to the germline genome in comparison to those that remain in the somatic genome (Zufall and Katz 2007).

Mating system evolution

In addition to diversity in genomic architecture, ciliates also display a wide range of diversity in life history traits. For example, we have found that many aspects of ciliate mating systems have experienced rapid diversification (Phadke and Zufall 2009). Tetrahymena thermophila has a particularly unusual mating system, with 7 sexes (mating types) with probabilistic genetic determination, i.e. an allele at the mating type locus specifies the probability that an individual will develop into one of the 7 sexes. Using a mathematical model to determine the effects of this unusual mating system on sex ratios in natural populations, we find that this sex determination mechanism can result in stable skewed sex ratios, in contrast to the common even (1:1) sex ratio predicted by Fisher’s sex ratio theory. These results confirm that the uneven sex ratios found in natural populations of this species can represent equilibria (Paixao et al. 2011). We are currently testing the predictions and a major assumption (random mating) of this model using experimental laboratory populations of T. thermophila (more here).

Tetrahymena population genetics

Tetrahymena thermophila is a model system in cell and molecular biology, e.g. telomerase and ribozymes were both first discovered in this species. However, unlike its molecular biology, the population biology of this species has been relatively unexplored. In collaboration with Paul Doerder (Cleveland State University), we are studying the distribution and population structure of T. thermophila in order to determine patterns of gene flow, effective population sizes, mutation rates, and the frequency of sexual vs. asexual reproduction. T. thermophila appears to be restricted to the eastern U.S., however we are continuing to sample to determine the limits of its distribution.