Accumulation of Spontaneous Mutations in the CiliateTetrahymena thermophila

Abstract

Knowledge of the rate and fitness effects of mutations is essential for understanding the process of evolution. Mutations are inherently difficult to study because they are rare and are frequently eliminated by natural selection. In the ciliate Tetrahymena thermophila, mutations can accumulate in the germline genome without being exposed to selection. We have conducted a mutation accumulation (MA) experiment in this species. Assuming that all mutations are deleterious and have the same effect, we estimate that the deleterious mutation rate per haploid germline genome per generation is U = 0.0047 (95% credible interval: 0.0015, 0.0125), and that germline mutations decrease fitness by s = 11% when expressed in a homozygous state (95% CI: 4.4%, 27%). We also estimate that deleterious mutations are partially recessive on average (h = 0.26; 95% CI: -0.022, 0.62) and that the rate of lethal mutations is ,10% of the deleterious mutation rate. Comparisons between the observed evolutionary responses in the germline and somatic genomes and the results from individual-based simulations of MA suggest that the two genomes have similar mutational parameters. These are the first estimates of the deleterious mutation rate and fitness effects from the eukaryotic supergroup Chromalveolata and are within the range of those of other eukaryotes. MUTATIONS are the ultimate source of variation responsible for evolutionary change. Thus, knowledge of the rate and fitness consequences of spontaneous mutations is essential to understanding evolution (Charlesworth 1996). These parameters have been estimated in a handful of species and have provided many important insights into the evolutionary process (reviewed in Lynch et al. 1999;Halligan and Keightley 2009;Lynch 2010). For example, the observation that the deleterious mutation rate is less than one per genome per generation in several species suggests that the mutational deterministic hypothesis is insufficient to explain the widespread maintenance of sexual reproduction (Kondrashov 1988; Halligan and Keightley 2009). However, among eukaryotes, these mutational parameters have been estimated only in Opisthokonta (animals, fungi, and relatives) and Archaeplastida (red and green algae, land plants, and relatives), leaving the majority of eukaryotic diversity unexamined.Mutation accumulation (MA) is the best experimental tool with which to study mutation rates and fitness effects. Typically, MA experiments consist of allowing spontaneous mutations to arise and fix in parallel, replicate populations over many generations. Small populations are used to reduce the effectiveness of natural selection in determining the fate of new mutations. The quality of the estimates of mutational parameters derived from MA experiments is constrained by the biology of the organism used. Organisms with long-generation times experience a slow rate of MA [e.g., one experiment on Arabidopsis thaliana (Shaw et al. 2000), which has a generation time of 10 weeks, lasted only 17 generations], leading to imp...

Extremely Rare Polymorphisms in Saccharomyces cerevisiae Allow Inference of the Mutational Spectrum

“…MA experiments allow the accumulation of mutations under minimal selection conditions in a controlled lab environment, usually over many generations [1–4]. If following individual clonal lineages is not feasible, minimal selection conditions are usually achieved in unicellular cultures through repeated extreme bottlenecks, sometimes down to a single individual, such as in Saccharomyces cerevisiae [5–13], Dictyostelium discoideum [14], Arabidopsis thaliana [1], and Chlamydomonas reinhardtii [15,16].…”

Hidden genetic variation in the germline genome of Tetrahymena thermophila

“…Second, we find that GE lines from a single wild isolate often differ from each other in fitness, revealing the presence of heterozygosity in the micronuclear genome. Both of these results match our expectation that selection is limited in its ability to operate on mutations in the micronuclear genome that accumulate during asexual division (Zufall et al ., ; Long et al ., ), allowing allelic diversity to be maintained for long periods of time (Morgens et al ., ). Because this genomic architecture can protect both dominant and recessive alleles from exposure to selection, it will be interesting to assess whether there are more dominant deleterious alleles in this species compared to other taxa that have no mechanism to protect dominant alleles from selection.…”

Mutational Robustness of Morphological Traits in the Ciliate Tetrahymena thermophila

“…All MA and GE lines were from the experiment described in Long et al. () and were stored in liquid nitrogen. Cell lines included in this study were chosen to evenly sample all of the MA lines, with respect to fitness of the corresponding GE lines.…”

“…Cell lines were grown for 1,000 generations of asexual reproduction, during which spontaneous mutations accumulated in the micronucleus but were not expressed (Long et al. ). We then assessed the morphological and fitness effects of these mutations after conjugation, which results in expression of the micronuclear mutations in progeny cells (Prescott ).…”