Research

I work at the intersection of evolutionary and molecular biology. I leverage model organisms to investigate big questions in evolution and to probe the specifics of how evolution can and does proceed. I primarily focus on the model yeast Saccharomyces cerevisiae, and I use both experimental evolution and analysis of existing species differences to test evolutionary theory. I believe that molecular-level insights are key in understanding evolution.

My work falls into two broad categories:

(1) The role of epistasis in adaptation and speciation

Epistasis, especially between beneficial alleles, can affect the predictability of evolution as well as contribute to reproductive isolation between populations. But how often does epistasis play a big role in adaptation? And how often are different evolutionary paths incompatible with each other?

My PhD work discovered that there is a surprising amount of negative epistasis between beneficial mutations from independent populations adapting to a common environment, with some mutant combinations even displaying the signature of postzygotic reproductive isolation (Bateson-Donzhansky-Müller incompatibilities; Ono et al. 2017, PLoS Bio).

I am now using a newly-developed technique (Bozdag, Ono et al. 2021, Curr Bio) to map nuclear gene-gene incompatibilities between two species of yeast – S. cerevisiae and its closest relative S. paradoxus – for the first time. This research helps build our understanding of how epistasis can contribute to reproductive isolation and speciation.

(2) Chromosome evolution in yeast

Yeast chromosome evolution is interesting in that there is wide-scale sequence divergence between species, but there are almost no fixed differences in ploidy or chromosomal arrangement. I have co-authored a mini-review on this paradoxical topic (Ono and Greig 2019, Curr Genet) and we explored this topic further, as well as other aspects of yeast species differentiation, in a full-length review (Ono et al. 2020, Annu Rev Microbiol).

During my PhD, I showed that adaptation to certain environments (in this case, high concentrations of copper) can occur through copy number changes and/or aneuploidy instead of nucleotide changes.

Also during my PhD, I found that differences in ploidy (haploidy vs. diploidy) can fundamentally change the adaptability of yeast. Haploids were able to adapt to a concentration of drug that diploids could not.

Using spore-autonomous fluorescent protein expression to quantify chromosome nondisjunction in both interspecific and intraspecific yeast hybrids, I helped show in my postdoc that sequence divergence is the primary reproductive barrier between S. cerevisiae and S. paradoxus (Rogers et al. 2018, PLoS Bio).

My past work has involved a variety of other systems and questions including:

How selectively bred and lab-created hybrid beer strains of yeast perform after multiple re-pitches.
Transcriptome evolution of cottonwood (Populus trichocarpa) in North America.
Discovering the genes involved in muscle cell extensions in Caenorhabditis elegans.
Characterizing genes involved in wax biosynthesis in Arabidopsis thaliana.

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