Understanding the chaos of plant adaptation

We study how complex changes in plant genomes drive coherent outcomes over evolutionary time in cultivated and wild plants. Plants have colonized nearly every conceivable terrestrial environment requiring the simultaneous tuning of thousands of traits to a particular niche. Despite this apparent precision, genome evolution is remarkably chaotic. The plant genome frequently undergoes massive expansion and contraction, does not necessarily contain the same basic set of functional information in the form of genes, and is subject to ongoing invasions by a host of parasitic elements. How these changes translate to increased fitness remains one of the most perplexing and important questions in biology. We deconstruct the principles of genome evolution using computational and statistical analysis of large-scale genomic datasets, simulation-based hypothesis generation, and phenotype focused wet lab and field experimentation. Our goal is to develop a mechanistic framework for predicting plant success in a changing environment relevant to natural and agricultural systems.

Lab Themes

Observing evolution in real time

Plant adaptation is typically studied by comparing  samples collected from different environments. We aim to gain a mechanistic understanding of the molecular underpinnings of the adaptive process through direct observation of evolution. To accomplish this goal, we study a one of a kind series of long-term agricultural experiments, the barley composite crosses. In these experiments thousands of barley genotypes were competed against one another for decades in several environments.  By directly observing evolution in the composite crosses we can link individual genetic changes to fitness across time and observe how they are combined into a single genome to facilitate adaptation.

The molecular basis of the rate of mutation

Plant genomes are astonishingly unstable over evolutionary time. With the passage of each generation,  mutations ranging from single base pair substitutions to large-scale chromosomal rearrangements can modify the genetic code. Changes in genome structure and content accumulate even after relatively short evolutionary periods, and the rate of genome content evolution is itself unstable. We use whole genome sequencing data to identify genes that alter the tempo and spectrum of mutation in natural plant populations and to understand how natural selection shapes the rate of mutation.

Lab Members

Oluwafemi Alaba

Postdoctoral Researcher

Ruth Sarahi Perez Alfaro

Assistant Specialist

Jill Marzolino

Graduate Student

Aimee Uyehara

Co-advised Graduate Student

Dr Dan Koenig


Joining the lab

Thank you for your interest in working with us!

Graduate Students: The lab accepts students from the Plant Biology; Genetics, Genomics, and Bioinformatics; and Ecology, Evolution, and Organismal Biology graduate programs. Please click the links to one of the programs to learn more. All three programs accept applications in the Fall of every year.

Postdoctoral Researchers: Please contact the lab PI to discuss the possibility of joining the lab. Please be specific in describing your research interests and how they may align with the lab's research. Postdoctoral researchers are encouraged to apply for fellowships, and the PI will be happy to assist in this process.

Undergraduate Researchers: We are always excited to host undergraduate researchers in the lab. Please contact the PI to discuss possible opennings.

Where to find us

University of California

Department of Botany and Plant Sciences

4412 Boyce Hall

3401 Watkins Dr.

Riverside, CA 92507

Lab Phone: (951) 827-4679

Office Phone: (951) 827-3212

email: dkoenig at ucr dot edu