Research

Genomics of Thermotolerance in Tomato Reproduction

We are part of the Genomics of Thermotolerance in Tomato Reproduction consortium (NSF Plant Genomes Research Program IOS#1939255) to understand the genomic basis of heat-tolerance during pollen tube formation in tomato (Solanum). We are using a combination of population (and meta-population) genomic variation, RNA-Seq differential expression experimentation, and biochemical analyses to reveal this mechanism. We will also use wild population variation and environmental data to understand the heat tolerance in the of natural populations. Read current work in Plant Cell and Current Biology and explore past work in Molecular Ecology and PLoS Biology.

African Acacia Eco-Evo-Genomics

We are leading the African Acacia Eco-Evo-Genomics consortium (NSF Bridging Ecology and Evolution DEBS#2105917) to explore the combined effects of fire, drought, grass competition, and herbivory on the evolutionary history and present ecological responses in the African acacias (Vachellia and Senegalia; Fabaceae). We are using a combination of population genomics, phylogenetics, ecological common garden, and RNA-Seq differential expression analyses to explore questions about the biology of these widespread and important savanna trees.

Genomics of Vertebrate Muscles

Our work focuses on understanding muscle-related gene expression through evolutionary analysis of conserved gene expression shifts, alongside sequence-based analysis of selection, protein structure, and gene family change. Read our past work in Proceedings of the National Academy of Sciences, and current work in PLoS Genetics. This work featured use of a new Phylogenetic Differential Gene Expression Tool (PhyDGET) developed by our group.

Comparative genomic data has revealed extensive gene flow, lineage sorting, and complex transcriptome expression patterns in a variety of systems. We are continuing to analytical approaches and computational methods to detect these patterns and how they overlap with speciation, complex trait adaptation, and patterns of sorting of ancestral variation. Current work focuses on continued development of molecular phylogenetic methods for detection of genomics discordance patterns, and expansion into understanding the relationship between molecular discordance and transcriptomic data. We are investigating these complex evolution histories using a combination of population genomic, coalescent, and phylogenetic techniques. Read example publication in PLoS Biology and Science, Systematic Biology, and The American Journal of Botany.