Research
The major themes in the lab are:
- Genome evolution
- Adaptation to extreme environments
- Conservation genomics
- Overwintering in cold environments
Genomic changes underlying adaptation
to extreme environments
Extreme environments impose strong selective pressures on phenotypes and provide a context within which to explore specific questions about differentiation and adaptation. Multiple species and populations of Poeciliids have independently colonized multiple springs with toxic concentrations of hydrogen sulfide (H2S). The sulfide spring fish provide a unique opportunity for an integrative approach to studying adaptation because: 1. the environmental gradients are clearly defined and replicated, 2. the environmental gradients are physiologically explicit, with known biochemical consequences; and 3. the divergence between populations is recent. Together with Dr. Michi Tobler at Kansas State University, we are studying multiple sulfide spring populations and related non-sulfidic populations in the family Poeciliidae to understand parallel adaptation, adaptive trait divergence, differentiation in gene sequences, and gene expression patterns. We are taking a multi-omics approach to determine the relative contributions of different regulatory processes to the convergent phenotypes we observe in the sulfidic species.
Antifreeze proteins in polar fish
One mechanism that polar species have evolved to survive in sub-freezing temperatures are antifreeze proteins (AFPs). AFPs have independently evolved multiple times in fish. AFPs interact with the leading edge of a forming ice crystal to reduce the freezing point and are identified as one of the key innovations that have lead to the radiation of species throughout the Southern Ocean. We combined Expressed Sequence Tag (EST) sequencing and proteomic analyses to demonstrate that antifreeze protein genes are under diversifying selection and all isoforms are expressed and translated in a single individual (Kelley, Aagaard et al. 2010 J Mol Evol). Eelpouts are globally distributed and Arctic and Antarctic eelpouts both have type III AFPs, which makes for a phenomenal global perspective on genome evolution.
We are sequencing, assembling and comparing the genomes of multiple polar and non-polar fishes, to clarify how rates of evolution vary in polar environments, identify general trends that shape the adaptive trajectories of cold-adapted marine fishes, and determine how functional differences shape the evolution of novel proteins by measuring thermal hysteresis activity of multiple AFP isoforms to link genotype to phenotype.
Functional genomics of seasonal
changes in brown bears
The brown bear experiences three major physiological shifts during a year, including active season, hyperphagia and hibernation. In collaboration with Profs. Charlie Robbins, Heiko Jansen and Omar Cornejo we are studying the transcriptional response to seasonal changes in brown bears. RNA-sequencing of multiple tissues has revealed complex regulatory changes that occur in response to extreme physiological changes. Currently, we are using additional functional genomics datasets, including single-cell resolution RNA-seq, ATAC-seq, and ChIP-seq, to better understand the regulation of key hibernation phenotypes. Ultimately, understanding the molecular mechanisms of hibernation in bears may enable the development of new treatments for human disease and injury.
Other ongoing projects in the lab include using functional, population, and evolutionary genomic analyses to understand the role of regulatory sequence evolution in the gain and loss of hibernation phenotypes across bears. This work aims to better understand how complex physiological adaptations evolve in vertebrates.
Conservation genomics of brown bears
Brown bears have experienced rapid population declines and ecosystem fragmentation in North America and have been listed as Threatened under the Endangered Species Act since 1975. In collaboration with Ellie Armstrong at UC Riverside, the US Geological Survey, and the US Fish and Wildlife Service, we are investigating the effects of this rapid population decline and recent conservation efforts on genomic diversity and population dynamics across North American brown bears. This work is funded by the Partnership to Advance Conservation Science and Practice program, a collaboration between NSF and the Paul G. Allen Family Foundation.
Currently, we are analyzing modern and historic samples to understand genomic diversity, population demography, and gene flow across North American brown bear populations. Using these data, we are building a range-wide database of genetic ancestry for North American bear populations and developing genetic tools (e.g., SNP panels) that can be used to monitor populations and inform management decisions. Using this large population genomic dataset, we are also investigating how the genomic landscape of diversity and relatedness of North American brown bears relates to features of life history, ecology, and environment that vary across the diverse ecosystems that they inhabit.