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. Poecilia mexicana and P. sulphuraria 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 using sulfide spring populations of Poecilia in three different river drainages to study parallel adaptation, adaptive trait divergence, differentiation in gene sequences, and gene expression patterns.
Genomic basis of behavioral and life-history traits in the self-fertilizing hermaphroditic killifish Kryptolebias marmoratus
The killifish (mangrove rivulus), Kryptolebias marmoratus, is the only known self-fertilizing hermaphroditic vertebrate. Rare males allow for infrequent outcrossing events. Wild-caught individuals are often naturally homozygous; each individual is essentially a recombinant inbred line. The unique nature of the killifish makes it an attractive vertebrate system, one that will provide many opportunities to answer questions about behavioral genetics and population genomics. We are interested in the evolution of sex determination, as well as questions about behavioral and other phenotypic differences. We have sequenced the genome of K. marmoratus, which lays the groundwork for developing K. marmoratus as a new model organism. The genome was published in 2016 in Genome Biology and Evolution. The research is in collaboration with Dr. Ryan Earley at University of Alabama.
Overwintering in polar environments
Transcriptional changes in response to 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 will reveal complex regulatory changes that occur in response to extreme physiological changes. Here’s a great video about the bear center and some of the research done at WSU: http://www.kcts9.org/programs/in-close/environment/fat-bears
De novo genome assembly of the Antarctic midge, Belgica antarctica
Coincident with my interest is adaptation to extreme environments, in collaboration with Dr. Dave Denlinger at Ohio State University, we have sequenced the genome of the Antarctic fly, Belgica antarctica. The goal of the research is to learn about desiccation and over-wintering and general genomic adaptation to the extreme environment of the Antarctic peninsula. In addition to providing a genomic resource for comparative studies of Chironomidae and Diptera, we have exciting results regarding genome size and transposable elements in these unusual flies. Specific research studying the gene expression response to dehydration and cryoprotective dehydration conditions was published in PNAS. The genome was published in Nature Communications. We are following-up on the genome assembly to study the population genomics of B. antarctica.
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 at least five 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 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). Arctic and Antarctic eelpouts both have type III AFPs; we are currently sequencing genomes to determine the precise evolutionary history of type III antifreeze proteins (AFPs).
Detecting natural selection
Inferences of demography and selection in Great Ape genomes
Great Ape genomes can lead to insight into the forces that have shaped variation in our own genome. Using over 80 fully sequenced great ape genomes, distributed across the four genera, we are identifying regions of the genomes that have been shaped by balancing and positive selection and to uncover ancestral demographic changes in great ape genomes. We recently published a project focusing on patterns of diversity and divergence in Western Gorillas, the manuscript is available on the bio archives and at MBE. We have also explored recombination rate evolution in great apes. The paper is available on the bio archives.