The Institute of Ecology and Evolution, University of Oregon IEE University of Oregon

Ecological & Evolutionary Functional Genetics and Genomics

We still have an incomplete understanding of how changes in allele frequencies affect distributions of developmental processes in natural populations, and, once evolved, how these developmental programs alter subsequent evolutionary change. The goal of our lab is to fill this gap in our knowledge, and provide answers for numerous evolutionary questions that remain incompletely or poorly answered:

  • How large are evolutionary steps, in terms of number of genes and their allelic effects?
  • What is the molecular, genetic and developmental basis of phenotypic parallelism and convergence?
  • How does genetic architecture, interacting with the environment, affect the input of new genetic variation and response to selection?
  • To what extent do genes and pathways that segregate variation within species also contribute to divergence among higher-level taxa?

We use a variety of molecular, developmental, population and quantiative genetic approaches to address these questions. Most of our empirical work focuses on the threespine stickleback, Gasterosteus aculeatus, and members of the closely related family Syngnathidae. Threespine stickleback fish are restricted primarily to marine, brackish and coastal freshwater habitats of the northern hemisphere. Freshwater stickleback populations have undergone rapid diversification in many recently deglaciated regions, giving rise not only to a diverse array of phenotypes, but also to new species.

Much of our work uses experimental crosses to map the genetic basis of traits, functional analyses to understand the developmental roles of identified loci, and comparative genomic and gene expression studies to understand divergence among species. We have also helped develop high throughput genotyping techniques using next generation Illumina sequencing to examine genome-wde patterns of divergence. In order to understand the genetic basis of divergence among lineages, our laboratory is also styudiying the formation of highly modified bony structures of pipefish and seahorses, members of the order Gasteriformes along with stickleback.

Lastly, we are studying the evolution of duplicated genes and genomes, and their relationship to organismal diversity. Half of all vertebrate species are teleost fish, and a whole-genome duplication event at the base of the ray-fin fish may have played a significant role in the teleost radiation.

Cresko Laboratory, Center for Ecology and Evolution at the University of Oregon
Lab News

May 2015 - Sophie Sichel presents at the U of O undergraduate symposium.

April 2015 - John Crandall is awarded a fellowship through the OURS Program and the University of Oregon Department of Biology to work with genetic mapping of divergent Stickleback populations as a tool to investigate recombination and chromosomal inversions.

January 2015 - Thom Nelson is awarded a Doctoral Dissertation Improvement Grant (DDIG) from the NSF to use genome-wide coalescent analyses to identify adaptation by standing genetic variation.

November 2014 - Sophie Sichel won an award for her oral presentation at ABRCMS in San Antonio, Texas.

October 2014 - Thom Nelson gives an invited talk called, 'Reconstructing the Past; Five years to K, and just a bit further' honoring his former advisor at Kalamazoo College.

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