After an initial 3-week ‘bridge-to-research’ bootcamp, each cohort will collaborate on the assembly and annotation of genomes from three eukaryotic species. Bridging this project into individualized laboratory-based experiential learning, each trainee will also have an independent research role in one of the following projects or a related project in one of these labs.

Project 1: Functional importance of new genes in new traits.

  • Leadership Team: Dr. Yaowu Yuan and Dr. Elizabeth Jockusch
  • Research Objectives/Hypotheses: Identify “new genes” and assay their functions in ecologically significant new traits; in aggregate, this work will test broader hypotheses about the extent to which the origin of new genes and new traits are linked. This project is illustrated using two lineages, the angiosperm clade Asteridae and the insect clade Hemiptera.

Project 2: Importance of new versus toolkit genes in rapidly evolving genomic regions

  • Leadership Team: Dr. Barbara Mellone and Dr. Rachel O’Neill
  • Research Objectives/Hypotheses: Test two hypotheses about the evolutionary significance of taxonomically restricted genes and diversification of existing genes. In order to restore parity during chromosome segregation as centromere sequences diverge among closely related species:
    • Hypothesis B1: ‘New’ genes are more likely than ‘toolkit genes’ to be deployed.
    • Hypothesis B2: Toolkit genes with known function in chromosome segregation are more likely to be under diversifying selection.
  • This project is described for two complementary model systems, drosophilids (Mellone lab) and macropodid marsupials (O’Neill lab), with tractable phylogenies, available genome assemblies, and known centromere sequence diversity.

Project 3: The genomic basis for adaptation to extreme environments.

  • Leadership Team: Dr. Rachel O’Neill and Dr. Jill Wegrzyn
  • Research Objectives/Hypotheses: Test whether taxonomically restricted genes or diversification of toolkit genes are responsible for novel phenotypes enabling adaptation to extreme ocean environments.
    • Hypothesis C1: ‘New’ genes are more likely than ‘toolkit genes’ to be deployed in the development of novel traits.
    • Hypothesis C2: ‘New’ genes are more likely to be deployed in the development of novel traits than in the development of conserved traits.

Project 4: From phenotype to genotype and back: the genetic basis of novel traits

  • Leadership: Dr. Yaowu Yuan
  • Research Objectives/Hypotheses: Identification and functional characterization of genes regulating the development of ecologically important floral trait innovation.

Project 5: From phenotype to genotype: the genetic basis of pathogen resistance

  • Leadership Team: Dr. Jill Wegrzyn and Dr. Jennifer Koch (USDA)
  • Research Objectives/Hypotheses: Identification of novel genes underlying resistance to the invasive pathogen, emerald ash borer in green ash (F. pennsylvanica).
    • Hypothesis E1: Multiple loci, including those associated with uncharacterized genes, contribute to the chemical defense responses and lingering phenotype in green ash.