Transposons Early in my career I became intrigued by the idea that so-called junk DNA, especially retroviral-like sequences, could contribute to gene evolution. Retrotransposons are the most abundant and wide spread class of eukaryotic transposable elements. For example, retrotransposons constitute ~10% of the Drosophila genome, ~40% of the human genome, and >90% of the genome of some lilies.

I’m working to understand the mechanisms underlying retrotransposon evolution and the impact these elements have on the evolution of the host genomes in which they reside. Using a number of bioinformatic techniques I have identifed and investigated endogenous retroviruses interacting with neighboring genes in the genomes of nematode worm, fruit fly, and mouse (C. elegans, D. melanogaster and M. musculus, respectively). Currently, I am identifying and characterizing the repeat content of the newly sequenced plant Mimulus guttatus.

Duplicate gene evolution Gene duplication may promote the evolution of novel gene functionality by relaxing selection and allowing greater mutation (divergence) between the duplicate genes. Generally, gene duplication may allow new functionality to evolve due to relaxation of selection on or both members of the pair, leading to greater mutation (divergence) between the duplicate genes.

One measure of divergence between two duplicate genes is the amount of change in transcription (gene expression). A number of large gene expression datasets are now freely available, and I have used these datasets to test models of duplicate gene retention in the plant Arabidopsis thaliana (Ganko, Meyers, and Vision 2007). Supporting previous studies, the divergence in expression profile appears to occur at or shortly after duplication. However, contrary to findings from other eukaryotic systems, there is a strong positive relationship between expression divergence and changes to the translated protein (nonsynonymous substitutions). Additionally, expression divergence is often highly asymmetric (demonstrated by the A and B genes on the right), with one copy predominantly expressed in all conditions sampled. This is especially true in non-polyploid pairs with little sequence divergence, a result at odds with the predictions of the model of duplicate gene preservation by subfunctionalization.

Genome rearrangements While transposons are known to move pieces of DNA around a genome, occasionally DNA will be transposed in the absence of a transposon. Due to difficulty in identifying such rearrangement, the mechanism and consequences (gene expression, genetic incompatibilites) are unknown. For the past several years I’ve been part of a collaborative project developing a microarray methodology to systematically identify and investigate the consequences of small genomic rearrangements (~500-1000bp changes). We plan to use this technology to address the mechanisms and evolutionary effect of small chromosomal rearrangements from one generation to the next.