Gene duplication occurs when multiple copies of the same gene are created and retained within an organism's genome. It is believed to play a key role in the evolutionary process by creating innovation in organism traits. Therefore, understanding how evolution acts on duplicate genes will provide key insights into how complex traits and novel forms have arisen. The main goal of this project is to determine the evolutionary forces responsible for the retention of duplicate genes in an organism's genome. The researchers will test the specific hypothesis that the evolution of functional duplicate genes (those that have a new function) is primarily a consequence of natural selection. Scientists have long thought this to be the case, but have never been able to experimentally test this hypothesis. This project uses an innovative method that allows this hypothesis to be tested for the first time. Results will help to understand how organism traits evolve within and among species. The award will have multiple broader impacts on the scientific community by supporting the training of undergraduate and graduate students, development of open source computer software, and dissemination of research findings in open access publications. Additionally, the researchers will design and teach courses on bioinformatics and genomics to local K-12 students at the Science-U camp hosted by Pennsylvania State University each summer. Curricula developed for these courses will also be made freely available on a website for teachers.
The proposed research will examine the impact of natural selection on duplicate gene functions via both sequence- and expression-level approaches. The researchers recently developed a phylogenetic approach for identifying duplicate genes with novel functions by quantifying differences between their gene expression profiles in closely related species. Application of this method to spatial gene expression profiles in Drosophila revealed that most young duplicates possess new functions, and that acquisition of new functions occurs rapidly. Conversely, in mammals, most young duplicates retain their ancestral functions, and functional divergence occurs more gradually. The contrast in functional divergence rates between duplicate genes in these lineages is reminiscent of the faster sequence-level evolution observed in Drosophila relative to mammals. Researchers will test the hypothesis that natural selection also plays an important role in acquisition of new functions by duplicate genes. Researchers will apply a combination of traditional sequence-based, as well as innovative, expression-based tests for natural selection on duplicate genes. The objectives of these analyses will be to elucidate the role of natural selection in functional divergence of duplicate genes, and to examine differences in selective forces acting on duplicates in populations of different sizes, over evolutionary time, and with varying levels of functional divergence.