A primary focus of the current projects in our lab is on investigating evolutionary outcomes of four key classes of genomic rearrangements: duplications, deletions, inversions, and translocations.
The goal of these projects is to answer two major questions:
1) What are the functional outcomes of each class of rearrangement?
2) What role does natural selection play in these functional outcomes?
Most of our recent work has concentrated on gene duplication, an important source of new genetic material that is thought to play a central role in the evolution of functional innovation. In the simplest scenario, gene duplication results in two identical copies of a gene. The most common fate of young duplicate genes is nonfunctionalization, in which one copy accumulates deleterious mutations and is pseudogenized. However, functional duplicates may be preserved via one of four processes: conservation, neofunctionalization, subfunctionalization, or specialization. Under conservation, both copies retain their ancestral functions. Under neofunctionalization, one copy retains its ancestral function, and the other acquires a new function. Under subfunctionalization, the ancestral function is subdivided between copies. Finally, under specialization, neofunctionalization and subfunctionalization act in concert, resulting in two copies that are functionally distinct both from each other and from the ancestral gene.
Our projects on gene duplication aim to classify these retention mechanisms and assess the role of natural selection in evolution after gene duplication. In particular, we have been designing novel computational and statistical approaches to quantify gene expression divergence and classify retention mechanisms after duplication. By combining these classifications with evolutionary and population-genetic inferences, we have been assaying the types, strengths, timing, and genic targets of natural selection after gene duplication. We are performing these analyses in species from several diverse taxonomic groups, enabling us to make general predictions about the principles of evolution by gene duplication across the tree of life.