The Stoltzfus group uses computer simulations and statistical data analysis to explore models and to test hypotheses about the evolution of genes, proteins, and genomes.

The evolution of introns is a long-standing interest. The diversity of intron sites observed in a eukaryotic gene family is due primarily, not to inheritance of primordial introns, nor to "intron sliding", but to the gain of introns (Stoltzfus, et al., 1997). Therefore our research focuses on models of intron gain (e.g., Qiu, et al., 2004). Recent work includes a model of intron gain that accounts largely for non-uniformity in the positions of introns relative to protein structure (De Kee, et al, accepted).

A second major topic is understanding the role of mutation in evolution. Contrary to conventional wisdom, mutation is non-uniform, and its non-uniformities impose non-uniformities on evolution, even adaptive evolution. This influence raises many questions. What is the population-genetic mechanism involved (see Yampolsky and Stoltzfus, 2001)? Can we tease apart mutational from fitness effects? (Yampolsky and Stoltzfus, 2005) Can mutation biases cause long-term trends (Stoltzfus, 2006b)? What are the implications for evolutionary biology (Stoltzfus, 2006a)?

Software tools used in our research often relate to a specific project and have a short lifespan. However, we also have long-term goals of developing i) a database system to automate the evolutionary analysis of gene family data; ii) a software pipeline that extracts and collates sets of gene family data extracted from sequence databases; iii) glue code for improving evolutionary interoperability (Hladish, et al., 2007).