Reconstructing the evolutionary history of species is a fundamental component of research in my lab. First, I need a robust estimate of phylogeny to reveal phylogenetically (statistically) independent pairs of species on which to do analysis. Second, I use phylogeny estimates to reconstruct rates and geographical patterns of speciation. We use molecular markers to estimate phylogenies, including mitochondrial DNA sequences and amplified fragment length polymorphisms (AFLPs). AFLPs are particularly useful for resolving relationships among very closely related species. Future work will continue to use these molecular markers to estimate phylogenetic relationships within subgenera of darters.