Phylogenetic methods are among the most important tools in comparative physiology because these allow us to use evolution as a natural experiment in traits of interest such as body size, diet, habitat, performance, and behavior. Hummingbirds are particularly useful organisms for studying the biomechanics and neural control of flight not only because of their extraordinary abilities, but also because they are one of the most diverse avian families with over 320 species. Hummingbirds vary in body size by an order of magnitude and live in a variety of challenging habitats including high elevations (up to 5000 m), extreme latitudes (from 55°S to 61°N), arid deserts, and tropical rainforests. We participate in a collaborative effort led by Jim McGuire (UC Berkeley) to generate a comprehensive phylogenetic hypothesis for hummingbirds with dense taxon sampling. Our first analysis (Altshuler et al., 2004) involved two nuclear and one mitochondrial gene for 75 ingroup (hummingbirds) taxa and one outgroup (swift) taxon. We confirmed the placement of most of the major lineages proposed from a previous study by Rob Bleiweiss and colleagues (1997), but we also discovered a novel clade of basal hummingbirds (Topazes) and a unique evolutionary position for the giant hummingbird (Patagona gigas). In our subsequent study (McGuire et al., 2007), we expanded the analysis to four genes for 151 hummingbirds to conduct a phylogeographical analysis, which revealed that hummingbirds originated in the South American lowlands and that there have been at least 30 independent invasions of other primary landmasses. In an additional paper, we proposed a formal phylogenetic taxonomy for hummingbirds (McGuire et al., 2008).