Properly addressing comparative questions can often feel daunting, because broad and robust base phylogenies are difficult to find. Fortunately, in recent years there have been a variety of initiatives to make this data more accessible, and techniques to approach this on your own. If you are interested in reconstructing a broad avian phylogeny I suggest visiting the the Tree of Life Web Project and Early Bird. The Tree of Life Web project is not only accessible through the web, as its name suggests, but also through programs such as Mesquite and R. Finding published matrix representation with parsimony (MRP) trees is another good place to start.
Knud A. Jønsson and Jon Fjeldså produced a massive super tree for 1724 oscine birds (2006) (accessible here). This has been a valuable resource for researchers since its publication, but unfortunately the tree was never created in a usable format (it was simply an Adobe image file). This has limited its applicability. I transcribed this phylogeny, with that of the Tree of Life project for a very comprehensive avian phylogeny (6704 species). There have been a number of improvements to the general patterns reported in Jønsson and Fjeldså (2006) that will substantially add to this number. With some additional effort, a number of comprehensive phylogenies can bulk up specific avian groups.
I will continue to cultivate this tree, and encourage those interested in helping or using it to contact me directly (dhanley@uoguelph.ca).
