I've been kicking a few ideas around for the independent project. Ideally, I was hoping to be able to analyze some of my own data. However, the data I collected last summer has already been analyzed as fully as I believe it could/should be. I'll be collecting more data over spring break, but I'm concerned that will be too late to begin the project.
Instead, I think I'll work with the niche breadth and complementarity dataset of Tom's, which I began working with last fall but was put on hold while we waited for some samples from Tom's former advisor. The dataset includes information on foraging height, arthropod species consumed, habitat, maneuvers used, substrate, et al. for about a dozen species of rainforest-dwelling insectivorous birds in Costa Rica (mostly in or near La Selva). We're testing to see whether there is an inverse relationship between habitat and food specialization in this guild resulting in niche diffferentiation. That is, we expect that species that consume similar diets will be separated spacially (by habitat, height, etc.) and vice versa. We intend to combine this with a phylogenetic analysis (perhaps phylogenetic independent contrasts? need to look into this further) to identify which differentiation (habitat vs. food) developed first - the prediction is that similar species will differentiate spatially fairly rapidly, while specialized food habits will take longer to involve.
We plan to test this using Mantel tests, which can be run using an add-on package for R which you can download from CRAN. I haven't looked into this yet, but had good success with the VEGAN package which I used last summer, and I expect this will be similar.