This is an interesting opinion piece in TREE: http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(13)00212-7.
I particularly like the idea of localised phylogenetic trees i.e. understanding all of the phylogenetic relationships between organisms within a certain area. With next gen sequencing and environmental DNA technology (see http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2012.05542.x/abstract) this is going to be a real possibility. I agree with the authors, that this coupled with functional trait data will be a powerful method to understand local ecology and will greatly contribute to our general understanding of biology. Creating meaningful phylogenies is the challenge….