I spent Monday in London at The Royal Society for a discussion meeting on Phylogeny, extinction risks and conservation. As someone who is increasingly using comparative phylogenetic tools to ask how evolutionary history might influence conservation decisions, I took away at least three points (several more rattling in my mind at present):
(1) Measures of phylogenetic diversity are increasingly being used to inform conservation decisions (or at least that was the perception I got).
Perhaps the most notable way this is being done is through the EDGE (evolutionarily distinct globally endangered) programme. EDGE classifies species based on the product of their IUCN Red List category and their evolutionary distinctiveness (ED). ED is itself calculated by dividing the lengths of each branch in a phylogenetic tree by the number of species that subtend that branch. These values are then summed for all the branches from which a species is descended.
(2) Risk of extinction is fairly clustered within evolutionary lineages – and this can lead to rather large losses in phylogenetic diversity (PD). Losing PD may reduce ecosystem function and limit the range of biodiversity features that can respond to future change – if in fact there is an association between PD and function – though this is debatable.
This of course also assumes that closely-related species are more likely to go extinct because they share similar traits that make them more vulnerable to threats. Large mammals are an excellent example of such a group. But this might not be true for plants, particularly in areas with rapid diversification where species most classified as threatened are the recently-evolved ones that cluster within short branches at the tips of phylogenies.
(3) Systematists are developing great new tools for assembling dated phylogenetic trees.
We heard about two specific resources. The first was TimeTree, which is essentially a curated database collating all published estimates of divergence times among organisms. By visiting the website, you can instantly search for a divergence time between any two species and find all published estimates, allowing you to not only get a date but also a statistical distribution for that estimate. Unfortunately this means that its only as good as the primary literature and the curators’ ability to keep up with it. I tried it quickly for two of our NZ alpine species (Ourisia macrocarpa and Veronica odora) but was told that “No molecular data available for this query”, which was surprising considering they do exist.
The second resource we heard about was the Open Tree of Life. As the name says, it’s essentially trying to assemble a giant “tree of life” that will be continuously updated by the scientific community. This is a really nice complement to TimeTree because rather than focusing on branch lengths, it’s just concerned with synthesizing tree topologies. You can begin to explore the tree here.
Ecology in a Gingko-covered building 
Sounds like it was an interesting meeting!
I think the point you make about the association between PD and function is an important one. It seems to me that two distinct rationals are commonly put forward to justify the use of PD in conservation. On the one side, there is an argument to be made in favor of attempting to preserve evolutionary distinctiveness and evolutionary potential potential, which per se constitutes a valuable facet of biodiversity. On the other hand, many researchers (among which I count myself) have suggested using PD as a surrogate measure of functional diversity, and here I think the link becomes more tenuous. Although some degree of trait conservatism can be expected among closely related species, I think the correlation between PD and FD will inevitably depend on the traits in question and the phylogenetic resolution at which the analysis is being carried out.
Just to add to your list of online resources for accessing, quantifying and visualizing phylogenetic data, OneZoom (http://www.onezoom.org/) is another good one!