This is not my idea, but I did find it useful to help answer your questions:
It is not enough to have just phylogeny on specie level. If you have phylogenetic tree with each branch corresponding to single species, and you can determine divergence time for lineages by means of node dating with molecular clock calibrated with fossil record, but this dating does not give you direct information on species age. The problem is that inside each linage there could be some extinct or non-discovered species, so the age of closest (most recent) node that separates any specie from the rest of the tree is not the same as specie age. This node age could be interpreted instead as maximum for range of possibilities for specie age. The real specie age could be much younger than this maximum limit value.
So you should analyze population from given specie, determine variability and calibrate molecular clock within specie limits. Potentially it is possible to determine age of last common ancestor of all populations that belongs to specie - that will be value close to the specie age, considering that there were no "bottleneck" events in specie evolution.
You can review methods used in Dick et al. (2013) though it seems that there are some issues with incomplete population sampling in this work.
Otherwise, this PDF should help you accomplish your goal (attached)
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