Why we can not assume that any phylogenetic tree which is based on sequenced data express evolutionary events?

Phylogenetic relationships can give relative times in the past that species shared common ancestors but with no reference points to tie them to actual times or ecosystems. This group is shown to have diverged twice as far back as another. The tree is showing two species are more related to each other than they are to a third. Phylogenetic trees show degrees of relationship.
http://archive.peabody.yale.edu/exhibits/treeoflife/branches.html


As yet we have only an estimated rate of molecular change.
http://en.wikipedia.org/wiki/Molecular_clock
A multigene analysis is done as well as using the best estimates for a molecular clock to predict rates of change both within and across the lineages. In general they agree well with other dating methods like fossil calibrations that show relevant structural changes to constrain the upper and lower limits of when the event occurred.
A Molecular Timeline for the Origin of Photosynthetic Eukaryotes
http://mbe.oxfordjournals.org/content/21/5/809.full