Phylogenetic trees are hypothesis and they can be tested by the following way:
1.) Phylogenetic trees, whether based on molecular techniques or from cladistic analysis of morphological characters are essentially independent of stratigraphy.
2.) Therefore, it is reasonable to compare the results of stratigraphy and phylogeny:
3.) If they (results) do not agree or lack congruence, then either the fossil record, or the phylogeny, or both are wrong.
4.) If the results are broadly congruent, then they are both probably telling the same story, and it can be assumed that it is the true story of the history of life.