From what I've read the contortions of the geneolical tree are at a very basic, fundamental level...
As Doolittle indicates, from the base of the tree of life, it is not "tree-like." In the "bush" below (Figure 3), it is impossible to reconstruct such trees, as the observed distribution of characters create something which looks more like a tangled thicket or a bush. The three major "domains" of life--Bacteria, Archaea, and Eukarya have a distribution of characteristics which does not allow a tree to be constructed to describe their alleged ancestral relationships. This is due to a character distribution which is not what one would predict if they inherited their genes through common ancestry