Here is an wonderful review paper on origin of eukaryotes by Bill Martin. Anyone interested in the topic should start with this paper.
Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote to eukaryote transition has a bioenergetic cause.
Dr. Martin starts with discussing how the tree concept is invalid in prokaryotes. He also reviews the current understanding on the major problems in biology. In addition to the paper itself, the review sections are excellent. You can learn a lot by seeing the comments from Graur, Koonin and others.