The universal tree of life depicts the evolutionary relationships of all living things by grouping them into one of three Domains of life; the Archaea (archaebacteria), Baaeria (eubacteria) and Eucarya (eukaryotes). The "canonical universal tree" topology is actually a composite of phylogenies based on single ribosomal RNA gene trees and duplicated, paralogous protein gene trees. The salient features of the canonical universal tree are: (1) all three Domains are mono/holophyletic; (2) Archaea and eukaryotes are sister groups with the Bacteria at the root; and (3) thermophilic bacteria are the earliest evolved bacterial lineage. Recent studies based on new genome sequence data suggest that the universal tree has been "uprooted" by extensive horizontal gene transfer (HGT). However, the scope of HGT is still unclear and reports of extensive trans-Domgdn HGT based on sequence homology, without supporting phylogenetic analysis, need careful reconsideration. Phylogenetic analysis of combined conserved proteins suggests that there is still underlying support for the concept of the universal tree.