Tree of life with and without extinct lineages.   Most depictions of the trees of life that are derived from molecular data only consider extant organisms (i.e. lineages that have representatives alive today).   Through horizontal gene transfer molecules from now extinct lineages might have survived in today's organism (more at Zhaxybayeva and Gogarten (2004): Cladogenesis, Coalescence and the Evolution of the Three Domains of Life.
Trends in Genetics 20 (4): 182- 187