Eukaryotes - more complex organisms such as plant and animal cells - present problems for determining a Tree of life, according to a recent article in Trends in Ecology and Evolution. For one thing, some key types of eukaryotes might have absorbed another life form early in their history, in a process called endosymbiosis (or symbiogenesis).
For example, the mitochondria (power plants of cells) and the chloroplasts of green plants may have originated as free-living bacteria but later gotten absorbed by another cell. That would explain why these structures inside the cell have their own genomes.
According to Christopher E. Lane and John M. Archibald, eukaryotes are hard to organize using a simple concept like a Tree of life, which assumes common ancestry and ancestor to descendant relationships. In "The eukaryotic tree of life: endosymbiosis takes its TOL," they point out that, in an effort to reduce the confusion surrounding eukaryotes, six eukaryotic supergroups have been proposed, but, "The strength of the evidence supporting these superassemblages (summarized in the accompanying Glossary) has been the subject of much debate [7] and the relationships between the supergroups are largely unknown. Indeed, whether molecular data can accurately resolve relationships between taxa that diverged ca. one billion years ago is unclear."
Relatively simple life forms like prokaryotes (Archaea and Monera) create problems for a different reason: They swap genes to an extent that makes constructing a "Tree of life" difficult. Prokaryotes might perhaps be better understood by a different ancient symbol, the river of life flowing on and blending its waters.
The conventional popular explanation for the origin of species is Darwin's theory that natural selection acts on random mutations in the genome. It somehow creates new adaptations and organs, thus producing the diversity that we see in life forms. However, belief in the power of natural selection as a creative force can fairly be described as a leap of faith. From what we observe, natural selection acts conservatively, rather than creatively. It eliminates life forms whose genes have expressed themselves in ways ill-suited to survival.
Lynn Margulis, the key proponent of symbiogenesis, argues that,
random mutation, long believed (but never demonstrated) to be the main source of genetic variation, is of only marginal importance. Much more significant is the acquisition of new genomes by symbiotic merger.
If so, "tree of life" is not the best way to understand eukaryote origins, just as it is not the best way to understand prokaryote origins. Would a corporate mergers and acquisitions diagram serve the eukaryotes better? Time will tell.
Abstract and citation:
Citation: The eukaryotic tree of life: endosymbiosis takes its TOL Christopher E. Lane and John M. Archibald Trends in Ecology & Evolution, Volume 23, Issue 5, May 2008, Pages 268-275
Abstract: Resolving the structure of the eukaryotic tree of life remains one of the most important and challenging tasks facing biologists. The notion of six eukaryotic ‘supergroups’ has recently gained some acceptance, and several papers in 2007 suggest that resolution of higher taxonomic levels is possible. However, in organisms that acquired photosynthesis via secondary (i.e. eukaryote–eukaryote) endosymbiosis, the host nuclear genome is a mosaic of genes derived from two (or more) nuclei, a fact that is often overlooked in studies attempting to reconstruct the deep evolutionary history of eukaryotes. Accurate identification of gene transfers and replacements involving eukaryotic donor and recipient genomes represents a potentially formidable challenge for the phylogenomics community as more protist genomes are sequenced and concatenated data sets grow.