Save the tree of life or get lost in the woods
Ruben E Valas and Philip E Bourne
DOI: 10.1186/1745-6150-5-44 © Valas and Bourne; licensee BioMed Central Ltd. 2010
Received: 10 June 2010Accepted: 1 July 2010Published: 1 July 2010
The wealth of prokaryotic genomic data available has revealed that the histories of many genes are inconsistent, leading some to question the value of the tree of life hypothesis. It has been argued that a tree-like representation requires suppressing too much information, and that a more pluralistic approach is necessary for understanding prokaryotic evolution. We argue that trees may still be a useful representation for evolutionary histories in light of new data.
Genomic data alone can be highly misleading when trying to resolve the tree of life. We present evidence from protein abundance data sets that genomic conservation greatly underestimates functional conservation. Function follows more of a tree-like structure than genetic material, even in the presence of horizontal transfer. We argue that the tree of cells must be incorporated into any new synthesis in order to place horizontal transfers into their proper selective context. We also discuss the role data sources other than primary sequence can play in resolving the tree of cells.
The tree of life is alive, but not well. Construction of the tree of cells has been viewed as the end goal of the study of evolution, where in reality we need to consider it more of a starting point. We propose a duality where we must consider variation of genetic material in terms of networks and selection of cellular function in terms of trees. Otherwise one gets lost in the woods of neutral evolution.
This article was reviewed by Dr. Eric Bapteste, Dr. Arcady Mushegian, and Dr. Celine Brochier.
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INTERESTING CONCLUSION EXCERPT/EXCERTO INTERESSANTE DA CONCLUSÃO:
We must keep in mind the humor of calling the central metaphor for evolution "the tree of life". The phrase first appears in Genesis 2:9:
And the LORD God made all kinds of trees grow out of the ground--trees that were pleasing to the eye and good for food. In the middle of the garden were the tree of life and the tree of the knowledge of good and evil.
There is irony in using the name of a tree central to the creation story to argue against that very myth. Therefore we doubt that any phrase will ever pack as much punch as the "tree of life", even if the pattern of common descent is more of a web. It is very important that the community stops labeling any tree derived from a single data source the TOL. The recent attempts to resolve the TOC using primary sequence should be labeled "universal sequence trees", a name that is grounded in the limitations of the data. The title TOC should be reserved for branch orders that are supported by several lines of independent evidence, and the TOL should be the synthesis of those branch orders and horizontal process.