This article is part of a series on Evolutionary Biology 150 years after the 'Origin': is a post-modern synthesis in sight?, edited by Dr Eugene V Koonin.

Research

Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life

Ruben E Valas¹ and Philip E Bourne²

¹  Bioinformatics Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

²  Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA

author email corresponding author email

Biology Direct 2009, 4:30doi:10.1186/1745-6150-4-30

Published:	25 August 2009

Abstract

Background

The root of the tree of life has been a holy grail ever since Darwin first used the tree as a metaphor for evolution. New methods seek to narrow down the location of the root by excluding it from branches of the tree of life. This is done by finding traits that must be derived, and excluding the root from the taxa those traits cover. However the two most comprehensive attempts at this strategy, performed by Cavalier-Smith and Lake et al., have excluded each other's rootings.

Results

The indel polarizations of Lake et al. rely on high quality alignments between paralogs that diverged before the last universal common ancestor (LUCA). Therefore, sequence alignment artifacts may skew their conclusions. We have reviewed their data using protein structure information where available. Several of the conclusions are quite different when viewed in the light of structure which is conserved over longer evolutionary time scales than sequence. We argue there is no polarization that excludes the root from all Gram-negatives, and that polarizations robustly exclude the root from the Archaea.

Conclusion

We conclude that there is no contradiction between the polarization datasets. The combination of these datasets excludes the root from every possible position except near the Chloroflexi.

Reviewers

This article was reviewed by Greg Fournier (nominated by J. Peter Gogarten), Purificación López-García, and Eugene Koonin.