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Systematic Biology 2008 57(6):835-843; doi:10.1080/10635150802555933
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© 2008 Society of Systematic Biologists

Evidence for a New Root of the Tree of Life

James A. Lake1,2,3,4, Jacqueline A. Servin2,4, Craig W. Herbold2,4 and Ryan G. Skophammer1,4

1 Department of Molecular, Cellular, and Developmental Biology, University of California Los Angeles, California 90095, USA; E-mail: Lake{at}mbi.ucla.edu (J.A.L.)
2 Molecular Biology Institute, University of California Los Angeles, California 90095, USA
3 Department of Human Genetics, University of California Los Angeles, California 90095, USA
4 UCLA Astrobiology Institute, University of California Los Angeles, California 90095, USA

Edited by Frank Anderson


  Abstract

Directed indels, insertions or deletions within paralogous genes, have the potential to root the tree of life. Here we apply the top-down rooting algorithm to indels found in PyrD (dihydroorotate dehydrogenase), a key enzyme involved in the de novo biosynthesis of pyrimidines, and HisA (P-ribosylformimino-AICAR-P-isomerase), an essential enzyme in the histidine biosynthesis pathway. Through the comparison of each indel with its two paralogous outgroups, we exclude the root of the tree of life from the clade that encompasses the Actinobacteria, the double-membrane prokaryotes, and their last common ancestor. In combination with previous indel rooting studies excluding the root from a clade consisting of the Firmicutes, the Archaea, and their last common ancestor, this provides evidence for a unique eubacterial root for the tree of life located between the actinobacterial–double-membrane clade and the archaeal-firmicute clade. Mapping the phylogenetic distributions of genes involved in peptidoglycan and lipid synthesis onto this rooted tree parsimoniously implies that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer.

Keywords: Actinobacteria; double-membrane; Firmicutes; indels; prokaryotes; root; tree of life

Received December 21, 2007; Revised February 29, 2008; Accepted August 26, 2008
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