Universal Tree of Life

Abstract

The universal tree of life represents the proposed evolutionary relationships among all cellular life forms, which are classified into three main urkingdoms or domains; the Archaea (archaebacteria), Bacteria (eubacteria) and Eucarya (eukaryotes). While the flood of whole genome deoxyribonucleic acid (DNA) sequences from species in all the three domains have provided rich data sets to reconstruct the universal tree, it has also raised important new questions about the evolution of life. In particular, early genome evolution might have been largely shaped by the widespread occurrence of lateral or horizontal gene transfer between distantly related species from different domains.

Keywords: universal tree of life; evolution; archaebacteria; bacteria; eukaryotes

Figure 1.

Schematic drawing of a universal rRNA tree showing the relative positions of evolutionary pivotal groups in the domains Bacteria, Archaea and Eucarya. The location of the root (the cenancestor) corresponds with that proposed by reciprocally rooted gene phylogenies. (Branch lengths have no meaning in this tree.) In addition to putative HGT events associated with the origin of mitochondria and chloroplasts (green and purple arrows), HGT between other groups have also been observed, such as between Spirochaetes and Archaea (a), between low G+C Gram‐positive bacteria and Archaea (b), and between thermophilic Bacteria and Archaea (c). The diagram shows the relative evolutionary positions of various groups of organism on the tree, but branch lengths are not to scale. Among eukaryotes there are protist groups, once called the Archezoa that are thought to have secondarily lost their mitochondria‐like organelles (yellow dashed arrows).

Figure 2.

Conceptual rooting of the universal tree using paralogous genes. Suppose that gene A was duplicated in the cenancestor such that all extant organisms have both genes, A1 and A2. Provided that some sequence similarity still exists between genes A1 and A2, then reciprocally rooted gene trees could be constructed. The positioning of Archaea and Eucarya as sister groups, with the Bacteria as the outgroup, has been consistently supported by such rootings.

Figure 3.

Universal tree constructed from the phylogenetic of the combined or concatenated alignment of 14 conserved proteins (from Brown JR, Douady CJ, Italia MJ, Marshall WE and Stanhope MJ (2001)). Although protein gene trees are frequently incongruent with trees based on 16S rRNA molecules, this phylogeny shows good agreement with the universal tree topology – i.e. Archaea, Bacteria and Eucarya are monophyletic groups and the thermophilic bacterial species are the first branch of the Bacterial clade. The tree is based on three different phylogenetic methods. As measures of statistical confidence, the numbers along the branches show the per cent occurrence of nodes in greater than 50% of either 1000 bootstrap replicates of maximum parsimony (plain text) or neighbour joining (italicized text) analyses or 1000 quartet puzzling steps of maximum likelihood analysis (in parentheses). Dashed lines show occasional differences in branching orders in different phylogenetic analyses. Bar, 100 amino acid residue substitutions, CFB Cytophaga–Flexibacter–Bacteroides group of bacteria.

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Further Reading

Brown JR (2003) Ancient horizontal gene transfer. Nature Reviews Genetics 4: 121–132.

Brown JR and Doolittle WF (1997) Archaea and the prokaryote‐to‐eukaryote transition. Microbiology and Molecular Biology Reviews 61: 456–502.

Brown JR, Douady CJ, Italia MJ, Marshall WE and Stanhope MJ (2001) Universal trees based on large combined protein sequence datasets. Nature Genetics 28: 281–285.

Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284: 2124–2128.

Keeling PJ (1998) A kingdom's progress – Archezoa and the origin of eukaryotes. Bioessays 20: 87–95.

Koonin EV, Aravind L and Kondrashov AS (2000) The impact of comparative genomics on our understanding of evolution. Cell 101: 573–576.

Kurland CG, Canback B and Berg OG (2003) Horizontal gene transfer: a critical view. Proceedings of the National Academy of Sciences of the USA 100: 9658–9662.

Martin W, Rujan T et al. (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proceedings of the National Academy of Sciences of the USA 99: 12246–12251.

Martin W and Embley TM (2004) Early evolution comes full circle. Nature 431: 134–135.

Rivera MC and Lake JA (2004) The ring of life provides evidence for genome fusion origin of eukaryotes. Nature 431: 152–155.

Woese CR (1987) Bacterial evolution. Microbiological Reviews 51: 221–271.

Woese CR, Kandler O and Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proceedings of the National Academy of Sciences of the USA 87: 4576–4579.

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How to Cite close
Brown, James R(Jan 2006) Universal Tree of Life. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0004125]