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Evolution: The Molecular Landscape

Cold Spring Harbor’s 74th Symposium
The Molecular Landscape
Edited by Bruce Stillman,
David Stewart, and
Jan Witkowski,
Cold Spring Harbor Laboratory


Chapter 5 Notes

The Last Universal Common Ancestor and the Tree of Life

Tracing Early Evolutionary History

Box 5.1 Evolutionary Trees

The University of California Museum of Paleontology provides a good general resource that includes an introduction to phylogenetic trees, homology, and related concepts. There are also teaching resources there.

The “Tree Thinking Group” at the University of Pittsburgh also has some good resources, including some excellent teaching materials.

The Concept of Descent with Modification Can Be Used to Infer Evolutionary Relationships

The inference of phylogenetic history is discussed in detail in Chapter 27. In this chapter we introduce some of the key aspects of this inference. We focus here on the general concept of working backward from comparisons of modern organisms and on how this can be done if one assumes that the path of evolution is by vertical descent. The occurrence of lateral gene transfer (see later in the chapter) complicates the reconstruction of evolutionary history somewhat.

For more on homology and analogy, try the University of California Museum of Paleontology’s web resource.

A useful discussion on convergence and parallel evolution can be found here.

Universal Homologies, LUCA, and the Tree of Life

The Existence of Universal Homologies Implies a Single Origin of Life and the Existence of LUCA

Two good papers on this topic are Kyrpides et al. (1999), which discusses using universal protein families to infer properties of LUCA, and Harris et al. (2003), which uses comparative genomics to infer the genetic core of the universal ancestor.

The Features of LUCA Can Be Inferred from Universal Character States or by Evolutionary Reconstructions

Character State Reconstruction

A good description of the phylogenetic methods for inferring the evolutionary history and processes of change in discretely valued characters can be found in Maddison (1994). In addition, a very helpful resource is the book that accompanies the computer software MacClade (e.g., Maddison and Maddison [2000]). Another useful paper is Cunningham et al. (1998), which contains a critical reappraisal of ancestral character states reconstruction.

Nonuniversal Genetic Code

A review of the “escaped triplet theory” as a possible origin of the genetic code is presented in Yarus et al (2005). Recent evidence for evolution of the genetic code is presented by Osawa et al. (1992).

Box 5.2 The Tree of Life: A Brief History

There are numerous resources available that delve more deeply into the history of tree of life studies. A good overview can be found in the Introduction to Assembling the Tree of Life (Cracraft and Donoghue 2004).

Some of the original sources mentioned in Box 5.2 are Generelle Morphologie der Organismen by Haeckel (1866), Titres et Travaux Scientifiques by Chatton (1937), and a paper by Whittaker (1969), entitled “New concepts of kingdoms of organisms.”

The alignment in Figure 5.16 is of RecA proteins. More discussion of alignment is in Chapter 27.

The important contributions of Carl Woese and his colleagues, who in analyzing the sequences of rRNA uncovered the existence of the Archaea, are detailed in many papers. Woese (1987) is still relevant and has a great discussion of rRNA, the history of phylogeny, and more. One of the first papers to show that rRNA cataloguing is useful for phylogeny was Fox et al. (1977). In Woese and Fox (1977) evidence for the existence of the Archaea is presented. The full text is available online. More evidence for the Archaea is in Woese et al. (1977). A formal proposal for constructing a system of organisms based on three domains: the Bacteria, the Archaea, and the Eukarya, is in Woese et al. (1990).

To Infer Properties of LUCA, We Need a Rooted Tree of Life

Inferring Nuclear Membrane Origins

Martin (2005) is a good review paper on the origin of the nucleus.

Initial Attempts to Root the Tree of Life Suggested That Archaea and Eukaryotes Are Sister Groups

Orthologs and Paralogs

The original definition of orthologs and paralogs is from Fitch (1970). A good overview of orthologs and paralogs can be found in Koonin (2005).

Rooting the Tree with Duplicated Genes

Iwabe et al. (1989) presents the use of duplicated genes EF-TU and EFG and ATPase α and β to infer the root of the tree of life. Gogarten et al. (1989) look at the evolution of ATPases to do the same thing.

Brown and Doolittle (1997) present a detailed analysis of the phylogeny of many gene families and what they mean for the rooting of the tree and the origin of eukaryotes.

LUCA and Modern Cells Share Features of Protein Translation

Galtier et al. (1999) discuss inferring the growth temperature of LUCA.

Kyrpides et al. (1999) discuss using universal protein families to infer properties of LUCA.

Harris (2003) uses comparative genomics to infer the genetic core of the universal ancestor.

Woese (1990) discusses the progenote hypothesis.

The Bacterial Rooting of the Tree of Life Has Been Challenged by Some Analyses

A good review of long branch attraction can be found in Gribaldo and Philippe (2002).

Microsporidial origins and long branch attraction are discussed in Keeling et al. (2000) and Keeling (2003).

For a discussion of challenges in rooting the tree of life, see Forterre (1997), Rivera and Lake (2004), and Brinkmann and Philippe (2007).

Philippe and Forterre (1999) and Forterre and Philippe (1999) discuss some of the limitations of the bacterial rooting of the tree of life. Poole et al. (1999) present alternative possibilities.

Penny and Poole (1999) discuss various theories on the nature of LUCA.

Bapteste and Brochier (2004) discuss the conceptual challenges in rooting the tree.

Rivera and Lake (2004) discuss the “ring of life” and some of the challenges in studying the relationships among the three domains.

The Occurrence of Gene Transfer between Species Means That Different Genes May Have Their Own LUCAs

An excellent overview of lateral gene transfer and what it could mean in phylogenetic classification can be found in Doolittle (1999). Eisen (2000) discusses genomic evidence for and against lateral gene transfer.

Genomic Analyses and Lateral Gene Transfer

Ge et al. (2005) discuss the “Cobweb of life.”

Kunin et al. (2005) present evidence for establishing the microbial phylogeny as a network—“the net of life.” Chapters 6 (pp. 131–133) and 7 (pp. 182–191) in Evolution contain more detail on lateral gene transfer.

Where Do Viruses Sit on the Tree of Life?

An excellent discussion of the issues involved in studying the origin and evolution of viruses can be found in Mindell et al. (2004).

The article by Lawrence et al. (2002) has a discussion of the challenges of building viral phylogenetic taxonomies in the face of gene exchange and other aspects of viral evolution.

Rohwer and Edwards (2002) discuss taxonomy challenges and introduce the “phage proteomic tree” concept.

A very interesting paper on possible origins of the three domains of life and how that connects to viruses is Forterre (2006a) (also see Forterre [2006b]).

Koonin et al. (2006) has a good discussion of possible ancient origin of viruses.


Bapteste E. and Brochier C. 2004. On the conceptual difficulties in rooting the tree of life. Trends Microbiol. 12: 9–13.

Brinkmann H. and Philippe H. 2007. The diversity of eukaryotes and the root of the eukaryotic tree. Adv. Exp. Med. Biol. 607: 20–37.

Brown J.R. and Doolittle W.F. 1997. Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61: 456–502.

Chatton E. 1937. Titres et travaux scientifiques. Sette, Sottano, Italy.

Cracraft J and Donoghue M., eds. 2004. Assembling the tree of life. Oxford University Press, New York.

Cunningham C.W., Omland K.E., and Oakley T.H. 1998. Reconstructing ancestral character states: A critical reappraisal. Trends Ecol. Evol. 13: 361–366.

Doolittle W.F. 1999. Phylogenetic classification and the Universal Tree. Science 25: 2124–2128.

Eisen J.A. 2000. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 10: 606–611.

Fitch W.M. 1970. Distinguishing homologous from analogous proteins. Syst. Zool. 19: 99–113.

Forterre P. 1997. Protein versus RNA: Problems in rooting the Tree of Life. ASM News 63: 89.

Forterre P. 2006a. Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain. Proc. Natl. Acad. Sci. 103: 3669–3674.

Forterre P. 2006b. The origin of viruses and their possible roles in major evolutionary transitions. Virus Res. 117: 5–16.

Forterre P. and Philippe H. 1999. Where is the root of the universal tree of life? Bioessays 21: 871–879.

Fox G.E., Pechman K.R., and Woese C.R. 1977. Comparative cataloging of 16S ribosomal RNA: Molecular approach to procaryotic systematics. Int. J. Syst. Bacteriol. 27: 44–57.

Galtier N., Tourasse N., and Gouy M. 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283: 220–221.

Ge F., Wang L.-S., and Kim J. 2005. The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol. 3: e316.

Gogarten J.P., Kibak H., Dittrich P., Taiz L., Bowman E.J., Bowman B.J., Manolson M.F., Poole R.J., Date T., Oshima T., et al. 1989. Evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. 86: 6661–6665.

Gribaldo S. and Philippe H. 2002. Ancient phylogenetic relationships. Theor. Popul. Biol. 61: 391–408.

Haeckel E. 1866. Generelle Morphologie der Organismen. Reimer, Berlin.

Harris J.K., Kelley S.T., Spiegelman G.B., and Pace N.R. 2003. The genetic core of the universal ancestor. Genome Res. 13: 407–412.

Iwabe N., Kuma K., Hasegawa M., Osawa S., and Miyata T. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl. Acad. Sci. 86: 9355–9359.

Keeling P.J. 2003. Congruent evidence from a-tubulin and b-tubulin gene phylogenies for a zygomycete origin of microsporidia. Fungal Genet. Biol. 38: 298–309.

Keeling P.J., Luker M.A., and Palmer J.D. 2000. Evidence from b-tubulin phylogeny that microsporidia evolved from within the fungi. Mol. Biol. Evol. 17: 23–31.

Koonin E.V. 2005. Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 39: 309–338.

Koonin E.V., Senkevich T.G., and Dolja V.V. 2006. The ancient Virus World and evolution of cells. Biol Direct. 1: 29.

Kunin V., Goldovsky L., Darzentas N., and Ouzounis C.A. 2005. The net of life: Reconstructing the microbial phylogenetic network. Genome Res. 15: 954–959.

Kyrpides N., Overbeek R., and Ouzounis C. 1999. Universal protein families and the functional content of the last universal common ancestor. J. Mol. Evol. 49: 413–423.

Lawrence J.G., Hatfull G.F., and Hendrix R.W. 2002. Imbroglios of viral taxonomy: Genetic exchange and failings of phenetic approaches. J. Bacteriol. 184: 4891–4905.

Maddison D.R. 1994. Phylogenetic methods for inferring the evolutionary history and processes of change in discretely valued characters. Annu. Rev. Entomol. 39: 267–292.

Maddison D.R. and Maddison W.P. 2000. MacClade 4: Analysis of phylogeny and character evolution. Sinauer Associates, Sunderland, Massachusetts.

Martin W. 2005. Archaebacteria (Archaea) and the origin of the eukaryotic nucleus. Curr. Opin. Microbiol. 8: 630–637.

Mindell D.P., Rest J.S., and Villarreal L. P. 2004. Viruses and the tree of life. In Assembling the tree of life (ed. J. Cracraft and M.J. Donoghue), pp. 107–118. Oxford University Press, New York.

Osawa S, Jukes TH, Watanabe K, and Muto A. 1992. Recent evidence for evolution of the genetic code. Microbiol. Rev. 56: 229–264.

Penny D. and Poole A. 1999. The nature of the last universal common ancestor. Curr. Opin. Genet. Dev. 9: 672–677.

Philippe H. and Forterre P. 1999. The rooting of the universal tree of life is not reliable. J. Mol. Evol. 49: 509–523.

Poole A., Jeffares D., and Penny D. 1999. Early evolution: Prokaryotes, the new kids on the block. Bioessays 21: 880–889.

Rivera M.C. and Lake J.A. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431: 152–155.

Rohwer F. and Edwards R. 2002. The Phage Proteomic Tree: A genome-based taxonomy for phage. J. Bacteriol. 184: 4529–4535.

Whittaker R.H. 1969. New concepts of kingdoms of organisms. Science 163: 150–160.

Woese C.R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221–271.

Woese C.R. 1990. Evolutionary questions: the “progenote”. Science 247: 789.

Woese C.R. and Fox G.E. 1977. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc. Natl. Acad. Sci. 74: 5088–5090.

Woese C.R., Kandler O., Wheelis M.L. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. 87: 4576–4579.

Woese C.R., Balch W.E., Magrum L.J., Fox G.E., and Wolfe R.S. 1977. An ancient divergence among the bacteria. J. Mol. Evol. 9: 305–311.

Yarus M., Caporaso J.G., and Knight R. 2005. Origins of the genetic code: The escaped triplet theory. Annu. Rev. Biochem. 74: 179–198.


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