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Review
. 2010 Jan;2(1):a002238.
doi: 10.1101/cshperspect.a002238.

Deep phylogeny--how a tree can help characterize early life on Earth

Eric A Gaucher  1 , James T Kratzer, Ryan N Randall
Affiliations
Review

Deep phylogeny--how a tree can help characterize early life on Earth

Eric A Gaucher et al. Cold Spring Harb Perspect Biol. 2010 Jan.

Abstract

The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history."You know, a tree is a tree. How many more do you need to look at?"--Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966.

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Figures

Figure 1.
Figure 1.
Tree of Life and its evolution over 100 years. (A) Taxonomy of life based on morphological characteristics (Chatton 1925). (B) Phylogenetic tree of life based on DNA sequence analysis (Woese and Fox 1977). (C) Competing views for the rooting of the phylogenetic tree of life. Initials A, B, and E represent Archaea, Bacteria, and Eukarotes, respectively. The tree on the left is based on membrane architecture and insertion/deletion events in gene (Cavalier-Smith 2002), the tree in the center is based on ancient gene duplication events (Gogarten et al. 1989; Iwabe et al. 1989; Brown and Doolittle 1995; Brown et al. 1997; Gribaldo and Cammarano 1998), and the tree on the right is based on phylogenetic analysis of hundreds of genes (Rivera and Lake 2004). (D) Most recent view about the tree of life in light of vertical and horizontal gene transmission (Fournier et al. 2009).
Figure 2.
Figure 2.
Distribution of modern hyperthermophilic organisms (Stetter 1996). Thick terminal branches lead to hyperthermophiles and thin terminal branches lead to nonhyperthermophiles. Thick internal branches are inferred based on the distribution and relatedness of modern hyperthermophiles.
Figure 3.
Figure 3.
Plot of ancestral EF melting temperatures versus geologic time in billions of years (Ga) (Gaucher et al. 2008). Molecular clock estimates and their confidence intervals (horizontal bars) from Battistuzzi et al., using a 2.3 Ga minimum constraint for the great oxidation event (Battistuzzi et al. 2004). Solid lines are temperature curves of the ancient ocean inferred from maximum δ18O (light gray [Knauth and Lowe 1978; Knauth and Lowe 2003], dark gray [Robert and Chaussidon 2006]). Although not shown, an analogous trend is seen with δ30Si isotopes (Robert and Chaussidon 2006).
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