Systematics and the Origin of Species On Ernst Mayr's 100th Anniversary (2005) / Chapter Skim
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Part IV--GENOMIC APPROACHES AND NEW INSIGHTS ON DIVERSITY: 14 Decoding the Genomic Tree of Life--ANNE B. SIMONSON, JACQUELINE A. SERVIN, RYAN G. SKOPHAMMER, CRAIG W. HERBOLD, MARIA C. RIVERA, AND JAMES A. LAKE
Part IV--GENOMIC APPROACHES AND NEW INSIGHTS ON DIVERSITY: 14 Decoding the Genomic Tree of Life--ANNE B. SIMONSON, JACQUELINE A. SERVIN, RYAN G. SKOPHAMMER, CRAIG W. HERBOLD, MARIA C. RIVERA, AND JAMES A. LAKE
Pages 265-285
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Another example lies in the paper by James Lake and colleagues, "Decoding the Genomic Tree of Life" (Chapter 14) , who use genomic data to reconstruct the process by which eukaryotes arose from prokaryotes.
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The final paper in the volume takes an explicitly forward look and describes the ongoing and future changes that are happening to the biological sciences. With genomic sequences for many organisms having been available for several years, many biologists are turning to the highly integrated study of cellular processes and networks, a field that is called Systems Biology (Hood, 2003)
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But genome fusions and horizontal gene transfer (HGT) seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life.
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One of the most recent evolutionary mechanisms to challenge our view of genome evolution is the massive horizontal gene transfer (HGT) that has recently become so apparent (Campbell, 2000; Doolittle, 1999a; Gogarten et al., 2002; Karlin et al., 1997; Koonin et al., 2001; Lawrence and Ochman, 1998, 2001; Rivera et al., 1998)
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. THE HGT REVOLUTION The possibility of analyzing complete genomes awakened interest in prokaryotic genome evolution and profoundly changed our understanding of genome evolution.
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Scientific opinion has now shifted and favors a significant role for HGT in prokaryotic genome evolution. HGT HAS PROFOUNDLY AFFECTED OUR UNDERSTANDING OF PROKARYOTIC GENOME EVOLUTION Three remarkable new findings, based on analyses of whole genomes, have engendered appreciation for the important role of HGT in prokaryotic evolution.
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. Of the yeast genes analyzed, approximately one-third were informational genes, and two-thirds were operational genes.
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Because codon usage is different in various organisms, the codon biases of some restriction-modification systems in the Pyrococcus genomes suggest that these systems have been acquired by horizontal transfer (Chinen et al., 2000)
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, which posits that informational genes are less likely to undergo horizontal transfer, because their products are members of large complexes with many intricate interactions. Operational genes, on the other hand, are generally not parts of large complexes, and thus are more readily transferred.
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. By rapidly introducing newly evolved genes into existing genomes, HGT circumvents the slow step of ab initio gene creation and thereby accelerates genome innovation (the acquisition of novel genes by organisms)
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This means that a species exchanging genes only with other members of its species would take 10,000 years to obtain the amount of genome innovation that would occur for an average exchange group in just 1 year. Indeed, HGT may be responsible for a remarkable increase in genome innovation that greatly exceeds anything that could have been accomplished by clonal evolution.
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With the availability of complete genomes, useful methods have been developed for whole-genome analyses (Fitz-Gibbon and House, 1999; Montague and Hutchison, 2000; Snel et al., 1999; Tekaia et al., 1999)
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One of the most remarkable properties of CR is that it can rigorously identify the merger of genomes, a process that until now could not be analyzed using gene sequence. A recently published application of this method has provided evidence that the eukaryotic genome was actually formed by a fusion of the genomes from two disparate prokaryotes.
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Fully and partially resolved rings are Lower Left and Lower Right, respectively. [Reproduced with permission from Rivera and Lake (2004)
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The ring opened into a tree only when both eukaryotes were simultaneously deleted from the analysis, indicating the eukaryotic genome had inherited genes from its prokaryotic fusion partners. This then demonstrated that eukaryotes are indeed the products of genome fusions.
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The data presented here argue against them, except of course chimeric theories that specifically propose genome fusions. At least half a dozen genome fusion theories have been proposed in which the eukaryotic genome originated from two diverse genomes (Gupta et al., 1994; Horiike et al., 2001; Lake and Rivera, 1994; Lake et al., 1982; Martin and Muller, 1998; Moreira and Lopez-Garcia, 1998)
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The ring of life does not explain why the fusion happened, but it provides a broad phylogenetic framework for testing theories for the origin and evolution of the eukaryotic genome. The genome fusion that created the ring of life may in some ways be the ultimate HGT.
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(2000) Comparison between Pyrococcus horikoshii and Pyrococcus abyssi genome sequences reveals linkage of restriction-modification genes with large genome polymorphisms.
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(2003) Horizontal gene transfer accelerates genome innovation and evolution.
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(2004) Deriving the genomic tree of life in the presence of horizontal gene transfer: Conditioned Reconstruction.
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(2000) Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Ba cillus subtilis.
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