Systematics and the Origin of Species On Ernst Mayr's 100th Anniversary (2005) / Chapter Skim
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17 Genomes, Phylogeny, and Evolutionary Systems Biology--MÓNICA MEDINA
17 Genomes, Phylogeny, and Evolutionary Systems Biology--MÓNICA MEDINA
Pages 332-350
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The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics, and computer science are now known as systems biology. Here, I present an overview, with an emphasis on eukary otes, of how the postgenomics era is adopting comparative ap proaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.
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These new genomic data have informed our understanding of phylogenetic relationships, and the emerging consensus topologies are adding new insight to the small subunit ribosomal RNA phylogenies. For example, the topology of the ribosomal eukaryotic tree has been recently redrawn with the use of genomic signatures that place the root of all eukaryotic life between two newly uncovered major clades, Unikonts and Bikonts (Fig.
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(Berbee et and 2002, (highlighted Cavalier-Smith, resolution (highlighted Unikonts and postgenomic phylogeny Ruiz-Trillo projects large although within Cavalier-Smith, by ,2001; al. consensus genome (Stechmann et and studied subclades recognized Medina (C)
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These comparisons were made between distantly related taxa, and the evolutionary implications were rarely mentioned or taken into account. The increasing importance of comparative analysis is evident in the growing proportion of new prokaryotic genome projects that have been chosen primarily because of their phylogenetic relationship to model organisms, such as Escherichia coli and Bacillus subtilis and their corresponding related taxa.
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(Dietrich et al., 2004; Dujon et al., 2004; Kellis et al., 2004) , although now more distantly related taxa including additional model organisms such as Neurospora crassa and Aspergillus nidulans have also been sequenced.
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Nonetheless, the first draft Plantae genome published was from Arabidopsis thaliana, a flowering plant model organism (Arabidopsis Genome Initiative, 2000)
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Because postgenomics research is taking place throughout the tree of life, comparative approaches are a way to combine data from many organisms to understand the evolution and function of biological systems from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use systems approaches to go in new uncharted directions.
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The extensive microarray gene expression datasets available for model and non-model organisms are starting to be incorporated into a comparative approach to study transcriptome evolution at multiple levels of divergence. At lower levels of divergence, studies in organisms including fish (Olesiak et al., 2002)
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The degree of accuracy in which genomes are annotated is affected by the quality of sequence assembly, gene prediction, and functional annotation by both bioinformatics and experimental data. This relationship is particularly critical in genome projects of non-model organisms where little genetic work has been performed in the past.All these factors, combined with the lack of network information outside the model organisms, point to the tradeoff between a comprehensive systems analysis of a particular network within a well-studied organism, versus the historical perspective introduced by evolutionary conservation or divergence of systems through time in phylogenetic comparisons.
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Regulatory Networks The characterization of the transcriptome is only a fraction of the information needed to understand global cellular processes because gene expression is driven by the spatio-temporal localization of regulatory networks and details of specific proteinDNA and proteinprotein interactions. Genomewide efforts to characterize transcriptional regulatory networks have already been fruitful in model organisms like yeast (Lee et al., 2002)
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. Protein Networks The proteome for several of the model organisms is now characterized, and this global scale information has been used to predict protein protein interaction networks (interactomes)
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. A pioneer example is the ENCODE initiative, which aims to identify all functional elements in the human genome by using coordinated computational and experimental efforts in a multispecies framework (ENCODE Project Consortium, 2004)
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Pilar Francino and Paramvir Dehal provided thoughtful insight for both the seminar and the manuscript. I also thank Mike Colvin, Benoît Dayrat, Jodi Schwarz, Rick Baker, Kevin Helfenbein, and an anonymous reviewer for helpful comments on previous versions of the manuscript.
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(2004) The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome.
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(2002) Transcriptional regulatory networks in Saccharomyces cerevisiae.
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(2002) A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians.
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(2003b) How the global structure of protein interaction networks evolves.
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