Abstract
Adaptive evolution is a process that influences and alters all biological organisms over time. Changes involved in adaptive evolution begin with genetic mutations and can lead to large changes in phenotypic behavior. Thus, the relationship between genotype and phenotype is a central issue in studying adaptive evolution.
The whole-cell phenotype of an organism is the result of integrated functions at various levels of cellular organization. As methods have been developed and improved to study the components involved with the different levels of cellular organization in a high-throughput and genome-wide scale, it is becoming possible to establish the link between genotype and phenotype. In this chapter, different means of studying and establishing connections between genotype and phenotype in the context of adaptive evolution will be discussed.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Elena SF, Lenski RE. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 2003;4(6):457–469.
Atwood KC, Schneider LK, Ryan FJ. Periodic selection in Escherichia coli. Proc Natl Acad Sci USA 1951;37(3):146–155.
Lenski RE, Travisano M. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci USA 1994;91(15):6808–6814.
Fong SS, Palsson BO. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 2004;36(10):1056–1058.
Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002;420(6912):186–189.
Riehle MM, Bennett AF, Long AD. Genetic architecture of thermal adaptation in Escherichia coli. Proc Natl Acad Sci USA 2001;98(2):525–530.
Velkov VV. New insights into the molecular mechanisms of evolution: Stress increases genetic diversity. Mol Biol 2002;36(2):209–215.
Fleischmann RD, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995;269(5223):496–498, 507–512.
Palsson BO. The challenges of in silico biology. Nat Biotechnol 2000;18 (November):1147–1150.
Burger RM. Willensdorfer, Nowak M.A. Why are phenotypic mutation rates much higher than genotypic mutation rates? Genetics 2006;172(1):197–206.
Schilling CH, Edwards JS, Palsson BO. Towards metabolic phenomics: Analysis of genomic data using flux balances. Biotechnol Progress 1999;15(3):288–295.
Fong SS, Marciniak JY, Palsson BO. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J Bacteriol 2003;185(21):6400–6408.
Bochner BR, Gadzinski P, Panomitros E. Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res 2001;11(7):1246–1255.
Kell DB, Brown M, Davey HM, et al. Metabolic footprinting and systems biology: the medium is the message. Nat Rev Microbiol 2005;3(7):557–565.
Riehle MM, Bennett AF, Lenski RE, et al. Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature. Physiol Genomics 2003;14(1):47–58.
Fong SS, Joyce AR, Palsson BO. Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res 2005;15(10):1365–1372.
Cooper TF, Rozen DE, Lenski RE. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc Natl Acad Sci USA 2003;100(3):1072–1077.
Ferea TL, Botstein D, Brown PO, et al. Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci USA 1999;96(17):9721–9726.
Sauer U. High-throughput phenomics: experimental methods for mapping fluxomes. Curr Opin Biotechnol 2004;15(1):58–63.
Fong SS, Nanchen A, Palsson BO, et al. Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem 2005;281(12):8024–8033.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this chapter
Cite this chapter
Fong, S.S. (2007). Genome-Scale Assessment of Phenotypic Changes During Adaptive Evolution. In: Choi, S. (eds) Introduction to Systems Biology. Humana Press. https://doi.org/10.1007/978-1-59745-531-2_10
Download citation
DOI: https://doi.org/10.1007/978-1-59745-531-2_10
Publisher Name: Humana Press
Print ISBN: 978-1-58829-706-8
Online ISBN: 978-1-59745-531-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)