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Chapter 4 : The Study of Microbial Adaptation by Long-Term Experimental Evolution

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Abstract:

Experimental evolution, the research approach discussed in this chapter, permits study of the fundamental processes of adaptation that underlie microbial evolution under controlled laboratory conditions. Long-term evolution experiments with microbes have displayed numerous elements of the complexity of natural systems and have therefore permitted the study of fundamental questions in evolutionary biology, ecology, physiology, and genetics. This chapter focuses on a few long-term, open-ended studies as well as other relevant experiments that best illustrate specific problems. Despite many excellent studies using fungal and viral models, the chapter is focused primarily on bacterial systems with occasional mention of viral systems. Specific topics under consideration include the dynamics of adaptation, the genetic and physiological bases of fitness, causes of specialization and functional losses, evolution of mutation rates, and models of the evolution of virulence. At the end of the chapter, the author addresses prospects for future experiments to study the evolution of pathogens. The author refers repeatedly to two longterm experiments throughout this chapter. The first involves the long-term experimental evolution of 12 populations of B, originally founded by Richard Lenski in 1988. The second experiment of this review was derived from this first one. The chapter discusses selected examples in which the mechanisms and consequences of genetic adaptation were discovered. The evidence that important steps in microbial evolution have been driven significantly, and perhaps mostly, by interspecies recombination continues to grow.

Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4

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Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4
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Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4
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FIGURE 1

Trajectory for mean fitness of 12 populations during 20,000 generations in minimal glucose medium. Each point is the population mean measured relative to the ancestor with fivefold replication. Curves are the best fit of a hyperbolic model.

Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4
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Image of FIGURE 2
FIGURE 2

Evolution of fitness during 1,000 generations in maltose, after 2,000 generations of prior evolution in glucose. (A) Derived versus ancestral values for mean fitness in the 36 experimental populations. Symbols A through L reflect 12 different progenitor genotypes. (B) Relative contributions of adaptation, chance, and history to mean fitness (triangles) and fitness after (circles) 1,000 generations in maltose. Error bars represent 95% confidence intervals. Reprinted from reference with permission.

Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4
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Image of FIGURE 3
FIGURE 3

A Wrightian landscape, illustrating that maladaptive “valleys” may separate two adaptive “peaks” of unequal relative value. A Fisherian landscape, on the other hand, would be dominated by a single adaptive peak. See reference for a more detailed discussion of these alternative population genetic models.

Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4
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Image of FIGURE 4
FIGURE 4

Punctuated evolution caused by periodic selection of beneficial mutations, which produced correlated increases in cell size. Data are from one population of adapting to a minimal laboratory environment. Reprinted from reference with permission.

Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4
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FIGURE 5

Frequency of Rbs cells over time in the 12 evolving LT populations. Seven of 12 populations became 100% Rbs by generation 500, which is best explained by genetic linkage to other “big-benefit” mutations (genetic hitchhiking). In the remaining five populations, ribose function acts as a marker for other selective sweeps (periodic selection), including positive selection on the Rbs mutation itself. Adapted from reference .

Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4
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Image of FIGURE 6
FIGURE 6

Nonsynonymous mutations in in eight independently evolved populations. Only the variable amino acid residues are shown, with the ancestor listed first and the eight mutant alleles shown below. Four other populations retained the ancestral sequence. Reprinted from reference with permission.

Citation: Cooper V. 2006. The Study of Microbial Adaptation by Long-Term Experimental Evolution, p 55-81. In Seifert H, DiRita V (ed), Evolution of Microbial Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815622.ch4
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