Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments

4. Experimental Evolution from the Bottom Up

67 4 EXPERIMENTAL EVOLUTION FROM THE BOTTOM UP Daniel E. Dykhuizen and Anthony M. Dean A BOTTOM-UP ANALYSIS OF THE LACTOSE SYSTEM OTHER APPROACHES DISCUSSION Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments, edited by Theodore Garland, Jr., and Michael R. Rose. Copyright © by the Regents of the University of California. All rights of reproduction in any form reserved. One of the most important uses of experimental evolution is the study of natural selection , its causes and its consequences. This involves mapping genotype onto phenotype (genetic architecture; Hanson 2006) and mapping phenotype onto fitness. Implicitly or explicitly, these mappings also include any impact the environment has on each. Natural selection is studied using two very different approaches in experimental evolution , which we call “top down” and “bottom up.” In the top-down approach, an experimenter sets up the environmental conditions, such as media, temperature, and growth regime, and allows the culture to evolve over thousands of generations (e.g., see Forde and Jessup this volume; Futuyma and Bennett this volume; Gibbs and Gefen this volume; Huey and Rosenzweig this volume). The usual output measured is change in fitness, but it also can be change in DNA sequence, change in protein expression, or change in any physiological process. The patterns that emerge are then compared to those expected from evolutionary theory. In contrast, the bottom-up approach attempts to predict fitness from first principles. For example, two strains, genetically identical except for a specific genetic difference of interest , are placed in competition against each other, and fitness is measured over a short period, usually less than a hundred generations and before a selective sweep incorporates other genetic changes. Next, the genetic difference or the environment is changed, and fitness is measured again. The observed pattern of fitness differences is then compared against the pattern predicted from biochemistry and molecular biology. In a classic example of the top-down approach, Bennett et al. (1992) studied temperature adaptation in Escherichia coli. A culture of E. coli was first evolved for two thousand generations in a serial transfer experiment—each day the culture was diluted 1 to 100 into fresh minimal medium plus glucose and shaken (not stirred) in a flask at 37°C (Lenski et al. 1991). A single bacterium from this culture was grown up as the common ancestor of multiple cultures that were then propagated for a further two thousand generations under identical conditions except for temperature: some were grown at 32°C, some at 37°C, some at 42°C, and some were shifted daily between 32° and 42°C. At the end of the experiment, fitness increases were measured in direct competition against the common ancestor (stored at –80°C). Cultures grown at 37°C showed little increase in fitness under all temperature regimes. Those grown at 32°C showed large increases in fitness at this temperature and minor changes in fitness at the other temperatures. Likewise, those evolved at 42°C showed large increases in fitness at 42°C and minor changes in fitness at the other temperatures . Cultures that were subjected to daily shifts in temperature increased in fitness at all temperatures, though never as much as those grown at a single temperature, except for those grown at 37°C. The temperature-shift cultures were also fitter at 37°C than the culture evolved solely at this temperature (Bennett and Lenski 1999). These results show that adaptation to temperature is specific to the culture temperature . Specialization arises simply because cultures adapt to their local environment— there is no evidence of fitness trade-offs at other temperatures. Additional experiments 68 • T Y P E S O F E X P E R I M E N T A L E V O L U T I O N show that thermal niche breath does not change as cultures adapt to temperatures near the upper and lower thermal limits, and that evolution in a changing environment does not increase phenotypic plasticity (Bennett and Lenski 1999). Thus, well-conceived topdown experiments can be used to test and reject theories in evolutionary biology. In an early example of a bottom-up experiment, Dykhuizen (1978) tested the energy conservation hypothesis, which states that organisms should benefit in direct proportion to the energy saved by not synthesizing compounds already present in the environment. E. coli strains, each carrying a gene disruption that abolished synthesis of tryptophan (an amino acid...