Adaptive evolution

The quantification of adaptation is difficult because it is unlikely that any plant is in a state of perfect adaptation to its environment since it is made up of a collection of ancestral characteristics and the process of adaptation is occurring continually. Indeed, Harper (1982) has argued that we should refer to abaptation rather than adaptation - evolution from rather than evolution towards. We can say that adaptation to an environment depends on the possession of an optimum combination of characters that minimises deleterious effects and maximises advantageous effects (Bradshaw, 1965). We must bear in mind, however, that non-adaptive characters may evolve in parallel with adaptive characters by pleiotropy, and that the direction of adaptive change is limited by the available genetic resources of the species (Harper, 1982). This is part of the reason why Harper (1982) argues that... 

Ibarra RU, Edwards JS, Palsson BO. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002 420 186-9. 

Moxon et al. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr Biol 1994 4 24-33. 

In a related application of this approach, Ferea et al. (1999) examined variations in gene expression of progeny during adaptive evolution. The yeast genomes were monitored in evolving strains subjected to growth under... 

Ferea, T.L., Botstein, D., Brown, P.O., and Rosenzwig, R.F., Systematic changes in gene expression patterns following adaptive evolution in yeast, Proc. Natl. Acad. Sci. USA, 96, 9721-9726, 1999. 

Neutral evolution is based on the hypothesis that most mutations made on the molecular level do not alter the fitness of an organism (Kimura, 1983 Kimura, 1991). This is in contrast to adaptive, or Darwinian, evolution, which asserts that mutational changes that survive selection usually have a beneficial effect. There is empirical evidence supporting both theories (King and Jukes, 1969 Kimura, 1991 Eanes et al., 1993 Hall, 1998). Recent efforts have focused on the relationship between neutral and adaptive evolution and insight has been provided into the mechanisms by which neutral evolution can drive adaptation. The neutral structure of a fitness landscape can aid the evolutionary search. Adaptive... 

The period when neutral drift dominates over adaptive evolution is called an epoch. If the fitness is plotted versus time, an epoch is a flat period showing no fitness improvement (Fig. 19). If a population becomes trapped at a suboptimal peak, it can remain trapped for a long time because it requires a specific series of mutations to escape the peak (Fontana et al., 1989). The time that a population remains trapped is longer for larger peaks. Neutrality helps the evolving population to overcome fitness barriers so that the highest fitness achieved by evolution increases with the size of the neutral network, as more sequence space can be explored (Newman and Engelhardt, 1998). 

The benefit of neutrality has yet to be captured with in vitro protein evolution. Neutral theory predicts the punctuated emergence of novel structure and function, however, with current methods, the required time scale is not feasible. Utilizing neutral evolution to accelerate the discovery of new functional and structural solutions requires a theory that predicts the behavior of mutational pathways between networks. Because the transition from neutral to adaptive evolution requires a multi-mutational switch, increasing the mutation rate decreases the time required for a punctuated change to occur. By limiting the search to... 

Levin, B.R., and C.T. Bergstrom (2000). Bacteria are different Observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. Proc. Natl. Acad. Sci. USA 97 6981-6985. 

Kimura s theory has not been universally accepted, and the debate between selectionism and neutralism is still going on, but the experimental data have changed for good our view of molecular evolution. Today, biologists are aware that neutral mutations are a fact of life, and that genetic drift is, at the molecular level, at least as important, if not more important, than natural selection. It must also be noticed that this does not diminish in the least the key role of natural selection in phenotypic evolution, and Kimura himself explicitely acknowledged that The basic mechanism of adaptive evolution is without doubt natural selection. He added however that Underneath the remarkable procession of life and indeed deep down... 

The physical separation between genotype and phenotype has an extraordinary consequence, because mental genotypes can be directly instructed by mental phenotypes, and this means that cultural heredity is based on a transmission of acquired characters. Cultural inheritance, in other words, is transmitted with a Lamarckian mechanism, whereas biological inheritance relies on a Mendelian mechanism which is enormously slower. As a result, cultural evolution is much faster than biological evolution, and almost all differences between biology and culture can be traced back to the divide that exists in their hereditary mechanisms. The discovery that human artifacts (i.e. cultural phenotypes) obey the Lotka-Volterra equations has two outstanding consequences. The first is that selection accounts for all types of adaptive evolution natural selection is the mechanism hy which all phenotypes - biological as well as cultural - diffuse in the world. 

Chemostats Used for Studying Natural Selection and Adaptive Evolution... 

Studies of adaptive evolution are long-term experiments, run for hundreds or thousands of hours, whose purpose is to elucidate the adaptive mutations occurring over time. These experiments are usually started with... 

Crespi B, Summers K, Dorus S. 2007. Adaptive evolution of genes underlying schizophrenia. Proc R Soc Lond B Biol Sci... 

Infante, J.J., Dombek, K.M., Rebordinos, L., Cantoral, J.M., Young, E.T. (2003) Genome-wide amplifications caused by chromosomal rearrangements play a mojor role in the adaptive evolution of natural yeast. Genetics, 165, 1745-1759. 

Further, they stressed that the convergent evolution of a fermentative foregut in these two groups of mammals has provided them with a unique opportunity to study adaptive evolution at the protein level. 

Hashiguchi Y, Nishida M (2007) Evolution of trace amine associated receptor (TAAR) gene family in vertebrates lineage-specific expansions and degradations of a second class of vertebrate chemosensory receptors expressed in the olfactory epithelium. Mol Biol Evol 24 2099-2107 Hashiguchi Y, Furuta Y, Kawahara R, Nishida M (2007) Diversification and adaptive evolution of putative sweet taste receptors in threespine stickleback. Gene 396 170-179 Hemess MS, Gilbertson TA (1999) Cellular mechanisms of taste transduction. Annu Rev Physiol 61 873-900... 

Hughes AL, Hughes MK (1993) Adaptive evolution in the rat olfactory receptor gene family. J Mol Evol 36 249-254... 

Shozo, Y. (2002). Evaluating adaptive evolution. Nature Genetics, 30, 350-1. 

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