One of the most widely applied uses of ancestral character state reconstruction is in the study of adaptation. The word adaptation is derived from the Latin ad (to, toward) and aptus (a fit), and is used to imply a feature or phenotype that evolved to serve a particular function or purpose. For example, the function or purpose of an animal central nervous system is to coordinate sensory information and motor output patterns; that is to say, a centralized brain is an adaptation for sensory-motor coordination. Adaptation is therefore used both as a noun to describe the features that arose because of natural selection, and as a verb, the process of natural selection through which the features originated. In an evolutionary context, an adaptation is not only a static description of the match between form and function, but is also an explanation for the origin of that relationship (Russell, 1916).

It is important to distinguish among several distinct uses of the word 'adaptation' in the biological sciences. A physiological adaptation is an organismal response to a particular stress: if you heat up from the sun you may respond by moving into the shade (a behavioral adaptation), or you may respond by sweating (a physiological adaptation). In an evolutionary context, adaptation is also a change in response to a certain problem, but the change is genetic. Evolutionary adaptations that result from the process of natural selection usually take place over periods of time considerably longer than physiological timescales. Traits are referred to as adaptations only when they evolved as the solutions for a specific problem; that is, for a particular function or purpose. A physiological response can itself be an adaptation in the evolutionary sense.

In reconstructing ancestral phenotypes it is important to bear in mind the primitive condition may be more or less variable than the conditions observed in living species. In some cases physiological or developmental plasticity is itself an evolutionary (genetic) specialization that permits organisms to adapt physiologically or behaviorally. For example, many species are characterized as eur-ytopic, or tolerant of a wide variety of habitats. Other species are stenotopic, or adapted to a narrow range of habitats. Similarly, individual characters may be more or less variable within a species, and this variability may itself be subject to evolutionary change. Flexible phenotypes may be more adaptive in a variable environment and stereotyped pheno-types more adaptive in a stable environment (van Buskirk, 2002).

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