In biology, adaptation has three related meanings. Firstly, it is the dynamic evolutionary process that fits organisms to their environment, enhancing their evolutionary fitness. Secondly, it is a state reached by the population during that process. Thirdly, it is a phenotypic or adaptive trait, with a functional role in each individual organism, that is maintained and has evolved through natural selection.
Jean-Baptiste Lamarck proposed a tendency for organisms to become more complex, moving up a ladder of progress, plus "the influence of circumstances," usually expressed as use and disuse. This second, subsidiary element of his theory is what is now called Lamarckism, a proto-evolutionary hypothesis of the inheritance of acquired characteristics, intended to explain adaptations by natural means.
Adaptation is not always a simple matter where the ideal phenotype evolves for a given external environment. An organism must be viable at all stages of its development and at all stages of its evolution. This places constraints on the evolution of development, behaviour, and structure of organisms. The main constraint, over which there has been much debate, is the requirement that each genetic and phenotypic change during evolution should be relatively small, because developmental systems are so complex and interlinked. However, it is not clear what "relatively small" should mean, for example polyploidy in plants is a reasonably common large genetic change. The origin of eukaryotic endosymbiosis is a more dramatic example.
Flexibility stems from phenotypic plasticity, the ability of an organism with a given genotype to change its phenotype in response to changes in its habitat, or to move to a different habitat. The degree of flexibility is inherited, and varies between individuals. A highly specialized animal or plant lives only in a well-defined habitat, eats a specific type of food, and cannot survive if its needs are not met. Many herbivores are like this; extreme examples are koalas which depend on Eucalyptus, and giant pandas which require bamboo. A generalist, on the other hand, eats a range of food, and can survive in many different conditions. Examples are humans, rats, crabs and many carnivores. The tendency to behave in a specialized or exploratory manner is inherited×it is an adaptation. Rather different is developmental flexibility: "An animal or plant is developmentally flexible if when it is raised in or transferred to new conditions, it changes in structure so that it is better fitted to survive in the new environment," writes evolutionary biologist John Maynard Smith.
A large diversity of genome DNAs in a species is the basis for adaptation and differentiation. A large population is needed to carry sufficient diversity. According to the misrepair-accumulation aging theory, The misrepair mechanism is important in maintaining a sufficient number of individuals in a species. misrepair is a way of repair for increasing the surviving chance of an organism when it has severe injuries. Without misrepairs, no individual could survive to reproduction age. Thus misrepair mechanism is an essential mechanism for the survival of a species and for maintaining the number of individuals. Although individuals die from aging, genome DNAs are being recopied and transmitted by individuals generation by generation. In addition, the DNA misrepairs in germ cells contribute also to the diversity of genome DNAs.
Habitats and biota do frequently change. Therefore, it follows that the process of adaptation is never finally complete. Over time, it may happen that the environment changes little, and the species comes to fit its surroundings better and better. On the other hand, it may happen that changes in the environment occur relatively rapidly, and then the species becomes less and less well adapted. Seen like this, adaptation is a genetic tracking process, which goes on all the time to some extent, but especially when the population cannot or does not move to another, less hostile area. Given enough genetic change, as well as specific demographic conditions, an adaptation may be enough to bring a population back from the brink of extinction in a process called evolutionary rescue. It should be noted that adaptation does affect, to some extent, every species in a particular ecosystem.