No Perfect Organism
Natural selection is a driving force in evolution and can generate populations that are adapted to survive and successfully reproduce in their environments. However, natural selection cannot produce the perfect organism. Natural selection can only select on existing variation in the population; it cannot create anything from scratch. Therefore, the process of evolution is limited by a population's existing genetic variance, the physical proximity of alleles, non-beneficial intermediate morphs in a polymorphic population, and non-adaptive evolutionary forces.
Natural Selection Acts on Individuals, not Alleles
Natural selection is also limited because it acts on the phenotypes of individuals, not alleles. Some alleles may be more likely to be passed on with alleles that confer a beneficial phenotype because of their physical proximity on the chromosomes. Alleles that are carried together are in linkage disequilibrium. When a neutral allele is linked to beneficial allele, consequently meaning that it has a selective advantage, the allele frequency can increase in the population through genetic hitchhiking (also called genetic draft).
Any given individual may carry some beneficial alleles and some unfavorable alleles. Natural selection acts on the net effect of these alleles and corresponding fitness of the phenotype. As a result, good alleles can be lost if they are carried by individuals that also have several overwhelmingly bad alleles; similarly, bad alleles can be kept if they are carried by individuals that have enough good alleles to result in an overall fitness benefit.
Polymorphism
Furthermore, natural selection can be constrained by the relationships between different polymorphisms. One morph may confer a higher fitness than another, but may not increase in frequency because the intermediate morph is detrimental.
Polymorphism in the grove snail
Color and pattern morphs of the grove snail, Cepaea nemoralis.The polymorphism, when two or more different genotypes exist within a given species, in grove snails seems to have several causes, including predation by thrushes.
For example, consider a hypothetical population of mice that live in the desert. Some are light-colored and blend in with the sand, while others are dark and blend in with the patches of black rock. The dark-colored mice may be more fit than the light-colored mice, and according to the principles of natural selection the frequency of light-colored mice is expected to decrease over time. However, the intermediate phenotype of a medium-colored coat is very bad for the mice: these cannot blend in with either the sand or the rock and will more vulnerable to predators. As a result, the frequency of a dark-colored mice would not increase because the intermediate morphs are less fit than either light-colored or dark-colored mice. This a common example of disruptive selection.
Not all Evolution is Adaptive
Finally, it is important to understand that not all evolution is adaptive. While natural selection selects the fittest individuals and often results in a more fit population overall, other forces of evolution, including genetic drift and gene flow, often do the opposite by introducing deleterious alleles to the population's gene pool. Evolution has no purpose. It is not changing a population into a preconceived ideal. It is simply the sum of various forces and their influence on the genetic and phenotypic variance of a population.