No Perfect Organism
Natural selection is a driving force in evolution and can generate populations that are better 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 does not create anything from scratch. Thus, it is limited by a population’s existing genetic variance and whatever new alleles arise through mutation and gene flow.
Natural selection is also limited because it works at the individual, not allele level, and some alleles are linked due to their physical proximity in the genome, making them more likely to pass on together (linkage disequilibrium). Any given individual may carry some beneficial and some unfavorable alleles. It is the alleles' net effect, or the organism’s fitness, upon which natural selection can act. As a result, good alleles can be lost if individuals who carry them also have several overwhelmingly bad alleles. Likewise, bad alleles can be kept if individuals who have enough good alleles to result in an overall fitness benefit carry them.
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 going from the less beneficial to the more beneficial trait would require going through a less beneficial phenotype. Think back to the mice that live at the beach. Some are light-colored and blend in with the sand, while others are dark and blend in with the patches of grass. The dark-colored mice may be, overall, more fit than the light-colored mice, and at first glance, one might expect the light-colored mice to be selected for a darker coloration. However, remember that the intermediate phenotype, a medium-colored coat, is very bad for the mice—they cannot blend in with either the sand or the grass and predators are more likely to eat them. As a result, the light-colored mice would not be selected for a dark coloration because those individuals who began moving in that direction (began selection for a darker coat) would be less fit than those that stayed light.
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: 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 the various forces that we have described in this chapter and how they influence the population's genetic and phenotypic variance.