Agents of Change

We begin this chapter by returning to the ideas of advantageous and deleterious genetic variants we alluded to in Chapter 4 . We use a well-studied example from the biology of the HIV virus and its resistance to the drug AZT. We discover that genetic variants (or alleles) beneficial when a drug is present can be deleterious in its absence. We then ask if alleles are always advantageous or deleterious. We argue that introns, the structure of the genetic code, and the prevalence of repetitive elements in the human genome suggest that there is a third class of variants: the neutral alleles that have no effect on fitness. We then ask how the frequency of such alleles might change in time in a population of finite size. We argue that effects such as the independent assortment of chromosomes in meiosis should cause generation-to-generation changes in frequency even for neutral alleles. We then develop a Python script to simulate this process. Running our simulations leads us to the conclusion that even neutral genetic variation is transient in finite populations, and that the time it takes to lose that variation is proportional to population size. We then compare our results to those from a theoretical model of this process of genetic drift and find that their predictions are very similar.