The evolution of living organisms is the consequence of two processes. First, evolution depends on the genetic variability generated by mutations, which continuously arise within populations. Second, it also relies on changes in the frequency of alleles within populations over time.

The fate of those mutations that affect the fitness of their carrier is partly determined by natural selection. On one hand, new alleles that confer a higher fitness tend to increase in frequency over time until they reach fixation, thus replacing the ancestral allele in the population. This evolutionary process is called positive or directional selection. Conversely, new mutations that decrease the carrier's fitness tend to disappear from populations through a process known as negative or purifying selection. Finally, it may happen that a mutation is advantageous only in heterozygotes but not in homozygotes. Such alleles tend to be maintained at an intermediate frequency in populations by way of the process known as balancing selection.

However, natural selection is not the only factor that can lead to changes in allele frequency. For example, consider a theoretical population in which all individuals, or genotypes, have exactly the same fitness. In this situation, natural selection does not operate, because all genotypes have the same chance to contribute to the next generation. Given that populations do not grow infinitely and that each individual produces many gametes, it follows that only a fraction of the gametes that are produced will succeed in developing into adults. Thus, in each generation, allelic frequencies may change simply as a consequence of this random process of gamete sampling. This process is called genetic drift. The difference between genetic drift and natural selection is that changes in allele frequency caused by genetic drift are random, rather than directional. Ultimately, genetic drift leads to the fixation of some alleles and the loss of others.

But what about mutations that do not affect the fitness of individuals? These so-called neutral mutations are not affected by natural selection and, hence, their fate is essentially driven by genetic drift. Interestingly, Darwin himself recognized that some traits might evolve without being affected by natural selection:

"Variations neither useful nor injurious would not be affected by natural selection, and would be left either a fluctuating element, as perhaps we see in certain polymorphic species, or would ultimately become fixed, owing to the nature of the organism and the nature of the conditions." (Darwin, 1859)

It is important to note, however, that the impact of genetic drift is not limited to neutral mutations. Because of genetic drift, most advantageous mutations are eventually lost, whereas some weakly deleterious mutations may become fixed.

Beyond selection and drift, biased gene conversion (BGC) is a third process that can cause changes in allele frequency in sexual populations. BGC is linked to meiotic crossing-over. When crossing-over occurs between two homologous chromosomes, the intermediate includes heteroduplex DNA—a region in which one DNA strand is from one homologue and the other strand is from the other homologue. Regardless of the ultimate resolution of the crossover intermediate (in other words, whether the regions on either side of the crossover junction recombine), base-pairing mismatches in the heteroduplex region must be resolved. As a consequence, when a given locus resides in the heteroduplex region, one allele can be "copied and pasted" onto the other one during gene conversion.

BGC is said to be biased if one allele has a higher probability of conversion than the other. In that situation, the donor allele will occur at higher frequency in the gamete pool than the converted allele. Hence, BGC tends to increase the frequency of such donor alleles within populations. There is evidence that BGC occurs in many eukaryotic species, and various observations suggest that it might result from a bias in the repair of DNA mismatches in the heteroduplex DNA formed during recombination (Marais, 2003). Again, it is important to note that the impact of BGC is not limited to the evolution of neutral mutations: BGC can favor the fixation of donor alleles even if these alleles are weakly deleterious (Galtier & Duret, 2007).