The ultimate source of evolution is mutation, a permanent, heritable change in the nucleotide sequence of a chromosome, usually in a single gene. Mutations occur at random and can vary in their effect. They may be neutral with no phenotypic expression, or cause variations to an individual's phenotype, which may range from small-scale to large-scale. Although mutations can affect an individual's survival, evolution is driven forward only if this mutation can be passed on to the next generation, thereby affecting that generation's survival rates as well.

Recombination is another source of variation in a population. It is a process whereby two homologous chromosomes exchange some of their genetic material producing two chromosomes that are genetically unique from the original, or parental, chromosomes. Recombination enlarges the amount of genetic diversity in the population by increasing the number of alleles at any given genetic locus.⁰⁸

Both mutations and recombination can alter the allelic frequencies from generation to generation and, at least in theory in small populations, can affect HWE. While mutation and recombination add to the variation within a population, their effects are limited.

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