Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new genomes that ultimately decide the adaptability of bacteria to varying environmental conditions.

During meiosis, when a single cell divides twice to produce four cells containing half the original number of chromosomes, HR leads to crossovers between genes. This means that two regions of the same chromosome with nearly identical sequences break and then reconnect but to a different end piece. The minor differences between the DNA sequences of the homologous chromosomes do not change the function of the gene but can change the allele or the phenotype of the gene. For example, if a gene codes for a trait such as hair color, its allele determines the specific phenotype, i.e. whether the hair would be black, blonde or red. Humans contain two alleles of the same gene, at each gene location, one from each parent. Recombination such as gene conversion changes this distribution, altering the gene’s form or manifestation in the offspring.