Gene conversion is the process by which one DNA sequence replaces a homologous sequence such that the sequences become identical after the conversion. Gene conversion can be either allelic, meaning that one allele of the same gene replaces another allele, or ectopic, meaning that one paralogous DNA sequence converts another.

Allelic gene conversion occurs during meiosis when homologous recombination between heterozygotic sites results in a mismatch in base pairing. This mismatch is then recognized and corrected by the cellular machinery causing one of the alleles to be converted to the other. This can cause non-Mendelian segregation of alleles in germ cells.

Recombination occurs not only during meiosis, but also as a mechanism for repair of double-strand breaks (DSBs) caused by DNA damage. These DSBs are usually repaired using the sister chromatid of the broken duplex and not the homologous chromosome, so they would not result in allelic conversion. Recombination also occurs between homologous sequences present at different genomic loci (paralogous sequences) which have resulted from previous gene duplications. Gene conversion occurring between paralogous sequences (ectopic gene conversion) is conjectured to be responsible for concerted evolution of gene families.

Conversion of one allele to the other is often due to base mismatch repair during homologous recombination: if one of the four chromatids during meiosis pairs up with another chromatid, as can occur because of sequence homology, DNA strand transfer can occur followed by mismatch repair. This can alter the sequence of one of the chromosomes, so that it is identical to the other.

Meiotic recombination is initiated through formation of a double-strand break (DSB). The 5' ends of the break are then degraded, leaving long 3' overhangs of several hundred nucleotides. One of these 3' single stranded DNA segments then invades a homologous sequence on the homologous chromosome, forming an intermediate which can be repaired through different pathways resulting either in crossovers (CO) or noncrossovers (NCO). At various steps of the recombination process, heteroduplex DNA (double-stranded DNA consisting of single strands from each of the two homologous chromosomes which may or may not be perfectly complementary) is formed. When mismatches occur in heteroduplex DNA, the sequence of one strand will be repaired to bind the other strand with perfect complementarity, leading to the conversion of one sequence to another. This repair process can follow either of two alternative pathways as illustrated in the Figure. By one pathway, a structure called a double Holliday junction (DHJ) is formed, leading to the exchange of DNA strands. By the other pathway, referred to as Synthesis Dependent Strand Annealing (SDSA), there is information exchange but not physical exchange. Gene conversion will occur during SDSA if the two DNA molecules are heterozygous at the site of the recombinational repair. Gene conversion may also occur during recombinational repair involving a DHJ, and this gene conversion may be associated with physical recombination of the DNA duplexes on the two sides of the DHJ.

Biased gene conversion (BGC) occurs when one allele has a higher probability of being the donor than the other in a gene conversion event. For example, when a T:G mismatch occurs, it would be more or less likely to be corrected to a C:G pair than a T:A pair. This gives that allele a higher probability of transmission to the next generation. Unbiased gene conversion means that both possibilities occur with equal probability.

GC-biased gene conversion (gBGC) is the process by which the GC content of DNA increases due to gene conversion during recombination. Evidence for gBGC exists for yeasts and humans and the theory has more recently been tested in other eukaryotic lineages. In analyzed human DNA sequences, crossover rate has been found to correlate positively with GC-content. The pseudoautosomal regions (PAR) of the X and Y chromosomes in humans, which are known to have high recombination rates also have high GC contents. Certain mammalian genes undergoing concerted evolution (for example, ribosomal operons, tRNAs, and histone genes) are very GC-rich. It has been shown that GC content is higher in paralogous human and mouse histone genes that are members of large subfamilies (presumably undergoing concerted evolution) than in paralogous histone genes with relatively unique sequences. There is also evidence for GC bias in the mismatch repair process. It is thought that this may be an adaptation to the high rate of methyl-cytosine deamination which can lead to C→T transitions.

The Fxy or Mid1 gene in some mammals closely related to house mice (humans, rats, and other Mus species) is located in the sex-linked region of the X chromosome. However, in Mus musculus, it has recently translocated such that the 3' end of the gene overlaps with the PAR region of the X-chromosome, which is known to be a recombination hotspot. This portion of the gene has experienced a dramatic increase in GC content and substitution rate at the 3rd codon position as well as in introns but the 5' region of the gene, which is X-linked, has not. Because this effect is present only in the region of the gene experiencing increased recombination rate, it must be due to biased gene conversion and not selective pressure.