All organisms suffer a certain number of small mutations, or random changes in a DNA sequence, during the process of DNA replication. These are called spontaneous mutations and occur at a rate characteristic for that organism. Genetic recombination refers more to a large-scale rearrangement of a DNA molecule. This process involves pairing between complementary strands of two parental duplex, or double-stranded DNAs, and results from a physical exchange of chromosome material.
The position at which a gene is located on a chromosome is called a locus. In a given individual, one might find two different versions of this gene at a particular locus. These alternate gene forms are called alleles. In the phase of meiosis known as Meiosis I, when the chromosomes line up along the metaphase plate, the two strands of a chromosome pair may physically cross over one another. This may cause the strands to break apart at the crossover point and reconnect to the other chromosome, resulting in the exchange of part of the chromosome.
Recombination results in a new arrangement of maternal and paternal alleles on the same chromosome. Although the same genes appear in the same order, the alleles are different. This process explains why offspring from the same parents can look so different. In this way, it is theoretically possible to have any combination of parental alleles in an offspring, and the fact that two alleles appear together in one offspring does not have any influence on the statistical probability that another offspring will have the same combination. This theory of "independent assortment" of alleles is fundamental to genetic inheritance. However, having said that, there is an exception that requires further discussion.
The frequency of recombination is actually not the same for all gene combinations. This is because recombination is greatly influenced by the proximity of one gene to another. If two genes are located close together on a chromosome, the likelihood that a recombination event will separate these two genes is less than if they were farther apart. Linkage describes the tendency of genes to be inherited together as a result of their location on the same chromosome. Linkage disequilibrium describes a situation in which some combinations of genes or genetic markers occur more or less frequently in a population than would be expected from their distances apart. Scientists apply this concept when searching for a gene that may cause a particular disease. They do this by comparing the occurrence of a specific DNA sequence with the appearance of a disease. When they find a high correlation between the two, they know they are getting closer to finding the appropriate gene sequence.