The technique of DNA-DNA hybridisation measures the degree of similarity between the genomes of different species, and therefore predicts genealogies of extant species by comparing the genetic resemblance between lineages that diverged millions of years ago.
The principle of the technique is simple and utilises a basic physical, structural property of DNA. When heated almost to boiling, the hydrogen bonds binding the two strands of DNA together in a double helix break, and the DNA is denatured, separated into two complimentary strands. Then allowed to cool, and incubated at between 50 and 60 degrees C, the single strands will associate with their complimentary partners and reform their double helix. Given enough time, all single strands will find partners and the DNA will reform virtually perfectly, as the strands are exact matches for each other. The double helix rebuilds when the hydrogen bonds between complimentary base pairs are reformed.
This property is exploited by DNA-DNA hybridisation. DNA from two species will share a certain degree of similarity, reflected in the sequences of their base pairs. Therefore, when single strands of two species are introduced and incubated, complimentary base pairs will align and the double helix will attempt to re-anneal. The extent to which this occurs is measured by gradually heating the 'hybrid DNA' formed by the association of the two species, until the hydrogen bonds between the strands become so strained that they break, or melt, yielding single strands once more. If the species are closely related they will share many complimentary base pairs, and consequently many hydrogen bonds will form within the hybrid. The greater the number of hydrogen bonds, the stronger the double strands will be, and therefore the higher the temperature required to break the unison. The hybrid DNA of more distantly related species will split at a lower temperature. Melting, or breaking of the hydrogen bonds is detected when radioactive fragments of DNA are released within the single strands. As a rule of thumb, a difference in melting temperature of one degree is equivalent to a difference in DNA sequence of one percent, (i.e, one nucleotide in a sequence of one hundred) (Lewin 1997).
The technique yields a measure of genetic distance between two species, but with no information about character state. It has the advantage of statistically rendering homoplasy (or analogy) insignificant, because as such a large proportion of a species genome can be studied, the number of nucleotide positions at which homoplasy is likely is tiny compared with the number of homologous positions within the genome.