Jukes-Cantor correction

The Jukes-Cantor correction solves the problem in phylogenetics when as the time of divergence between two sequences increases the probability of a second substitution at any one nucleotide site increases and the increase in the count of differences is slowed. This makes these counts not a desirable measure of distance. In some way, this slow down must be accounted for.

The solution to this problem was first noted by Jukes and Cantor (1969). Instead of calculating distance as a simple count take the distance as

K(A,B) = -3/4 * loge[1 - 4/3 * D(A,B)]

This is the Jukes-Cantor correction equation for homoplasy.

Example

• Un-corrected distance:

             *     *    *       *
Species A: ATGCT CGTAG CTGCT ACGTC
Species B: ATCCT CGAAG CAGCT ACGAC

Count the changes (*) and divide by the length:

D(A,B) = 4/20

• Jukes-Cantor correction distance:

             A     B
Species A: ----  0.20
Species B: 0.23  ----

Apply the equation above to these data.

References

• Kimura and Ohta (1972). J Mol Evol 2:87-90.
• Jukes TH and Cantor CR (1969). Mammalian Protein Metabolism, H. N. Munro, Ed. (Academic Press, New York), pp. 21-132.