McDonalds & Kreitman test (MKT)


McDonalds & Kreitman test (MKT)search for term

McDonald and Kreitman (1991) propose a test of the neutral mutationrandom drift (NM-RD) hypothesis, the central claim of the neutral theory of molecular evolution. The test involves generating predictions from the NM-RD hypothesis about patterns of molecular substitutions. Alternative selection hypotheses predict that the data will deviate from the predictions of the NM-RD hypothesis in specifiable ways. The test compares the number of DNA sequence changes between species and within species. The number of DNA differences is an indicator of the evolutionary rate of the gene. Based on the test they conclude that there is strong evidence for adaptive protein evolution at particular sites in the gene. (http://pforber.squarespace.com/storage/forber-MKtest.pdf). McDonald-Kreitman test compares the ratio of the number of nonsynonymous to synonymous 'polymorphisms' within species to that ratio of the number of nonsynonymous to synonymous 'fixed' differences between species in a 2x2 table. The most direct method of showing the presence of positive selection is to compare the number of nonsynonymous (dN) to the number of synonymous (dS) substitutions in a locus. A high (>1) value of (dN/dS) substitutions suggest fixation of nonsynonymous mutations with a higher probability than neutral (synonymous) ones. The dN/dS ratio tests take into account of transition/transversion rate bias and codon usage bias.(http://dorakmt.tripod.com/evolution/popgen.html )