MacDonald 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. To conduct the test Mac- Donald and Kreitman examine the evolutionary dynamics of the alcohol dehydrogenase (Adh) gene in three species of Drosophila. 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 Adh gene. Based on the test they conclude that there is strong evidence for adaptive protein evolution at particular sites in the gene. Understanding the test requires some basic knowledge about molecular terms and the predictions of neutral theory. The two important terms are fixed differences and polymorphisms. These are determined by comparing DNA sequences made up of thousands of individual nucleotide sites. A site that is unchanged within a species but different from a related species counts as a fixed difference. These are mutations that occur in some common ancestor of the lineage such that all descendants inherit the change. A site that differs within a species counts as a polymorphism. Determining the number of fixed differences and polymorphisms requires placing 1 each individual gene sequence onto a phylogenetic tree. A coalescent tree charts the ancestral relationships for a set of individual gene sequences. Sequences sampled from within a species form a within-species tree. The common ancestors of each within-species tree form a between-species tree. A detected difference counts as a polymorphism or a fixed difference depending on where it occurs in the phylogenetic tree (cf. Table 1). The test uses the numbers of polymorphisms and fixed differences as indicators of evolutionary rates..
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