An improved method for estimating the rate of fixation of favorable mutations based on DNA polymorphism data.

The hitchhiking effect has frequently been used as a method to detect the action of past directional selection at the DNA sequence level in natural populations of several Drosophila species (Aguade et al. [ 1989 1; Stephan and Langley [ 19891; Miyashita [ 19901; Begun and Aquadro [ 199 11; Berry et al. [ 199 11; references to later papers can be found in Golding’s [ 19941 volume) and in natural isolates of Escherichia coli (Guttman and Dykhuizen 1994). Advantageous mutations going to fixation leave footprints of reduced DNA sequence variation which can most easily be identified in genomic regions of very low recombination. Mathematical models of the hitchhiking effect have explored the observed correlation between DNA sequence variation and levels of crossing-over (Maynard Smith and Haigh 1974; Kaplan et al. 1989; Stephan et al. 1992). Following this work, a method for estimating the rate of fixation of favorable mutations from DNA polymorphism data has been proposed (Wiehe and Stephan 1993). A formula describing the functional relationship between expected nucleotide diversity, rc, and recombination rate (per nucleotide site), P, has been derived for an with one selected locus: equilibrium hitchhiking model