The detection and measurement of recombination from sequence data

There are two types of recombination that we may wish to detect: rare recom binants between members of different populations or species and repeated re combination within a population. Methods appropriate in the former context are inappropriate in the latter because they depend on recognizing the exis tence of runs of nucleotides with similar ancestry. If recombination is suf ficiently frequent, no such runs will be present. Several methods, includin g the homoplasy test and the incompatibility test, are described that are a ppropriate for detecting repeated recombination and for measuring its impor tance, relative to mutation, in causing genetic change. The sensitivity of these tests is investigated by simulating populations with varying frequenc ies of mutation and recombination and calculating the various statistics on samples.