Estimation of rates of recombination and migration in populations of plant pathogens

A method of estimating the frequency of recombination in field populations of ascomycete fungi is presented. This is a development of a technique described by J. Zhan, C. C. Mundt, and B. A. McDonald, in which field plots were inoculated with isolates of Mycosphaerella graminicola of known genotypes and then, later, the proportions of the fungal populations in the plots that originated as recombinant progeny of matings between the inoculated isolates or as immigrants from the local population were estimated, It is argued that J. Zhan, C. C. Mundt, and B. A. McDonald's method is inappropriate in terms of its approach to statistical inference and that the lack of confidence intervals for rates of recombination (r) or immigration (NZ) is a further weakness. An improvement to their method would involve the use of inoculated isolates that can be clearly distinguished from the local population, for instance, by the use of DNA markers. There should also be sufficient markers for there to be a negligible probability that progeny of matings between inoculated isolates will have the same genotype as either of their parents. With this experimental design, estimates of r and m can be found by a standard maximum likelihood method, while confidence intervals for the parameters can be estimated by a simple bootstrap procedure. The method appears to be about an order of magnitude more efficient than are the existing ways of estimating the frequency of recombination in ascomycete fungi.