Gene flow is the movement of individuals among populations and can be estimated indirectly through isozyme analysis as the number of migrants per generation (Slatkin and Barton 1989) or by analysis of "private" alleles—those limited to a single species or population. Different species usually have highly differentiated allele frequencies and a higher number of private alleles compared to individuals from a single panmictic population. The computer program popgene, among others, can perform this type of analysis.
Applications of isozyme analysis to epidemiology have included monitoring the spread of specific genotypes of Phytophthora infestans (Goodwin et al. 1995; Legard and Fry 1996), determining the influence of various evolutionary forces on the composition of inoculated populations of the barley scald pathogen Rhynchosporium secalis (Goodwin et al. 1994), and estimating the size of and boundaries between individuals of the puffball Lycoperdon pyriforme on decaying logs (Huss 1993).
The first real attempt to use isozymes to analyze the genetic structure of fungal populations was for Neurospora intermedia by Spieth (1975). That analysis revealed a high level of genetic variation within but low differentiation among populations. Spieth's pioneering work was followed by additional studies within a decade and this has accelerated during the 1990s. Many of these studies have had similar results and demonstrated high gene diversity within but low differentiation among populations of a wide diversity of fungi (Andrews et al. 1988; Goodwin et al. 1993; Huss 1996; Tuskan et al. 1990). Other authors have found varying degrees of subdivision among populations, usually among host-associated forms (Harvey et al. 2001; Leuchtmann and Clay 1989; 1990) and, more rarely, among physiological races (Welz et al. 1994).
Gene flow analysis of isozyme markers also can indicate when taxa have become sufficiently isolated reproductively to be considered separate species. Existence of separate species was shown conclusively for several closely related groups in the genus Phytophthora (Goodwin et al. 1999; Man in't Veld et al. 2002; Nygaard et al. 1989) which could not have been discovered without the use of molecular markers. A similar approach identified distinct biological species within the mushroom Pleurotus eryngii (Urbanelli et al. 2002).
Isozyme analyses of some populations of fungi and oomycetes have revealed extremely low levels of genetic variation reflective of a highly clonal population structure. This occurred for rice-infecting isolates of the rice blast fungus Magnaporthe grisea (Leung and Williams 1986), asexual populations of cereal rusts (Burdon and Roelfs 1985a,b), and worldwide populations of the oomycete
Phytophthora infestans (Spielman et al. 1991; Tooley et al. 1985). Populations of fungi infecting conifer hosts in the western United States also appeared to be highly clonal and specific clones are characterized by fixed heterozygosity (Otrosina et al. 1992; Vogler et al. 1991).
Differences in levels of genetic variation among locations can help identify the center of origin of a species. The most diverse populations genetically should occur at or near the center of origin, as these populations will have had the longest time in which mutations can accumulate; derived populations usually will contain only a subset of the total species diversity. This idea has been combined with isozyme analysis to indicate that the edible mushroom Agaricus bisporus may be indigenous to North America (Kerrigan and Ross 1989) and that Phytophthora infestans, P. palmivora, and P. megakarya probably originated in central Mexico (Tooley et al. 1985), southeast Asia (Mchau and Coffey 1994), and central Africa (Nyasse et al. 1999), respectively. Very limited genetic diversity indicated that the plant pathogens Puccinia graminis f. sp. tritici, Phytophthora cinnamomea, and Dilophospora alopecuri had only very limited introductions into Australia (Burdon et al. 1982; Old et al. 1984; Riley et al. 1998), although the original source populations for the introductions could not be identified for certain.
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