For practical purposes, the individual has to be defined using a working definition and these units must be recognizable using objective detection criteria. The basidiomycetes themselves recognize self from non-self by an incompatibility system termed somatic incompatibility or vegetative incompatibility (Rayner et al., 1984; Rayner, 1991b; Worrall, 1997; Malik and Vilgalys, 1999). This is an intraspecific postfusion recognition system that normally reduces the exchange of cytoplasm between dissimilar individuals. The system has been shown to be composed of one to three or possibly more genes with multiallelic loci (Hansen et al., 1993b, 1994; Rizzo et al, 1995; Guillaumin, 1998; Malik and Vilgalys, 1999; Marcais et al., 2000; Kauserud et al., 2006; Lind et al., 2007). The exact molecular nature of the interaction is unknown, but recent advances in genome sequencing of basidiomycetes might offer new possibilities to track the actual genes. In Ascomycota, the recognition systems between hyphae have been studied in more detail (Glass et al., 2000). Between 7 and 11 loci have been identified and both allelic (e.g. Neurospora crassa, Perkins, 1988) and non-allelic (Podospora anserina, Esser and Blaich, 1994) interactions between these have been reported. Protein products from these genes include mating factors, leucine-rich repeats, signal peptides, serine proteases, G-protein, ribonucleotide reductase and a prion analogue (Glass et al., 2000). It is likely that the vegetative incompatibility systems in Asco- and Basidiomycota share some molecular characters but differ in others, for example in some ascomycete species the mating factor is involved in vegetative incompatibility but mating genes have never been shown to be involved in basidiomycete vegetative incompatibility.
The mitochondrial genome is normally uniparentally inherited in basidio-mycetes and clonally propagated with genotypic diversity arising from mutation alone (May and Taylor, 1988). However, in the laboratory recombination between mitochondrial genomes can be demonstrated (Matsumoto and FukumasaNakai, 1996). Moreover, Saville et al. (1996) provided evidence from field samples of Armillaria gallica indicating recombination in the mitochondrial genome in the wild.
Genetic markers such as isozymes, RAPD, AFLP, microsatellites etc. have been used to identify genotypes and delimit individuals (Stenlid, 1985; Smith et al., 1992; Roy et al., 1997; Vainio and Hantula, 2000; Johannesson and Stenlid, 2004). Normally the results of the various methods are congruent from samples from nature (Stenlid, 1985; Guillaumin et al., 1996; Roy et al., 1997; Vasiliauskas and Stenlid, 1999). The power of resolution differs among methods. In outcrossing and outbreeding species, somatic incompatibility normally can detect genets in a local population, yet to reach the same level of discrimination ten or more randomly chosen loci of microsatellites, RAPD or AFLPs may be needed depending on the variation present in the population. One advantage of molecular markers compared to somatic incompatibility tests is that, when studying large numbers of specimens, comparisons can be made directly on banding patterns instead of having to perform a geometrically increasing number of pairing tests. When studying inbred situations with limited genetic differentiation, such as mycelia originating from spore progenies of the same fruit body, a suite of markers might be needed to identify genotypes (Korhonen, 1978a). One recently studied example of a highly inbred wood-decomposer basidiomycete is the dry-rot fungus Serpula lacrymans (Kauserud et al., 2007). Here the genetic variation is very low due to several population genetic bottlenecks during the process of adaptation to a life in buildings. Almost no variation is detectable in AFLP (Kauserud et al., 2004), somatic incompatibility (Kauserud, 2004) and microsatellite loci (Hogberg et al., 2006) in Europe, while slightly higher variation is found in Asian populations indicating several more recent lines of infestation in Asia.
The evolutionary relevance of maintaining a non-self detection system has been suggested to be a restriction of cytoplasmic virus infection (Milgroom, 1999). Another important aspect of the incompatibility system is that it functions as a way to maintain the integrity of the individual mycelium (Rayner, 1991b). However, the somatic incompatibility barrier is leaky, for example in Heterobasid-ion annosum both dsRNA and mitochondria, as well as nuclei, could move through the barrier (Ihrmark et al., 2002). The leakiness can perhaps be seen as a trade-off between maintaining the resources for a specific nuclear combination and the possibilities offered by reassorting of nuclei mentioned above (Johannes-son and Stenlid, 2004).
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