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Lichens are a classic example of symbiosis ["Zusammenleben ungleichnamiger Organismen" (1)], with interactions ranging from mutualistic to parasitic (2). Hyphae of the fungal symbiont may lie within a matrix of algal cells, adhere to these cells as appressoria, invaginate these cells as haustoria, or occasionally penetrate cell walls and plasmalemmae (3). Long-term survival of the lichen association depends on balanced growth of the symbionts, yet this balance does not preclude killing or saprobic digestion of the algal symbiont (4). Lichen-forming fungi represent many diverse lineages of Dicaryomycotina (5) that traditionally have been studied under the rubric of lichenology. These lineages are not descended from a single lichen-forming ancestor, yet it is not known how many times, and in which groups, the lichen habit originated. By examining the phylogenetic position of lichen-forming fungi relative to saprobic or pathogenic fungi, we can address a fundamental question of symbiont evolution: whether mutualistic symbioses are derived from more parasitic forms (6).
To determine the origins of the lichen habit, we included lichen-forming fungi within a phylogenetic analysis of Amastigomycota, members of Eumycota that lack motile stages. The major lineages of Amastigomycota--Basidiomycetes, Ascomycetes, and the paraphyletic zygomycetous fungi (7)--have few comparable morphological characters to serve as the basis for phylogenetic hypotheses. For example, the group Dicaryomycotina is distinguished by the single morphological feature of dikaryotic hyphae (5). Even the sexual structures used to define these groups do not allow for comparisons. Additionally, many fungi lack sexual structures and cannot be unambiguously classified.
Unlike morphological characters, molecular characters allow direct comparisons among extant Eumycota. Specifically, sequences of small subunit ribosomal DNA (SSU rDNA) have been used to propose phylogenetic hypotheses for fungi (8). The inclusion of SSU rDNA sequences from four lichen-forming representatives has produced a highly resolved phylogeny for Ascomycetes and has demonstrated that lichen-forming fungi are a key to understanding ascomycete relations (9). Our study used SSU rDNA sequences from 10 lichen-forming fungi and 65 other fungi in a cladistic analysis, which produced two equally parsimonious cladograms that differed only in sister taxa relations within one clade of three fungi (10) (Fig. 1). (Fig. 1 omitted) These phylogenetic hypotheses support Dicaryomycotina, Basidiomycetes, and Ascomycetes as monophyletic and resolve their relations (11). In the topologies, we identified the phylogenetic positions...