FUNGI AND THEIR ALLIES
MEREDITH BLACKWELL AND JOSEPH W. SPATAFORA
A BROAD VIEW OF EUKARYOTES 8 KINGDOM FUNGI 9 PHYLUM CHYTRIDIOMYCOTA (ZOOSPORIC FUNGI) 10 PHYLUM ZYGOMYCOTA 11 CLADE GLOMALES 12 PHYLUM ASCOMYCOTA 12 Class Archiascomycetes 12 Class Saccharomycetes 13 Class Euascomycetes 13 PHYLUM BASIDIOMYCOTA 15 Class Ustilaginiomycetes 16 Class Urediniomycetes 16 Class Hymenomycetes 17KINGDOM STRAMINIPILA (HETEROKONT ZOOSPORIC ORGANISMS) 18 Oomycota 19 Hyphochytriomycetes 19 Labyrinthulales and Thraustochytriales (and Aplanochytrium) 20 SLIME MOLDS 20 Plasmodiophorales (Parasitic Slime Molds) 20 Myxomycetes, Protostelids, and Dictyostelids (Plasmodial and Cellular Slime Molds) 20 Acrasid Slime Molds 20 CONCLUSIONS 20
Fungi are heterotrophic organisms that permeate ourenvironment. With few exceptions fungi have ﬁlamentous bodies enclosed by cell walls, are nonmotile, and reproduce both sexually and asexually by spores. During the last decade, mycologists have made unprecedented progress toward producing a phylogenetic classiﬁcation of fungi; a skeleton phylogeny based on analyses of DNA characters was developed relatively early on (Bruns et al. 1991; Alexopoulos et al.1996; McLaughlin et al. 2001). Such a phylogeny serves as a basis on which hypotheses of fungal evolution can be developed. One important ﬁnding has been that “fungi” are polyphyletic (Table 1.1); their morphologies are convergent, having been derived independently from among several independent eukaryotic lineages (Fig. 1.1). A monophyletic group, exclusive of slime molds and oomycetes, is welldeﬁned and supported as “true fungi,” a kingdom-level taxon (Barr 1992; Bruns et al. 1993; Baldauf et al. 2000; Keeling et al. 2000). Historically fungi have been compared with plants and included in the study of botany. Contemporary studies, however, indicate that members of Kingdom Fungi are most closely related to animals, not plants, possibly through a choanoﬂagellate-like ancestor (Barr 1992;Baldauf and Palmer 1993; Wainright et al. 1993; Ragan et al. 1996; Baldauf et al. 2000; Cavalier-Smith 2001). The phylogenetic positions of other groups once considered as fungi are not always well deﬁned among eukaryotes (see “Kingdom Straminipila” and “Slime Molds,” later in this chapter). Thus far, fewer than 800 fungi or fungus-like taxa have been included together in any single phylogeneticrecon-
Meredith Blackwell and Joseph W. Spatafora TABLE 1.1 Fungi and Fungus-like Organisms Previously Classiﬁed as Fungi*
Fungi Chytridiomycota Zygomycota Ascomycota Basidiomycota Straminipila Oomycota Hyphochytriomycota Labyrinthulales Thraustochytriales Slime molds Plasmodiophorales Myxomycota Dictyosteliomycota Acrasiomycota * Taxonomic ranks of the clades are not indicated (seetext).
struction (Tehler et al. 2000), a number representing less than 1% of the 80,000 currently listed species (see Hawksworth et al. 1995). Estimates of up to 1.5 million species of fungi (six times more than the number of recognized species of land plants) are daunting; the missing fungi must be discovered, identiﬁed, and incorporated into the taxonomic framework. In addition to the relativelylow numbers of taxa included in the trees, taxonomic coverage across higher taxa is limited. Until now only molecular characters from ribosomal RNA genes (rDNA) have been used widely in phylogenetic studies of fungi. The recent increase in use of other DNA regions and incorporation of phenotypic characters to resolve conﬂicting trees based on single genes and analytical approaches is encouraging.Fungal classiﬁcation, as opposed to phylogeny, is in a state of ﬂux. Ideally, classiﬁcations should reﬂect phylogenetic relationships, but the relationships of all the groups covered in this volume have not been resolved nor have all of the groups been represented in analyses. Thus, the formal and complex classiﬁcation systems that have been devised (e.g., Cavalier-Smith 2001) may vary in...