Genome-based analyses are providing
enhanced resolution and support for the
higher-level relationships of Agaricomycetes,
although so far only a few broad-scale phylo-
genomic studies of Agaricomycetes and other
Fungi have been published (Hibbett et al.
2013 ). As of this writing, the most inclusive
published analysis contains representatives of
8 orders of Agaricomycetes (Floudas et al.
2012 ), but over 70 Agaricomycete genomes
have been completed, many by the Joint
Genome Institute of the US Department of
Energy (Grigoriev et al. 2012 ). The phylogeny
in Fig.14.1represents a consensus of pub-
lished (Binder et al. 2013 ; Floudas et al. 2012 ;
Padamsee et al. 2012 ) and unpublished (L.
Nagy, D. Floudas, D. Hibbett, and R. Riley,
unpublished) phylogenomic analyses that col-
lectively draw on more than 40 whole-genome
sequences from 15 orders of Agaricomycetes,
as well as representatives of Dacrymycetes,
Tremellomycetes, Wallemiomycetes, and
other Fungi. Gomphales, Hysterangiales, Lepi-
dostromatales, Phallales, Thelephorales, and
Trechisporales have yet to be included in
phylogenomic analyses; placements of these
groups in Fig.14.1are based on studies com-
bining rRNA genes with protein-coding genes
(Hodkinson et al. 2013 ; Hosaka et al. 2006 ;
Matheny et al. 2007 ).
Phylogenomic analyses have confirmed
some aspects of the phylogeny of Agaricomy-
cetes that had been resolved in earlier studies of
rRNA and protein-coding genes, such as the
monophyly of Agaricomycetidae (Agaricales,
Boletales, Atheliales, Amylocorticiales, and
Lepidostromatales) and its sister group rela-
tionship to Russulales. Novel results from phy-
logenomics include the placements of Jaapiales,
Corticiales, and Gloeophyllales. In previous
analyses combining rRNA and protein-coding
genes,Jaapiawas placed as the sister group to
Agaricomycetidae, and the higher-level posi-
tion of Gloeophyllales was unresolved (Binder
et al. 2010 ; Garcia-Sandoval et al. 2011 ). Recent
phylogenomic analyses indicate that Jaapiales,
Gloeophyllales, and Corticiales form a strongly
supported clade, but its higher-level position is
ambiguous.
B. Taxonomic Characters and Ecological
DiversityAgaricomycete systematists have traditionally
used morphological, biochemical, and ecologi-
cal characters to formulate phylogenetic
hypotheses and structure classifications, and a
rich descriptive literature has evolved (Cle ́men-
c ̧on 2004 ; Donk 1964 ;Ju ̈lich 1981 ;Ku ̈hner 1984 ;
Oberwinkler 1977 ; Petersen1971a; Reijnders
and Stalpers 1992 ; Singer 1986 ). Nonmolecular
characters that have been emphasized include
anatomical features (e.g., shapes and staining
reactions of spores, basidia, and cystidia,
hyphal systems of fruiting bodies, rhizomorph
structures), macromorphology of fruiting bod-
ies (including developmental characters), pig-
ment chemistry, and cytological characters
(e.g., nuclear behavior in basidiosporogenesis).
Cultural characters, wood-decay modes (white
rot vs. brown rot), and asexual reproductive
forms have also been used to address relation-
ships and provide tools for identification
(Nakasone1990a; Redhead and Ginns 1985 ;Stal-
pers 1978 ). The previous version of this chapter
(Hibbett and Thorn 2001 ) contained a review of
nonmolecular characters and ecological modes
across major groups of Agaricomycetes, which is
not repeated here. Part II of the present chapter
summarizes the major morphological and
ecological features within each order of Agarico-
mycetes, as informed by recent phylogenetic
studies. The following sections discuss septal
pore ultrastructure (Fig.14.2), the evolution of
fruiting body forms (Figs.14.3,14.4,14.5,14.6,
14.7,14.8,and14.9), and the phylogenetic distri-
bution of major ecological modes (Table14.1a, b)
across the major groups of Agaricomycetes.- Septal Pore Ultrastructure
Septal pore ultrastructure provided clues to the
higher-level relationships of Agaricomycetes
long before the advent of molecular characters.
The union of Dacrymycetes and Agaricomy-
cetes is supported by their shared possession
of dolipores that are surrounded at each side by
a more or less dome-shaped modified ER
(endoplasmic reticulum) cisterna, the so-called376 D.S. Hibbett et al.