doubtful. Many holocarpic isolates form a
monophyletic clade (Fig. 3.5) (Beakes et al.
2006 ; Hatai 2012 ), whilst others intercalate
amongst thosePythiumclades with predomi-
nantly filamentous sporangia (Fig.3.14l), as
indeed does the genusPythiogeton(Fig.3.5b)
(Huang et al. 2012 ; Schroeder et al. 2012 ). Nei-
ther the orderMyzocytiopsidalesnor the family
Myzocytiopsidaceae(Table3.4) proposed by
Dick ( 1997 ,2001a) has any molecular support,
and both are rejected and omitted from our
revised taxonomic scheme (Table3.5).
The largest and most comprehensively
studied genus in this family is Pythium
(Fig.3.14k–w).Pythiumwas last monographed
by Plaats-Niterink ( 1981 ) and will soon be
updated (previewed by de Cock et al. 2012 ).
This genus has well over 100 species, most of
which have been sequenced (Bala et al. 2010 ;
Bedard et al. 2006 ; Briard et al. 1995 ;Le ́vesque
and de Cock 2004 ; Martin 2000 ; Schurko et al.
2004; Villa et al. 2006 ; Uzuhashi et al. 2010 ).
Early molecular studies found that species
assigned toPythiumspecies fell intoten clades,
designated A–K (Le ́vesque and de Cock 2004 )
(Fig.3.5b). Unfortunately, there are few com-
mon morphological features which characterize
every species within a given clade. Although
some broad overall morphological trends are
recognizable, there are always exceptions to
the norm, which makes it difficult to define
clade synapomorphies (de Cock et al. 2012 ).
There is a monophyletic cluster of clades (A–
D: Fig.3.5b) whose species predominantly have
simplefilamentous(Fig.3.14l)toirregularly
inflated(Fig. 3.14m, n) zoosporangia (Le ́v-
esque and de Cock 2004 ). These simple spor-
angia are found in the earliest diverging clades
(if lagenidiaceous genera are excluded) and are
considered to represent an ancestral state. This
group includes thetype species(clade A:P.
monospermum) and, as was recently proposed,
represents thegenusPythiums. str.(Uzuhashi
et al. 2010 ). This basal group contains species
that are opportunistparasites of seaweeds(e.g.
Pythium chondricolaandPythium porphyrae)
and vertebrates (e.g. Pythium insidiosum;
Schurko et al. 2004 ). However, even this
redefined Pythium s. str. group of clades
(Uzuhashi et al. 2010 ) has nested within it the
Pythiogetonsubclade(Huang et al. 2012 ), as
well as many holocarpic isolates, previously
assigned to the genera ~LagenidiumandMyzo-
cytiopsis(as in Fig.3.5b) (Schroeder et al. 2012 ),
and is therefore still in need of revision.
A second group ofPythiumclades (E–J)
(Le ́vesque and de Cock 2004 ) that share a com-
mon ancestor contains species with predomi-
nantly ovoid to globose sporangia that
frequently proliferate internally (Fig.3.14r, s)
and have oogonium walls that are often spiny
(e.g. P. amasculinum, Fig.3.14u). These are
considered to represent a derived state and
include the important root-infecting plant
pathogen P. ultimum(Fig.3.14v, w), whose
genome sequence was recently published (Le ́v-
esque et al. 2010 ). Uzuhashi et al. ( 2010 ) also
proposed that the species in clades E–G and I–J
(such asP. multisporum, clade E, Fig.3.14r)be
transferred to a new genus,Globisporangium,
and those in the sister clade (Clade H, e.g.P
undulatum, Fig.3.14s) to the genusElongispor-
angium, although these new names have not
been widely adopted.c) Peronosporaceae s. lat.
This is a species-diverse, predominantly plant-
pathogenic family that contains a significant
proportion of the total number of known
oomycete species (Thines and Kamoun 2010 ).
The expandedPeronosporaceaeproposed here
contains many economically important species
that account for and have been the focus of
much research effort, particularly in relation
to unravelling the basis of theirpathogenicity
(e.g. Kemen and Jones 2012 ; Lamour et al. 2007 ;
Randall et al. 2005 ; Thines and Kamoun 2010 ;
Tyler et al. 2006 ; Voglmayr 2008 ). Hulvey et al.
( 2010 ) proposed maintaining thebroad circum-
scriptionof the family Peronosporaceae, so that
it includes all downy mildews, ~Phytophthora
and many ~Halophytophthoraspp., in order to
avoid the creation of a plethora of poorly differ-
entiated families.Peronosporaceae(Fig.3.15)as
redefined here includes the genera Phyto-
pythium(formerly thePythiumK-clade) (Bala72 G.W. Beakes et al.