This document discusses the phylum Parabasalia, which includes amitochondriate protists that are known parasites of vertebrates or symbionts in the hindguts of wood-eating cockroaches and termites. The phylum is currently divided into 6 classes based on flagellar, cytoskeletal and nuclear characteristics. Many species remain unclassified or misclassified due to challenges in distinguishing morphological traits. Ongoing research aims to improve phylogenetic classification and understand the evolutionary transitions among Parabasalia lineages.

1. PARABASALIA
(Excavata,
Metamonada)
Vera
Tai1,
Erick
R.
James2,
Patrick
J.
Keeling2
1BC-­‐CFE
in
HIV/AIDS,
St.
Paul’s
Hospital,
Vancouver,
BC,
Canada
 Amitochondriate
proOsts
(but
have
hydrogenosome)
that
are
best
known
as
parasites
of
vertebrate
hosts
(eg.
Trichomonas
vaginalis,
Tritrichomonas
foetus)
 Greatest
diversity
is
found
as
symbionts
in
the
hindguts
of
wood-­‐eaOng
cockroaches
and
termites
 Phylum
is
named
aUer
the
parabasal
apparatus
which
consists
of
a
parabasal
body
(modified
Golgi)
with
parabasal
fibres
that
are
aWached
to
basal
bodies
 Most
have
an
axostyle
which
is
a
hollow
tube
of
a
rolled
row
of
microtubules
 Ancestor
is
thought
to
be
a
trichomonad-­‐like
cell,
simple
in
structure,
bearing
4
flagella,
one
of
which
is
recurrent
and
underlain
by
the
costa
forming
an
undulaOng
membrane
 Assumed
to
have
evolved
from
simple
to
complex
and
was
divided
into
two
classes,
the
simpler
Trichomonadida
and
the
mulOflagellated
HypermasOgida
 This
view
was
overly
simplisOc
and
current
classificaOon
includes
6
classes
of
Parabasalia
implying
several
transiOons
of
mulOplicaOon
and
reducOon
in
flagellar,
cytoskeletal,
and
nuclear
elements
 Many
are
misclassified,
especially
smaller
ones,
due
to
misunderstanding
of
morphological
evoluOon
 Many
other
parabasalids
remain
unclassified
because
new
taxonomic
groups
need
to
be
defined
are needed. In the present study, Spirotrichonymphea and
Hypotrichomonadea are represented by only two taxa and a
further taxon sampling may improve the resolution; however,
Hypotrichomonadea comprises only two genera [26] both of
which are included in the analyses and Spirotrichonymphea cells,
usually small in size, are very hard to distinguish by light
microscopy if multiple species occur simultaneously in the gut of
termites (and they very often do).
Table 3. Shimodaira-Hasegawa (SH) and approximately
unbiased (AU) tests for parabasalian root positions.
Root position P value
SH AU
a 0.012* 0.001*
b 0.088 0.044*
c 0.005* ,0.001*
d 0.019* 0.001*
e 0.367 0.161
f 0.378 0.013*
g 0.491 0.148
h 0.009* 0.002*
i 0.018* 0.001*
j 0.065 ,0.001*
k Best Best
Root positions are depicted in Figure 3. Asterisks indicate that the root position
was significantly different from the best ML topology at P,0.05.
doi:10.1371/journal.pone.0029938.t003
Figure 4. Maximum likelihood tree based on concatenation of GAPDH, actin, EF-1a, and SSU rRNA gene sequences and rooted by
Trimastix. Unambiguously aligned amino acid sites of GAPDH (257), actin (268), and EF-1a (274), and nucleotide sites of SSU rRNA (1338) gene
sequences were concatenated and analyzed in 28 parabasalian species with Trimastix as an outgroup. The tree was estimated in RAxML using the
CAT model (CATMIX). The parameters and branch length were optimized for each gene partition individually. The supporting values (bootstrap in
RAxML/Bayesian posterior probability) are indicated at the nodes. Values below 50% or 0.5 are indicated by hyphens. Vertical bars to the right of the
tree represent the parabasalian classes. The scale bar corresponds to 0.10 substitutions per site.
doi:10.1371/journal.pone.0029938.g004
Table 4. Exclusion of parabasalian taxa and the effect on
their root.
No. of parabasalian taxa
excluded 23 outgroup taxa 13 outgroup taxa
3 10 NT
6 10 NT
12 10 10
16 4 8
18 5 6
Values represent the number of occurrences of root position k (shown in
Figure 3) in 10 replicates of the random taxa exclusion analyses in each defined
number of excluded taxa. NT, not tested. The 23 outgroup taxa correspond to
the concatenate dataset of EF-1a, actin, and SSU rRNA gene sequences using 23
outgroup taxa as shown in Figure 3, whereas the 13 outgroup taxa correspond
to those remained after excluding 10 long-branch outgroup taxa (as
investigated in Table S1). Note that in the cases of 16 and 18 taxa exclusions, all
other replicates demonstrated the root position at the branch leading to
Trichonymphea (position g).
doi:10.1371/journal.pone.0029938.t004
Phylogeny and Evolution of Parabasalia
PLoS ONE | www.plosone.org 8 January 2012 | Volume 7 | Issue 1 | e29938
C. Trichomonadea
O. Trichomonadida
F. Trichomonadidae
O. Honigbergiellida,
F. Honigbergiellidae
F. Hexamastigidae
F. Tricercomitidae
C. Hypotrichomonadea
O. Hypotrichomonadida
F. Hypotrichomonadidae
C. Tritrichomonadea
O. Tritrichomonadida
F. Tritrichomonadidae
F. Dientamoebidae
F. Monocercomonadidae
C. Cristamonadea
O. Cristamonadida
F. Lophomonadidae
C. Trichonymphea
O. Trichonymphida
F. Hoplonymphidae
F. Staurojoenidae
F. Trichonymphidae
F. Teranymphidae
F. Spirotrichosomidae
C. Spirotrichonymphea
O. Spirotrichonymphida
F. Holomastigotoididae
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CURRENT
CLASSIFICATION
based
on
Cepicka
et
al.
2010
Cristamonadida
Trichonymphida
Spirotrichonymphida
Trichomonadida
Tritrichomonas muris
Image caption: Scanning electron micrograph of cells from a rodent.
image
by
G.
Brugerolle
image
by
G.
Brugerolle
Tritrichomonadida
Hypotrichomonadida
image
by
J.
Cole
2Department
of
Botany,
University
of
BriOsh
Columbia,
Vancouver,
BC,
Canada
ARTICLE IN PRESS
I. Cepicka et al.418
PHYLOGENY
OF
MAJOR
LINEAGES
Noda
et
al.
2012
EVOLUTION
of
MORPHOLOGICAL
TRAITS
Cepicka
et
al.
2012
EXAMPLE
IMAGES
of
MAJOR
LINEAGES
MANY
DESCRIBED
ORGANISMS
ARE
UNCLASSIFIED
or
MISCLASSIFIED,
MANY
MORE
ARE
BEING
DISCOVERED,
WITH
PARTICULARINTEREST
ON
FREE-­‐LIVING
ONES
THAT
MAY
SHED
LIGHT
ON
THE
ROOT
OF
THE
EXCAVATA
Figure 5. Phylogenetic relationships between Cthulhu, Cthylla, environmental sequences, and closely related parabasalians. Bayesian
Cthulhu and Cthylla
Ctuhlhu
and
Cthylla
are
possibly
members
of
a
yet
to
be
described
order
of
Trichomonadida
(James
et
al.
2013)
Cthulhu
Kofoidia
Kofoidia
is
a
Cristamonad,
but
taxa
known
as
the
lophomonads
(*)
are
polyphyleOc
and
the
type
genus
of
the
family
Lophomonadidae
groups
outside
of
the
Cristamonadea.
A
redefined
taxonomy
is
needed
for
the
cristamonads
(Tai
et
al.
2015)
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5 7 -
*
*
*
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Calonymphidae?
Devescovinidae?
Kofoiididae?
Deltotrichonymphidae?
Coronymphidae??
REFERENCES
Cepicka
et
al.
2010.
CriOcal
taxonomic
revision
of
parabasalids
with
descripOon
of
one
new
genus
and
three
new
species.
Pro8st.
161:
400-­‐433
Tai
et
al.
2015.
The
phylogeneOc
posiOon
of
Kofoidia
loriculata
(Parabasalia)
and
its
implicaOons
for
the
evoluOon
of
the
Cristamonadea.
J
Euk
Micro.
62:
255-­‐259
James
et
al.
2013.
Cthulhu
macrofasciculumque
n.
g.,
n.
sp.
and
Cthylla
microfasciculumque
n.
g.,
n.
sp.,
a
newly
idenOfied
lineage
of
parabasalian
termite
symbionts.
PLoSONE.
8:
e58509
Noda
et
al.
2012.
Molecular
phylogeny
and
evoluOon
of
Parabasalia
with
improved
taxon
sampling
and
new
protein
markers
of
acOn
and
elongaOon
factor-­‐1α.
PLoSONE.
7:
e29938