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Diversity and classiﬁcation of dinoﬂagellates
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Chapter 1
DIVERSITY AND CLASSIFICATION

OF DINOFLAGELLATES
Fernando Gómez
Puerto de Santa María, Spain
ABSTRACT
This chapter summarizes the diversity of dinoflagellates divided into several groups:
basal dinoflagellates (i.e., Syndineans and Noctilucales), unarmored dinokaryotes and
thecate forms such as Prorocentrales and Dinophysales, Gonyaulacales, Peridiniales, thin-
walled dinoflagellates and unclassified taxa. The morphology of the main representatives
are illustrated, phylogenetic trees of each group and a scheme on the tentative evolution
are provided. The trends on dinoflagellate biodiversity research, problematic and
unresolved issues (i.e., biases in the availability of molecular markers for the less
accessible taxa, recent proposals on nomenclature, etc.) are outlined. A classification
scheme for dinoflagellate levels above genus is proposed within a context of unresolved
relationships of higher ranks in the molecular phylogenies.
Keywords: dinoflagellata biodiversity, Dinophyta classification, Dinophyceae systematics,

alveolate evolution, protist diversity
INTRODUCTION
Dinoflagellates (Alveolata, Dinophyceae) are protists with a truly remarkable diversity in
lifestyles (free-living, parasites and mutualistic symbionts), habitats (marine, freshwater,
plankton, benthos), and trophic modes (heterotrophic, chloroplast-containing) (Gómez
2012a). Dinoflagellates and ciliates are the most diverse groups of alveolates. About ~2400
species of dinoflagellates are currently accepted (Gómez 2012b), several tens of new species
are described every year, and the environmental molecular surveys reveal numerous lineages

Corresponding Author’s Email: fernando.gomez@fitoplancton.com

2 Fernando Gómez
of basal dinoflagellates that has not been documented yet (Guillou et al. 2008). This chapter
summarizes the main groups of dinoflagellates and its classification, with illustrations of the
diversity, and some brief notes on ecological aspects and problematic issues.
A first issue is to delimitate what a dinoflagellate is. In a strict sense, a dinoflagellate is a
dinokaryote which is characterized by a peculiar nucleus, the dinokaryon, devoid of histones
and with permanently condensed chromosomes, and a huge genome with peculiar
characteristics (Lin 2011). Most of these biflagellate cells have a wavy transversal flagellum,
although this character is missing in the desmokont (prorocentroid) dinokaryotes. The
cingulum or girdle, a groove that encircles the cell harboring the transversal flagellum, is not
only missing in prorocentroids. It is also apparently absent in planktonic (Podolampas) or
benthic species (Adenoides) that have the wavy transversal flagellum. Alternatively, if the
cingular plates are not in a depressed or sunken groove, they can be mistaken for the
precingular or postcingular plate series (Gómez et al. 2015c).
BASAL DINOFLAGELLATES
Unexpectedly, the earlier molecular studies reveal the phylogenetic relationship between
the dinoflagellates and the apicomplexans that include agents of human diseases
(Plasmodium, Toxoplasma; Gunderson et al. 1987). Since then, the molecular phylogeny has
placed numerous lineages between the apicomplexans and the dinokaryotes (Figure 1).
Among these groups of basal dinoflagellates are parasites such as the perkinsids (Dinovorax,
Parvilucifera, Perkinsus, Snorkelia; Figure 2A; Goggin and Barker 1993, Nóren et al. 1999,
Reñé et al. 2017), the ellobiopsids (Thalassomyces, Ellobiopsis, Figure 2B; Silberman et al.
2004, Gómez et al. 2009a) and the free-living heterotrophic genus Oxyrrhis (Figure 2C,
Saldarriaga et al. 2003a). The nuclei of the syndineans have intermediate characteristic
between the typical eukaryotic and dinokaryotic nucleus (Ris and Kubai 1974). The
syndineans are divided into two groups: the euduboscquellids with Ichthyodinium, a parasite
of fish eggs (Figure 2D–E), and Euduboscquella, a parasite of ciliates (Figure 2F–G; Yuasa et
al. 2007, Harada et al. 2007, Coats et al. 2010, Gómez and Gast 2018) and the Syndiniales
with the parasites of crustaceans Hematodinium and Syndinium (Figure 2H, Skovgaard et al.
2005) and the dinophagous parasite Amoebophrya (Figure 2I–K, Gunderson et al. 1999). The
genera Syndinium, Hematodinium and Amoebophrya can be placed in the Syndiniales or
Syndinea, and Euduboscquella and Ichthyodinium can be placed in the family
Euduboscquelliaceae or alternatively in the order Coccidiniales following Cachon and
Cachon (1987). These basal dinoflagellates remain unreported in epicontinental waters, and
they have an important role in the marine ecosystems, including the control of the
proliferations of harmful dinoflagellates (Chambouvet et al. 2008). The molecular data reveal
a huge genetic diversity of basal dinoflagellates (Guillou et al. 2008). The lack of distinctive
characters, even in the dinospores, make difficult the species characterization. In the past, the
species names were proposed citing the host as the species epithet. This could be interpreted
as a high host-specificity. Further studies have revealed that the relationship between host and
parasite is not often species specific, and a single parasitic species may infect different
species of hosts, and a host species may be infected by different syndinean parasites
(Salomon et al. 2003).

Diversity and Classification of Dinoflagellates 3
Figure 1. The phylogenetic position of dinoflagellates and other alveolate lineages based on Maximum
Likelihood analysis inferred from SSU rRNA gene sequences. Bootstrap values ≥70 are noted to the
left of internodes. The stramenopile Bolidomonas pacifica was used as outgroup. Scale bar = 0.05
substitutions site−1.
The Noctilucales are the basal dinoflagellates closer to the dinokaryotes, and have
dinokaryotic characteristics in some life stages. Noctiluca scintillans was the first observed
dinoflagellate because it is the biggest species, bioluminescent and common in coastal
temperate waters. The other noctilucaceans have received less attention and numerous species
remain undescribed (Gómez 2010). Noctiluca scintillans (Figure 2L) and Spatulodinium spp.
are closely related in the molecular phylogenies (Gómez et al. 2010a), and they share a
tentacle-like extension used for feeding. In some tropical areas, Noctiluca may harbor a free-
swimming chlorophyte, Spatulodinium possesses chloroplasts of an unknown nature
(Figure 2O), and Pomatodinium possesses a photosynthetic endosymbiont (Figure 2P). A
close relative is Kofoidinium, which possesses an extracellular dome as well as Spatulodinium
used for prey capture (Figure 2M–N). The members of the Leptodiscaceae are even less
known due to their fragility. These heterotrophic species have highly flattened cell bodies and
able of fast changes of shape. Leptodiscus (Figure 2Q) and Cymbodinium (Figure 2R) swim
like a medusa, and Abedinium and Scaphodinium (Figure 2S) are also able of sudden
contractions. The molecular data on the Leptodiscaceae are restricted to partial ribosomal
RNA gene sequences of Abedinium (Gómez et al. 2010a). The phylogenetic position is
instable, being more distantly related to the other noctilucaceans (Figure 1). The Noctilucales
are characterized by sequences with long branches in the ribosomal RNA gene phylogenetic
trees. This is associated with the long-branch attraction artefact that is a form of systematic

4 Fernando Gómez
error where distantly related lineages with long branches appear closely related in the
phylogenetic trees (Philippe et al. 2005).
Figure 2. Light micrographs of basal dinoflagellates. A. Parvilucifera in Podolampas. B. Ellobiopsis on

a copepod. The inset shows the infective spores. C. Oxyrrhis. D–E. Ichthyodinium. F–G.
Euduboscquella. H. Syndinium. The inset shows the infective spore. I–K. Amoebophrya in
Protogonyaulax, Schuettiella and Tripos. L. Noctiluca. M–N. Kofoidinium. O. Spatulodinium. P.
Pomatodinium. Q. Leptodiscus. R. Cymbodinium. S. Scaphodinium. Scale bar = 20 μm.
UNARMORED DINOFLAGELLATES (GYMNODINIPHYCIDAE)

The dinoflagellates have been traditionally classified as armored (thecate) and unarmored
dinoflagellates (athecate or naked dinoflagellates). As all the known basal dinoflagellates are
unarmored, we could speculate that this is an ancestral trait and the thecate dinoflagellates
constituted the most derived forms. Recent data based on dinoflagellate transcriptomes
confirmed this view and placed the unarmored dinoflagellates as a basal group among the
dinokaryotic dinoflagellates (Janouškovec et al. 2017).

Figure 3. The phylogenetic position of dinoflagellates based on Maximum Likelihood analysis inferred
from SSU rRNA gene sequences, with especial focus on the unarmored forms. Bootstrap values ≥70 are
noted to the left of internodes. The syndinean Syndinium turbo was used as outgroup. Scale bar = 0.02
substitutions site−1.
There is an important gap in the knowledge between unarmored and armored

dinoflagellates due to practical reasons. When compared to the thecate dinoflagellates, the
naked forms are easily damaged by net sampling, cells lysis or the morphology is distorted
due to the manipulation and common fixatives. Modern methods such as the cultures provide
abundant material fresh material that allow reducing the gap of knowledge between naked
and thecate species. Although the bias remains for the heterotrophic species that predominate
in the open oligotrophic ocean (Gómez 2014). In the earlier studies, most of the free-living
unarmored dinoflagellates were placed in the genus Gymnodinium, and later new genera were

6 Fernando Gómez
proposed based on characters such as the degree of cingular displacement (Gyrodinium),

number of turns of the cingulum (Cochlodinium), or the relative height of the cingulum
(Amphidinium, Torodinium) (Kofoid and Swezy 1921). The molecular data revealed that
genera such as Gymnodinium, Amphidinium or Cochlodinium were not monophyletic, and
these classical diagnostic criteria were not supported (Daugbjerg et al. 2000, Jørgensen et al.
2004a, Gómez et al. 2017a). The modern generic diagnoses are based on a combination of
features with an especial relevance of the shape of the apical groove (Takayama 1985,
Daugbjerg et al. 2000).
Figure 4. Light micrographs of unarmored dinoflagellates: Amphidinioids and Gymnodiniales sensu

stricto. A. Amphidinium (photosynthetic). B. Amphidinium (heterotrophic). C. Testudodinium. D.
Togula. E. Ankistrodinium. F. Apicoporus. G. ‘Amphidinium’ scissum. H. Gymnodinium catenatum. I.
G. impudicum. J. Lepidodinium viride. K. Gymnodinium venator. L. Spiniferodinium. M. Polykrikos
kofoidii. N. nematocyst. O. Polykrikos lebouriae. P. Polykrikos hartmannii. Q. Pheopolykrikos
beauchampii. R. Warnowia sp. with chloroplasts and Polykrikos. S. Nematopsides. T–U.
Erythropsidinium. V. Gymnoxantella. W. Dissodinium. X. Chytriodinium. Y. Syltodinium. Z.
Myxodinium. Scale bar = 20 μm.

The unarmored dinoflagellates with a very anterior cingulum have been placed under the
genus Amphidinium (Kofoid and Swezy 1921). The earlier life stages of Kofoidinium
(Figure 2N) and Spatulodinium (Figure 2O) resemble species formerly placed in the genus
Amphidinium (Figure 4D–F), and we could speculate that the amphidinioids represent the
most ancestral morphology of the dinokaryotes. In the earlier evolutionary schemes,
Amphidinium was placed as a basal dinoflagellate after the prorocentroids (Kofoid and Swezy
1921, p. 86). Based on the ribosomal DNA such as the SSU rRNA gene, the sequences of the
clade of the type species Amphidinium operculatum are characterized by long branches, and
often clusters closer to the basal dinoflagellates that have also long branches, raising the
question of whether Amphidinium is really a basal group among the dinokaryotes or its
position is artificial due to the long-branch attraction (Figure 3). Based on multigene (Zhang
et al. 2007) and transcriptome phylogenies (Janouškovec et al. 2017), Amphidinium is
considered as the most basal lineage of the dinokaryotes clustering between the Noctilucales
and the other dinokaryotes. As occurred with other earlier genus of naked dinoflagellates,
under the genus Amphidinium were placed unrelated genera of unarmored dinoflagellates that
share a very anterior cingulum and consequently a small episome (Jørgensen et al. 2004a)
(Figure 3). The clade Amphidinium sensu stricto (Figure 4A–B) is a basal group, and species
such as Gymnodinium venator (Figure 4K) belongs to the Gymnodiniales or other former
members of Amphidinium are currently placed in new genera such as Testudodinium
(Figure 4C), Togula (Figure 4D), Ankistrodinium (Figure 4E), Apicoporus (Figure 4F), and
new amphidinioid genera have been proposed (i.e., Bispinodinium). Other species of
Amphidinium still needs a new generic placement (Figure 4G) (Jørgensen et al. 2004b,
Sparmann et al. 2008, Hoppenrath et al. 2012, Horiguchi et al. 2012, Yamada et al. 2013).
According to Janouškovec et al. (2017) Amphidinium sensu stricto is the most basal lineage
of the dinokaryotes, and Togula is a sister group of clade of Gymnodiniales sensu stricto.
There are no transcriptome sequences of the other amphidinioid genera that in the SSU rRNA
gene phylogenies are dispersed in the dinokaryote core without a clear relationship with other
dinoflagellates to establish a suprageneric classification (Figure 3).
The order Gymnodiniales is restricted to the clade that contains the type species of
Gymnodinium, G. fuscum (Figure 3, Daugbjerg et al. 2000). This is the most specious, and
morphologically and ecologically diverse clade of unarmored dinoflagellates. Blooms of the
colonial species Gymnodinium catenatum have received attention as responsible of Paralytic
Shellfish Poisoning (Figure 4H), and sometimes confused with other colonial non-toxic
species such as G. impudicum (Figure 4I). In addition to the typical peridinin-containing
chloroplast, other species possess a chloroplast derived from a chlorophyte with chlorophyll b
(Lepidodinium, Figure 4J), and the members of the family of Nusuttodinium and
Spiniferodinium (Figure 4L) have a chloroplast derived from a cryptophyte. The polykrikoid
dinoflagellates are constituted of multinucleate ‘pseudocolonies’ of zooids (Figure 4M–P).
Polykrikos possesses two nuclei and the species are heterotrophic (Figure 4M, R) or with
chloroplasts (Figure 4O–P). All the species have ejectile organelles or extrusomes with
analogies to the nematocyst found in metazoans such as the cnidarians (Figure 4N; Gavelis et
al. 2017). Other genus constitutes by zooids is Pheopolykrikos that possesses an equal number
of nuclei and zooids (Figure 4Q). The warnowiids possess an elaborate photoreception
organelle with analogies the ocelloid of pluricellular organisms (Figure 4R–U; Gómez et al.
2009b, Gavelis et al. 2015). The described species are heterotrophic, but at least one species
may contain chloroplasts (Figure 4R). The highest degree of ultrastructural sophistication is

8 Fernando Gómez
found in Erythropsidinium that also has a piston (Figure 4T–U, Gómez 2017). Among the
symbiotic forms, Gymnoxantella lives in symbiosis with pelagic radiolarians and it was
overlooked with the thecate dinoflagellate Zooxanthella (Figure 4V, Yuasa et al. 2016). The
members of the family Chytriodiniaceae are parasites of copepod eggs (Dissodinium, Figure
4W; Chytriodinium, Figure 4X; Syltodinium, Figure 4Y; Gómez et al. 2009c, 2019a), and
Myxodinium (Figure 4Z) that feeds on the microalgae Halosphaera, probably as an alternative
host in absence of eggs. The rRNA gene sequences of parasitic forms have often longer
branches than the free-living relatives. This results in unstable topologies in the phylogenetic
trees as often occurs with the sequences of Chytriodinium (Figure 3). Mixotrophic species
such as Gymnodinium aureolum are closely related to the Chytriodiniaceae (Figure 3).
Based on currently avalaible transcriptome phylogeny, the brachidiniaceans
(Brachidiniales) are placed between the Amphidiniales and the Gymnodiniales sensu stricto
(Janouškovec et al. 2017). The members of the Brachidiniales are photosynthetic species
containing fucoxanthin, a typical accessory pigment of haptophyte. Recently, a new genus,
Gertia, with a chloroplast containing peridinin and lacking fucoxanthin has been decribed
(Takahashi et al. 2019). The brachidiniaceans cluster into two groups in the SSU rRNA gene
phylogenies (Figure 3). One group for the species which apical groove is linear straight such
as Asterodinium (Figure 5A), Brachidinium and Karenia (Figure 5B; Daugbjerg et al. 2000,
Gómez et al. 2005, Benico et al. 2019), and other group for species with a sigmoidal apical
groove such as Karlodinium and Takayama (de Salas et al. 2003). The order Ptychodiscales
was a catch-all of species with a supposed strongly developed cell covering or pellicle,
pooling thecate forms such as Kolkwitziella, unarmored forms such as Balechina and
Ceratoperidinium, the Brachidiniales, and species with a endoskeleton such as Monaster
(=Achradina) (Fensome et al. 1993). The order Ptychodiscales remains only for Ptychodiscus
(Figure 5C–D), with straight apical groove and yellow pigmentation, tentatively with
fucoxanthin-containing plastids, that suggests an affinity with the Brachidiniales that is not
well supported in the molecular phylogenies (Figure 3; Gómez et al. 2016a).
The family Ceratoperidiniaceae contains up to date species with a circular apical groove,
which is also present in other lineages of unarmored dinoflagellates (Cochlodinium,
Cucumeridinium). All the described species of the Ceratoperidiniaceae are photosynthetic
with the typical peridinin-containing plastids, a smooth cell surface, and the cells are often
enclosed in a hyaline membrane. There are species with the typical gymnodinioid outline,
Kirithra, and cells with body extensions and ventro-dorsally compressed (Ceratoperidinium,
Figure 5E), laterally compressed (Gynogonadinium, Figure 5F) or slightly or non-compressed
such as Pseliodinium (Figure 5G–I) (Reñé et al. 2013, Boutrup et al. 2017). The torsion or the
cingular displacement, features traditionally used for the diagnoses, have low diagnostic value
for the generic split as evident for two closely related species such as Pseliodinium fusus
(Figure 5G–H) and P. pirum (Figure 5I) (Gómez 2018). The latter species was placed in the
new genus Torquentidium using as diagnostic character that the cingulum encircled the cell
1.5 times (Shin et al. 2019). The use of this arbitrary numeric morphometric character, aslo
found in Polykrikos geminatum or the warnowiids, is not supported by the molecular data.
This new genus proposal only contributes to the excesive proliferation of new genera of
dinoflagellates.

Figure 5. Light micrographs of unarmored dinoflagellates. A. Asterodinium. B. Karenia. C–D.

Ptychodiscus. E. Ceratoperidinium. F. Gynogonadinium. G–H. Pseliodinium fusus. I. Pseliodinium
pirum. J. Akashiwo. K. Levanderina. L. Margalefidinium. M–N. Gyrodinium. O. Cochlodinium. P.
Cucumeridinium. Q. Torodinium. R–S. Lebouridinium. T. Kapelodinium. U. Kapelodinium and
‘Amphidinium’ sphenoides. V. Balechina. W–X. Actiniscus. Y. Dicroerisma. Z–AA. Monaster. Scale
bar = 20 μm.
Other species that were first described as members of the genus Gymnodinium or
Cochlodinium constitute independent lineages of photosynthetic species with a smooth cell
surface such as Akashiwo (Figure 5J), Levanderina (Figure 5K) or Margalefidinium
(Figure 5L, Gómez et al. 2017a). Based on the avaliable transcriptome phylogenies, Akashiwo
is the closer relative to the thecate dinoflagellates (Janouškovec et al. 2017). Longitudinal
striae in the cell surface and encapsulated nucleus are common features in several
heterotrophic genera. This could be an adaptation to engulf large preys. We have to be
cautious to consider the surface striation as a diagnostic character for a clade. For example,
nearly all the members of the Gymnodiniales sensu stricto have a smooth surface, while
Erythropsidinium, able to ingest large preys, has reinforcements of the cell surface that can be
interpreted as longitudinal striae (Figure 4U, Gómez 2017). Longitudinal striae are found in
Gyrodinium (Figure 5M–N), Cochlodinium (Figure 5O), Cucumeridinium (Figure 5P), and
taxa with a reduced episome such as Torodinium, that also have chloroplasts (Figure 5Q), and
Lebouridinium for the species previously known as Katodinium/Gyrodinium glaucum
(Figure 5R–S) (Hansen and Daugbjerg 2004, Takano and Horiguchi 2004, Gómez et al.

10 Fernando Gómez
2015a,d). Boutrup et al. (2016) proposed Kapelodinium vestifici for the cold water species
Gymnodinium vestifici (Figure 5T–U), and they considered that Katodinium/Gyrodinium
glaucum and Amphidinium extensum as synonyms. The synonymy of Gymnodinium vestifici
and Katodinium/Gyrodinium glaucum (now Lebouridinium) is unsupported. Gymnodinium
vestifici is an amphidinioid cell, with a small episome and missing the cap-like structure, fine
longitudinal striation and closely related to species such as ‘Amphidinium’ extensum or
‘Amphidinium’ sphenoides (Figure 5U). The cells of Katodinium/Gyrodinium glaucum have a
small hyposome, an apical cap-like structure, and coarse longitudinal striation (Figure 5R–S).
The true Gymnodinium vestifici has not been investigated by modern methods and the
molecular data labelled as Kapelodinium vestifici correspond to Lebouridinium glaucum
(Figure 3). The longitudinal striation is not the exclusive of the phagotrophic species. The
genus Balechina (=Gymnodinium gracile) possesses a thick and smooth cell covering that is
able to sudden changes of shape (Figure 5V, Gómez et al. 2015d).
Other unarmored dinoflagellates have an internal skeleton. Actiniscus possesses a pair of
endoskeletal elements of silicate (Figure 5W–X), Dicroerisma has an inverted Y-shaped
endoskeleton of unknown nature (Figure 5Y), and Monaster (=Achradina) has as
endoskeleton of celestite, strontium sulfate. This type of skeleton is only known in Acantharia
and some radiolarians, opening the hypothesis of a gene transfer as numerous Rhizaria live in
symbiosis with dinoflagellates (Figure 5Z–AA; Gómez et al. 2017b). The cell covering of
Monaster may contain thin thecal plates, and it may constitute other group of the so-called
thin-walled dinoflagellates among the thecate dinoflagellates.
THECATE DINOFLAGELLATES (PERIDINIPHYCIDAE)

Prorocentroids and Dinophysoids
One century ago, the prorocentroids were considered as the most primitive forms of
dinoflagellates, even more basal dinoflagellates than Noctiluca and Amphidinium (Kofoid and
Swezy 1921, p. 86). The most typical armored and unarmored dinoflagellates are dinokonts,
in which the two flagella are inserted ventrally, and the wavy transversal flagellum is usually
placed in the cingulum, and the smooth longitudinal flagellum is placed in the sulcus. In
contrast, the prorocentroid dinoflagellates are desmokonts, with both smooth flagella and
inserted anteriorly. The grooves such as the sulcus or cingulum are not evident. This
configuration is closer to some flagellate groups (e.g., Cryptophyta) suggesting that
Prorocentrum could constitute the most basal group representing the ancestral morphology of
the dinoflagellates (Kofoid and Swezy 1921). However, in the ribosomal RNA gene
phylogenies, Prorocentrum is well-placed among the dinokaryotic core (Figure 6), and in the
transcriptome phylogenies is, together with the dinophysoids, a basal group of the thecate
dinoflagellates (Janouškovec et al. 2017).
The theca of prorocentroids is composed of two large plates joined by a sagittal suture,
and numerous tiny plates near the flagellar pore (periflagellar platelets). In molecular
phylogenies based on a single ribosomal RNA gene marker, the prorocentroids clustered into
three clades within the dinokaryotic core (Figure 6), while the monophyly appears using
several genes (Zhang et al. 2007, Murray et al. 2009). We have to take into account that these

multigene phylogenies are built with a less taxonomically representative dataset of different
species of other dinoflagellates. The clade of Prorocentrales sensu stricto with the type
species, P. micans, contains planktonic or tychoplanktonic species taxa, often with an apical
spine or tooth (Figure 7A–C). Benthic or epiphytic species (Figure 7D–E), often with toxic
species (i.e., Prorocentrum lima) constitute a second clade. The third clade also contains
several benthic species, which first described member was P. panamense (Grzebyk et al.
1998).
from SSU rRNA gene sequences, with especial focus on prorocentroids and dinophysoids. Bootstrap
values ≥70 are noted to the left of internodes. The basal dinoflagellate Amoebophrya was used as
outgroup. Scale bar = 0.02 substitutions site−1.
The dinophysoid dinoflagellates possess prorocentroid organization because the theca is

fundamentally divisible into two halves by a sagittal suture, but they have a cingulum
separating the epitheca and hypotheca, with the typical wavy flagellum that corresponds to
the dinokont organization. Consequently, the dinophysoids could be regarded as
morphologically intermediate between the desmokonts and dinokonts (Figure 7). In the rRNA

12 Fernando Gómez
gene phylogenies, the dinophysoids cluster into three clades. The Dinophysales sensu stricto
comprised the most specious and ecologically diverse group. The genus Dinophysis
(Figure 7F) comprises numerous toxic species that are responsible of Diarrhetic Shellfish
Poisoning. These species contains chloroplasts with a controversy on whether they are
permanent or kleptoplastids that need a periodical replacement. Other species of Dinophysis
in a more basal position are heterotrophic and have an antapical spine (Figure 7G). Several
oceanic taxa such as Citharistes (Figure 7H), Histioneis (Figure 7I–J) and Ornithocercus
(Figure 7K) survive to the prevailing oligotrophic conditions in circumtropical seas with
ectosymbiotic bacteria in the ‘phaeosome’ chamber or attached to the cingular or sulcal lists.
The family Oxyphysiaceae is highly diverse with most of the species placed in the genus
Phalacroma, mainly composed of heterotrophic and some species with plastids of different
origins (Figure 7L–O). The most basal group contains the highly elongated cells of
Triposolenia (Figure 7P) and Amphisolenia (Figure 7Q) with a much reduced epitheca, and
endosymbionts in numerous taxa. A second clade of dinophysoids contains the planktonic
heterotrophic genera Metaphalacroma (Figure 7R) and Pseudophalacroma (Figure 7S), and
the third clade contains the benthic heterotrophic species of Sinophysis (Figure 7T–U) that in
some species may also harbor photosynthetic endosymbionts (Gómez et al. 2011b, 2012b).
Figure 7. Light micrographs of thecate dinoflagellates: prorocentroids and dinophysoids. A.

Prorocentrum micans (dissociated valves). B. P. gibbosum (dissociated valves). C. Prorocentrum
rostratum. D–E. Prorocentrum sp. (dissociated valves). Note the excavation of the right valve. F.
Dinophysis acuta. G. D. alata. H. Citharistes. I. Histioneis highleyi. J. H. gubernans. K. Ornithocercus.
L–O. Phalacroma. P. Triposolenia. Q. Amphisolenia. R. Metaphalacroma. S. Pseudophalacroma. T–U.
Sinophysis. Scale bar 20 μm.

Gonyaulacales
The most evolved dinoflagellates lack the two large valves, and the theca shows
latitudinal series of plates (apical, anterior intercalary, precingular, cingular, postcingular,
posterior intercalary, antapical) that reach a higher number of series >10 in the so-called thin-
walled dinoflagellates. The number of plates is variable, and we can observe a high plate
multiplication or fragmentation of plates in Pyrophacus (Figure 9L). The Gonyaulacales is
the more recently proposed classical order, previously considered as a peridinioid family
(Taylor 1980, Fensome et al. 1993). It should be noted that Pyrocystis is the type of the order
Pyrocystales Apstein 1909 that was proposed before the Gonyaulacales Taylor 1980. The
article 11.3 of the I. C. N. states that the correct name is the earliest legitimate, but from
family to genus. The type genus of the Gonyaulacales is Gonyaulax that shows a marked
asymmetry due to the left-handed torsion of the epitheca as well as an asymmetrical first
apical plate (Figure 9M), while the Peridiniales tend to show a bilateral symmetry, with a
more-or-less symmetrical first apical plate (Figure 11A). Among other characteristics, the
Peridiniales have additional plates such as the canal plate near the apex that is missing in the
gonyaulacoids (Fensome et al. 1993).
Up to date, the Gonyaulacales is the only classical major order that is monophyletic,
although species such as Peridiniella catenata with a gonyaulacoid appearance clusters
within the short-branching dinokaryotic core together with peridinioid taxa (Daugbjerg et al.
2000). In the molecular phylogenies, the rRNA gene sequences of the Gonyaulacales are
characterized by long branches, especially for the genera Pyrophacus, Ostreopsis and
Gambierdiscus. This problem is evident in the case of Pyrophacus and Ostreopsis that
artificially cluster together due to the long-branch attraction artefact (Figure 8). If Ostreopsis
is removed, Pyrophacus clusters with Fragilidium and Pyrocystis. The most diverse clade of
gonyaulacoids includes Centrodinium (Figure 9A) that is a tropical open ocean form of the
best known genera Alexandrium, Gessnerium and Protogonyaulax (Figure 9B). Contrary to
all previous taxonomical schemes, Gómez (2012b) placed Centrodinium in the same
subfamily of the toxicologically important genus Alexandrium. The morphological and
molecular data of Centrodinium punctactum (Li et al. 2019), and typical species of
Centrodinium such as C. eminens (Figure 8) evidended that Alexandrium is not monophyletic,
and the need of the re-instatement of the genera Protogonyaulax and Gessnerium, and a new
genus for the clade of Alexandrium affine (Gómez and Artigas 2019). Within the family
Ostreopsidaceae, these planktonic genera are closely related to benthic genera also associated
with harmful events such as Coolia (Figure 9C) and Ostreopsis (Figure 9D). Other clade
contains the planktonic and benthic genera such as Pyrrhotriadinium (nom. illeg.) [formerly
Goniodoma (nom. rejic.)] (Figure 9E), Psammodinium (Figure 9F), Fukuyoa (Figure 9G),
Gambierdiscus (Figure 9H), and the more distantly related bioluminescent Pyrodinium
(Figure 9I) that may be also placed in the Ostreopsidaceae or an independent family (Gómez
et al. 2015b, Reñé and Hopperanth 2019). Family names such as Goniodomataceae or
Triadiniaceae are not considered valid because they are based on a peridinioid type
(Kretschmann et al. 2015). Pyrocystis (Figure 9J) is other bioluminescent genus closely
related to genera with an exceptional multiplication/fragmentation of thecal plates such as
Fragilidium (Figure 9K), and very especially Pyrophacus (Figure 9L).

14 Fernando Gómez
from SSU rRNA gene sequences, with especial focus on gonyaulacoid dinoflagellates. Bootstrap values
≥70 are noted to the left of internodes. The apicomplexan Eimeria was used as outgroup. Scale bar =
0.02 substitutions site−1.

Figure 9. Light micrographs of gonyaulacoid dinoflagellates. A. Centrodinium. B. Protogonyaulax. C.

Coolia. D. Ostreopsis. E. Pyrrhotriadinium. F. Psammodinium G. Fukuyoa. H. Gambierdiscus. I.
Pyrodinium. J. Pyrocystis. K. Fragilidium. L. Pyrophacus. M. Gonyaulax. N. Spiraulax (ecdysis). O.
Lingulodinium (ecdysis). P. Ceratium. Q. Two species of Tripos. R. Schuettiella. S. Protoceratium. T.
Ceratocorys. U–V. Two species of Thecadinium. Scale bar 20 μm.
The second main group of gonyaulacoids contains the type Gonyaulax (Figure 9M), and
Spiraulax (Figure 9N) and generic names based on fossils such as Ataxiodinium,
Bitectatodinium, Impagidinium or Spiniferites. It should be noted that the fossil names have
not priority if a name of an extant taxa is available (I. C. N. Art. 11.8). Other closely related
clade is composed of Lingulodinium (Figure 9O) and Amylax that could be placed in the
family Lingulodiniaceae or alternatively also placed in the Gonyaulacaceae (Figure 8). Based
on the molecular data, other lineages are Dapsilidinium, the Ceraticeae for Ceratium (Figure
9P) and Tripos (Figure 9Q), and in a more divergent position the Protoceratidaceae with
Schuettiella (Figure 9R), Protoceratium (Figure 9S), Pentaplacodinium and Ceratocorys
(Figure 9T). The placement of the benthic genus Thecadinium (Figure 9U–V) among the
Gonyaulacales is unstable (Figure 8). In some phylogenies, the genera Amphidiniella or
Halostylodinium may cluster among the basal gonyaulacoids, but this is uncertain whether
this reflects a real phylogenetic relationship or more likely an artefact of long-branch
attraction as also occurred between Protoperidinium and the long-branch group of the
Gonyaulacales.

16 Fernando Gómez
Peridinioids
A more restricted tabulation scheme for the Peridiniales is an epitheca with seven
precingular plates (7′′), several anterior intercalary plates (1–3a), four apical plates (4′), and
often additional plates such as the canal plate or ×-plate near the apical pore. This is the most
extended scheme for planktonic peridinioids that shows a more or less globular cell shape
with an equatorial cingulum. When the cell is compressed and the cingulum is more anterior,
as usual in benthic forms, this pattern is altered and the interpretation of the tabulation is more
difficult. The Peridiniales are polyphyletic, and we must restrict the Peridiniales sensu stricto
to the clade that contains Peridinium (Figure 11A), a clade of freshwater photosynthetic taxa
with few species (P. cinctum, P. bipes, P. willei), and tentatively we can add other freshwater
genera such as Glochidinium, Palatinus, Parvodinium or Thompsodinium (Figure 10). The
marine species of Peridinium were placed in the genus Protoperidinium, being the most
specious genus that was inflated to over 200 described species (Figure 11B–D). Most of the
species of Protoperidinium cluster together, with the exception of several species such as P.
depressum (section Oceanica) that cluster with the members of the Diplopsalis-group (Figure
11E), the latter also divided into two groups (Figure 10). The members of the Diplopsalis-
group show variations in the number of hypothecal and epithecal plates that have resulted on
the description of numerous genera (Diplopsalis, Gotoius, Huia, Niea, Preperidinium, Qia,
etc.). The nomenclature of the diplopsalid genera is also complicated because sometimes a
genus has been proposed with different names under the Botanical and Zoological Codes of
Nomenclature. Other species of Protoperidinium such as P. americanum, P. monovellatum
and Archaeperidinium (P. minutum) cluster with benthic genera such as Amphidiniopsis
(Figure 11F–G) and Herdmania (Figure 11H) that can be placed in the Amphidioniopsidaceae
(Figure 10; Gómez et al. 2011a, Yamaguchi et al. 2011). All the members of the
Protoperidiniaceae are heterotrophic forms known as pallium-feeders (Figure 11B), and at
least one species, Protoperidinium cf. diabolum possesses photosynthetic endosymbionts with
similar morphology to those in Podolampas (Figure 11I–J).
The shape of Podolampas (Figure 11I–J) reminds some species of Protoperidinium, but
with an important difference because Podolampas and its relatives (Gaarderiella,
Lissodinium, Mysticella, Heterobractum, Blepharocysta; Figure 11K) lack of a series of
depressed or sunken plates that harbor the transversal flagellum that could be interpreted as
the cingulum, although the transversal flagellum encircles the cell at the position where is
expected to find the cingulum. As occurred with Herdmania or Amphidiniopsis, the molecular
phylogenies have unexpectedly revealed a relationship of the pelagic podolampadaceans and
the benthic genera Roscoffia (Saldarriaga et al. 2003b; Gómez et al. 2010b). The available
sequences of the sand-dwelling dinoflagellate Cabra (Figure 11L) are highly divergent and it
is not easiy to confirm the affinity with the Podolampadaceae proposed by Yamaguchi et al.
(2018). The sequences of other sand-dwelling genera such as Planodinium (Figure 11M),
Plagiodinium and Chrysodinium have similarities with the Podolampadaceae, but this feature
is poor supported in the molecular phylogenies (Figure 10, Gómez et al. 2019b). Lessardia,
with a fusiform antero-posteriorly elongated cell (Figure 11N), was related to the
Podolampadaceae in the earlier phylogenies (Saldarriaga et al. 2003b), but more complete
phylogenies support the placement in its own family as suggested by Carbonell-Moore
(2004). It is not common to find highly antero-posteriorly elongated cells in the planktonic

peridinioids such as in some species of Oxytoxum (Figure 11O), that together with
Corythodinium (Figure 11P) conforms the family Oxytoxaceae (Gómez et al. 2016b).
Figure 10. The phylogenetic position of dinoflagellates based on Maximum Likelihood analysis
inferred from SSU rRNA gene sequences, with especial focus on peridinioid dinoflagellates. Bootstrap
values ≥70 are noted to the left of internodes. The apicomplexan Eimeria was used as outgroup. Scale
bar = 0.02 substitutions site−1.
Other peridinioids with endosymbionts are the members of the Kryptoperidiniaceae, the
so-called ‘dinotoms’ because they contains a diatom as endosymbiont (Yamada et al. 2017).
Up to date this family remains unrepresented in the open ocean, all the known members live
in coastal, brackish or freshwater environments such as the genera Blixaea (Figure 11Q),
Dinothrix, Durinskia (Figure 11R), Galeidinium, Kryptoperidinium and Unruhdinium. One of
the most specious and ecologically diverse clade of peridinioid dinoflagellates are the

18 Fernando Gómez
members of the family of Scrippsiella (Figure 11S) that is able to produce calcareous cysts
that have been described as different genera names (Calcigonellum, Pernambugia, Leonella,
Posoniella). The whole family and order is placed in the Thoracosphaerales, based on
Thoracosphaera heimii that was first described as a coccolithophorid. In addition to the free-
living planktonic photosynthetic species (Scrippsiella), there are other planktonic forms
(Apocalathium, Caladoa, Calcicarpinum, Chimonodinium, Fusiperidinium, Laciniporus,
Naiadinium, Speroidinium, Stoeckeria, Theleodinium, Tyrannodinium), and also
heterotrophic benthic forms (Aduncodinium, Figure 11T). Many of new planktonic genera
derived from freshwater taxa first described as species of Peridinium, Peridiniopsis,
Glenodinium or Glenodiniopsis. An important group of species is the pfiesterids (Pfiesteria,
Pseudofiesteria, Luciella, Cryptoperidiniopsis) (Figure 11U) that cause fish mortalities in
estuaries (Steidinger et al. 1996). The Thoracosphaerales also includes parasitic forms, such
as parasites of diatoms (Paulsenella, Figure 11V), parasites of ciliates (Duboscquodinium,
Tintinnophagus, Figure 11W; Coats et al. 2010) and fishes (Amyloodinium, Figure 11X; Levy
et al. 2007, Gómez and Gast 2018). In a more basal position of the Thoracosphaerales are
marine species Pentapharsodinium and Ensiculifera, but the phylogenetic position is
unstable.
In the classical taxonomic schemes, most of parasitic dinoflagellates were placed in the
orders Syndiniales and Blastodiniales, placing the dinokaryotic parasites in the latter order.
Currently, the Blastodiniales must be restricted to the clade that contains the type species of
Blastodinium, B. pruvotii, and even the monophyly of the genus is not always evident
(Figure 10, Skovgaard et al. 2007). Nearly all the species of Blastodinium contain
chloroplasts and carry out the photosynthesis inside the copepod hosts (Figure 11Y). The
members of the Heterodiniaceae are free-living heterotrophic species that live preferentially
in deep waters of warm oceans, and the most distinctive species are characterized by highly
flattened cell body as typical in other members of the ‘shade flora’ (Figure 11Z, Gómez et al.
2012a). The order Heterocapsales was proposed for the genus Heterocapsa (Figure 11AA;
Fensome et al. 1993). Based on the combination of several genes, Heterocapsa was placed as
a basal dinoflagellate, a sister group of Amphidinium (Zhang et al. 2007), but recent analyses
based on dinoflagellate transcriptomes placed Heterocapsa within the Peridiniales sensu lato
(Janouškovec et al. 2017).
The nomenclatural issues also affect Symbiodinium, a dinoflagellate genus with a high
ecological interest for the functioning of the coral reefs that have recently split in several
genera (LaJeunesse et al. 2018). The symbionts of the coral reefs invertebrates are commonly
referred as zooxanthellae, and this is source of confusion with the genus name Zooxanthella.
The type of the genus Zooxanthella, Z. nutricula, is a symbiont of pelagic radiolarians such as
Collozoum (Figure 12A; Gast and Caron 1996). Zooxanthella nutricula is a thecate
dinoflagellate, and it was unnecessarily transferred to Scrippsiella and Brandtodinium (nom.
illeg.) (Probert et al. 2014). Planktonic radiolarians may also contain an unarmored
dinoflagellate symbiont such as Gymnoxanthella (Figure 3V). The genus Zooxanthella has
been placed among the Thoracosphaerales, but this is not well supported in the molecular
phylogenies (Figure 10). In that case, the order Zooxanthellales proposed in 1970 and
Thorascophaerales in 1982 may have the priority, although the article 11.3 of the I. C. N.
states that the correct name is the earliest legitimate, but from family to genus. The type
species of Symbiodinium was already transferred into Zooxanthella (Loeblich and Sherley
1979), and more recently all the species of Symbiodinium have been placed into Zooxanthella

(Guiry and Andersen 2018). Zooxanthella is a thecate genus that lives in pelagic radiolarians
(Figure 12A), and Symbiodinium is a thin-walled dinoflagellate that live in benthic
invertebrates (Figure 12M). The species of these unrelated genera are placed together (Guiry
and Andersen 2018) althought there is no a morphological or phylogenetic relationship
(Figure 13). The parasites of fishes Amyloodinium (Figure 11V) and Piscinoodinium have
been placed in the family Oodiniaceae (Cachon and Cachon 1987, Fensome et al. 1993), but
they are members of the order Thoracosphaerales and Symbiodiniales, respectively (Levy et
al. 2007). The Oodiniaceae is restricted to the type Oodinium, an ectoparasite of
appendicularians (Figure 12B, Gómez and Skovgaard 2015). The rRNA gene sequences of
Oodinium, as occurred with other parasites, have long branches in the phylogenetic trees,
which resulted in unstable topologies, often clustering in basal positions.
Figure 11. Light micrographs of peridinioid dinoflagellates. A. Peridinium. B–D. Protoperidinium. B.

See the pallium, a feeding organelle. C. Purple pigmentation. D. Carotenoid globules. E. A member of
the Diplopsalis-group. F–G. Amphidiniopsis spp. H. Herdmania with hyposomal spines. I. Podolampas
bipes and Protoperidinium cf. diabolum with the same unidentified photosynthetic endosymbiont. J.
Podolampas bipes. K. Blepharocysta feeding on a microalga. L. Cabra. M. Planodinium. N. Lessardia.
O. Oxytoxum. P. Corythodinium. Q. Blixaea. R. Durinskia. S. Scrippsiella. T. Aduncodinium. U.
Unidentified pfiesterid species. V. Paulsenella. W. Tintinnophagus. X. Amyloodinium. Y.
Blastodinium. Z. Heterodinium. AA. Heterocapsa. Scale bar = 20 μm.

20 Fernando Gómez
Figure 12. Light micrographs of peridinioid and thin-walled dinoflagellates. A. Zooxanthella nutricula.
B. Oodinium. C. Azadinium caudatum. D. Amphidoma nucula. E. Cladopyxis. F. Bysmatrum. G.
Rhinodinium. H. Sabulodinium. I. Pseudadenoides. J. Adenoides. K. Thaumatodinium. L. Undescribed
thecate dinoflagellate. M–N. Symbiodinium s.l. Scale bar = 20 μm.
Since the proposal of the genus Azadinium (Tillmann et al. 2009), more than 10 new
species have been added. The species Amphidoma caudata (Figure 12C) was transferred into
Azadinium, and more recently new of species of Amphidoma have been proposed, placing
Amphidoma and Azadinium in the Amphidomataceae. A genus and family is defined by the
type species, and Amphidoma nucula (Figure 12D) has not been investigated by modern
methods. Although A. nucula and A. caudata showed a superficial resemblance (Figure 12C–
D), they are unrelated species, and Azadinium and the recently described species of
Amphidoma do not belong to the Amphidomataceae. The members of the Cladopyxiaceae
have been classified among the Gonyaulacales (Fensome et al. 1993). Molecular data are
missing of genus such as Clapopyxis (Figure 12E) with abundant information in the fossil
records. Numerous genera of thecate dinoflagellates cluster as independent lineages within
the dinokaryotic core, especially benthic dinoflagellates. Clear affinities with pelagic genera
have been found for Amphidiniopsis, Herdmania or Roscoffia, but numerous benthic genera
cluster as independent lineages of uncertain suprageneric classification (Figure 10). Some
species have more typical peridinioid morphology with an median cingulum such as
Bysmatrum (Figure 12F) and Rhinodinium (Figure 12G), while other have an anterior
cingulum that remind the dinophysoids such as Sabulodinium (Figure 12H), and a very
reduced episome (Pseudadenoides, Figure 12I), and without an apparent cingulum such as
Adenoides (Figure 12J) that reminds the prorocentroids. Other thecate dinoflagellates, even
with distinctive morphology, remain unreported since the original description such as
Thaumatodinium (Figure 12K) or undescribed (Figure 12L).

Thin-Walled Dinoflagellates
A thecate life stage has been reported in the life cycle of the unarmored dinoflagellate
Margalefidinium polykrikoides (Kim et al. 2007), but this supposed thecate life stage is a
misidentification for an Alexandrium species. It is common to observe how armoured
dinoflagellates leave behind the theca and continue as unarmored forms (i.e., Figure 9N–O),
but from a phylogenetic point of view armoured and unarmoured dinoflagellates are distinct
groups. At a first sight, the so-called ‘thin-walled’ dinoflagellates could be considered as
intermediate between unarmored and thecate dinoflagellates, and consequently showing the
characteristics of the hypothetical ancestor of the thecate dinoflagellates. The recent
transcriptome phylogenies suggest that the thin-walled dinoflagellates such as Symbiodinium
have evolved from thecate dinoflagellates (Janouškovec et al. 2017). This could be interpreted
as that the thin-walled dinoflagellates are thecate dinoflagellates that have reduced the
thickness of the thecal plates, and the plate multiplication or fragmentation resulted in
numerous latitudinal plate series. The proliferation of plates also occurs in other thecate
dinoflagellates such as Pyrophacus (Figure 9L). If the thecal plates are considered as
defensive structures, thick thecal plates are not necessary when living as an endosymbiont,
but not all the genera of the thin-walled dinoflagellates are endosymbionts. The thin-walled
dinoflagellates are not a monophyletic group (Figure 13), suggesting that the loss of the thick
thecal plates that are replaced by more numerous delicate plates have occurred independently
several times in the evolution.
The symbiotic Symbiodinium and its recently derived new genera are essential for the life
of the coral reefs (LaJenneuse et al. 2018). It has been intensively investigated by ecologists,
more interested on aspects as the host specificity than in the morphological differences among
the species. Symbiodinium has been recently split into several genera (Breviolum,
Durusdinium, Effrenium, Fugacium, Gerakladium; Figures 12M–N) based on molecular data
(Figure 13) and ecological aspects such as the type of host or geographical information, and
missing information on the morphology such as the plate arrangement in the generic
diagnoses (LaJeunesse et al. 2018). The ecologists do not always know or respect the rules of
the Nomenclature, and the species of Symbiodinium have experienced a convulse history of
typifications and validations, and finally the generic name Symbiodinium have been attributed
to three different authorities. The recent proposal by Guiry and Andersen (2018) placing all
the species of Symbiodinium into the distantly related thecate genus Zooxanthella is other
source of confusion. The family Symbiodiniceae also contains Pelagodinium, a symbiont of
pelagic Foraminifera, parasites of fishes such as Haidadinium and Piscinoodinium, free-living
species such as Polarella, Protodinium and numerous new genera have been recently added
(Ansanella, Asulcocephallum, Biecheleria, Biecheleriopsis, Dactylodinium, Leiocephalium,
Yihiella). This clade is often reported as the Suessiaceae, based on a fossil genus Suessia. The
article 11.8 of the International Code of Nomenclature (I. C. N) reports that fossil type has no
priority over names of extant species, and at the family level the use of Symbiodiniaceae
seems to be more coherent because we cannot verify with molecular data the relationship of
these taxa with the extinct Suessia. Other thin-walled dinoflagellate clades are mainly
freshwater taxa placed in recently erected families as the Borghiellaceae (Baldinia,
Borghiella) and the Tovelliaceae/Tovelliales (Bernadinium, Esoptrodinium, Jadwigia,
Tovellia) (Moestrup and Calado 2018). Nearly all these families and orders are based on
species described from accessible localities in Europe, but new names that can be superfluos

22 Fernando Gómez
are proposed without a re-investigation of the type of other existing suprageneric names
(Cystodiniaceae, Desmomastigales, Dinamoebidiales, Dinamoebales, Dinococcales,
Dinotrichales, Dinosphaeraceae, Hemidiniaceae, Glenodiniopsidaceae, Lophodiniales,
Phytodiniales, Woloszynskiaceae). The thin-walled dinoflagellates are often named
woloszynskioid dinoflagellates, being based on species that were previously described as
Woloszynskia, Gymnodinium or Glenodinium. New genera, families and even orders are
proposed without a re-investigation of the genus Woloszynskia, type of the family
Woloszynskiaceae.
Figure 13. The phylogenetic position of dinoflagellates based on Maximum Likelihood analysis
inferred from SSU rRNA gene sequences, with especial focus on thin-walled dinoflagellates. Bootstrap
values ≥70 are noted to the left of internodes. The syndinean Syndinium was used as outgroup. Scale
bar = 0.01 substitutions site−1.

CURRENT ISSUES
The most important advances in our knowledge of the dinoflagellate classification are
due to the molecular phylogeny that has allowed to test the hypotheses in the evolution and
the morphological characters of diagnostic value. Since the surprising relationship between
dinoflagellates and human parasites such as the apicomplexans (Gunderson et al. 1987), the
molecular phylogenies have modified the diagnostic criteria used for the classification
(Saldarriaga et al. 2004). The examples are evident in the unarmored dinoflagellates with split
of the genera Gymnodinium, Amphidinium and Cochlodinium (Daugbjerg et al. 2000,
Jørgensen et al. 2004a, Gómez et al. 2017a). Among the thecate dinoflagellates, the tabulation
is considered a stable diagnostic character, but again we fail in the interpretation of the
tabulation when the species have lost the typical globular morphology with an equatorial
cingulum of the pelagic species. The cell compression and the small epitheca, as usually
occurred in the benthic species, is associated with a re-arrangement of the thecal plates. Only
with the aid of the molecular phylogeny, we are able to relate Roscoffia and Podolampas
(Saldarriaga et al. 2003b, Gómez et al. 2010b) or Herdmania and Amphidiniopsis with species
of Protoperidinium (Gómez et al. 2011a, Yamaguchi et al. 2011). The use of molecular
markers (SSU-, LSU- and ITS rRNA genes) is unable to resolve the evolution and
suprageneric classification of dinoflagellates, although the resolution is slightly better in a
few groups (Gymnodiniales sensu stricto, Thoracosphaerales, Gonyaulacales). Sequences of
transcriptomes are a promising tool to resolve the deep branching relationships, but at the
present the number of available sequences of different species is low (Janouškovec et al.
2017). As usual, the application of the new tools shows a strong bias towards the cultivable
species or easily accessible coastal species (Gómez 2014). The open ocean is mainly studied
with techniques such as the metabarcoding (Le Bescot et al. 2016). These short environmental
sequences allow a view of the relative abundance of groups of dinoflagellates, but the studies
are not accompanied with microscopic observations. The microscope is an instrument to
banish together with the taxonomists. Research and academic positions are offered for
molecular biology and bioinformatics. Beyond the research groups focused on the monitoring
of the harmful algae blooms, the general taxonomy of dinoflagellates persists in a few groups
in Denmark, Germany and Japan, and as it occurs in other research fields such as the ciliates
with an important increase of the taxonomical studies in China.
There are no significant advances on several topics. The molecular phylogeny reveals a
huge diversity of syndinean dinoflagellates (Guillou et al. 2008), but in the last decade there
is no advance because the sequences are not identified at the species level, and the syndineans
remains restricted to five genera. Other tentative syndinean genera such as Actinodinium,
Atlanticellodinium, Caryotoma, Coccidinium, Dogelodinium, Keppenodinium, Merodinium or
Sphaeripara do not receive the amount of attention that they deserve. Coats et al. (2012)
proposed the transfer of the species associated with the sequences previously identified as
Duboscquella in the new genus Euduboscquella, but they did not solve the identity of the
dinokaryotic genus Duboscquella. Coats et al. (2012) proposed the family
Euduboscquellaceae, but this clade of Euduboscquella and Ichthyodinium needs to be ranked
at least at the order level. We can use the order Coccidinales following Cachon and Cachon
(1987), although cautiously because Coccidinium has not been investigated by modern
methods. Our knowledge on the phylogeny of Noctilucales remains limited to the few partial

24 Fernando Gómez
sequences in Gómez et al. (2010a). It is uncertain if the leptodiscaceans are really basal
dinoflagellates or they should be placed among the dinokaryotic dinoflagellates (Figure 1).
The nature of chloroplasts of Spatulodinium or the endosymbionts of Pomatodinium remain
unknown.
In the last two decades, there is an increase of the descriptions of new taxa, mainly of
unarmored and thin-walled dinoflagellates, while numerous species described by
Wołoszyńska, Skvortsov, van Goor, van Meel, Conrad & Kufferath, or Schiller remains in
most of the cases restricted to the original descriptions (Thessen et al. 2012). The proposals of
new genera, often based on a single species, have largely increased, revealing the inability to
relate the morphology of the new taxa with other existing species. In other cases, superflous
new genus names are proposed without molecular support such as the case of Torquentidium
(Shin et al. 2019). Several attempts have tried to propose new genus names for species such
as Gymnodinium catenatum and other species of Gymnodinium just only based on the
distance in the molecular phylogenies to the type species G. fuscum. The question could be
the reverse, why to place all the species of the Gymnodiniaceae into Gymnodinium?
Similarly, we could place the species of the genera Alexandrium, Episemicolon, Gessnerium
and Protogonyaulax into Centrodinium. On the other hand, numerous benthic species of
Prorocentrum have been described in the last two decades, but many of them should be
placed into another genus because they are distantly related to the type species, the spine-
bearing planktonic Prorocentrum micans. Sometimes, we are splitters in the
Gymnodiniaceae, Alexandrium/Centrodinium or the Pfiesteriaceae (Pfiesteria,
Pseudofiesteria, Luciella, Cryptoperidiniopsis), while lumpers in Prorocentrum. This is the
dilemma of being a splitter or a lumper taxonomist.
New species are described from coastal isolates or germination of cysts that are able to
grow well with the standard culture media. In contrast, most of the oceanic species are
uncultivable with the current methods, and the studies must be based on the few cells
available. This paucity of material renders the detailed studies that are not comparable to the
morphological, ultrastructural and molecular studies when billions of cells are available in a
culture. Unfortunately, this limitation is not well understood, and the requirements for
publication discourage researchers to study the heterotrophic species that predominates in the
open ocean (Gómez 2014). It is embarrassing that we have not solved classical issues such as
whether Pronoctiluca is or is not a dinoflagellate and the molecular affiliation of Cladopyxis.
In addition to the excessive proliferation of new genus names (i.e., Torquentidium), there
is an increase of the proposal of suprageneric names, families and orders, based on the
characteristics of a single genus. If we are unable to find relatives based on the ribosomal
RNA gene sequences, it does not mean that each taxon constitutes a new family or even
order. Moestrup and Calado (2018) proposed new families (Gyrodiniaceae, Amphidiniaceae,
Sphaerodiniaceae) or even an order (Amphidiniales) based on a single genus. If this practice
extends, new suprageneric names will appear everywhere. Several new families or even
orders of freshwater taxa have been proposed such as Borghiellaceae, Sphaerodiniaceae or
Tovelliales (Moestrup and Calado 2018). Tens of new taxa of the so-called ‘woloszynskiods’
are proposed without a study of the identity of Woloszynskia. The detail of the earlier species
descriptions is not comparable to the current description, but we have the option of the
typification.
The consideration of the earlier descriptions is important, but sometimes they have scarce
detail that may result in subjective interpretations. Gottschling and collaborators have recently

re-interpreted the identity of species illustrated by Ehrenberg in the 1830’s that are the
basionyms of the Stein’s genera Goniodoma, Heterocapsa or Blepharocysta (Stein 1883).
Proposals appears such as the consideration that the description of Peridinium splendormaris
in the Mediterranean Sea, basionym of the type of the genus Blepharocysta, corresponds to an
earlier description of Alexandrium balechii, a species that lives in the mangroves of the
Caribbean Sea. Ehrenberg’s Peridinium splendormaris looks like Lingulodinium polyedra, a
common bioluminescent dinoflagellate in the Mediterranean Sea. Gottschling et al. (2019)
considered that the basionym of the type species of Heterocapsa, Peridinium triquetrum, is a
species of the genus Kryptoperidinium. There is no a phylogenetic relation between
Kryptoperidinium and the species that we know as Heterocapsa (Figure 10). Then, the genus,
family and order of Heterocapsales is dismantled when the type is placed in another genus.
Kretschmann et al. (2015) re-interpreted that the basionym of the type of Goniodoma is a
peridinioid cell of the genus Scrippsiella instead of a gonyaulacoid dinoflagellate. The genus
named Goniodoma is rejected, as well as related families such as Goniodomatadaceae or
Triadiniaceae (Prud’homme van Reine 2017), without reporting an alternative because
Pyrrhotriadinium is an illegitimate name. The changes may not stop here. The most common
species of Scrippsiella, S. trochoidea, is now S. acuminata (Kretschmann et al. 2015). In the
molecular phylogenies, Duboscquodinium is very closely related to the type species of
Scrippsiella, S. sweeneyae (Figure 10). In case of congenerity, Duboscquodinium Grassé
1952 has the priority over Scrippsiella Balech 1959. There is no molecular data of
Duboscquella, type genus of the Duboscquellaceae, which could be closely related to
Duboscquodinium. Then, the family name Duboscquellaceae has the priority over the
Thoracosphaeraceae. As consequence of nomenclatural changes, the free-living genus
Goniodoma traditionaly used for gonyaulacoid dinoflagellates is a posterior synonym of a
peridinioid parasite of ciliates. Other studies are not good examples of the observance of the
recommendations in the Nomenclature. Gottschling et al. (2017) proposed Blixaea and
Unruhdinium for species of the family Kryptoperidiniaceae, when other tentative related taxa
such as Dinothrix have not been investigated. According the Recommendation 20A of the I.
C. N.: “Not dedicate genera to persons quite unconnected with botany, mycology, phycology,
or natural science in general”. Blixaea and Unruhdinium are in honor of musicians. At least, I
will prefer the use of the orthography ‘Unruhidinium’. Based on an inexistent proposal to
reject the name Zooxanthella, Probert et al. (2014) proposed the new name Brandtodinium to
replace Zooxanthella, the thecate endosymbiont of pelagic radiolarians. The conflicts on
nomenclature must be solved by the Committee for Algae of International Association for
Plant Taxonomy. Most of the members of the Committee that vote the recommendation or
rejection of proposals are not experts on taxonomy of dinoflagellates and decision remains in
the hands of a few people. The decision to recommend or to reject a proposal may delay for
several years being associated with uncertainty during that period. John et al. (2014) proposed
to reject the Gonyaulax catenella, basionym of an important toxicologically species of
Protogonyaulax. In the decision, Prud’homme van Reine (2017) reported “Alexandrium
fundyense and A. catenella are certainly conspecific, and then ‘catenella’ has nomenclatural
priority”. Is it really the same species responsible of the blooms in the Canadian Atlantic and
California? Members of the Committee placed all the species of Symbiodinium into
Zooxanthella (Guiry and Andersen 2018), when the morphology and molecular phylogeny
evidence that Zooxanthella and Symbiodinium are independent genera (Figure 13).

26 Fernando Gómez
CLASSIFICATION
The names that we use for the classification of dinoflagellates are in continuous evolution
due to the new taxonomical innovations, re-classifications based on the molecular data, and
the nomenclatural changes. There is nothing more risky for an author than to propose a
suprageneric classification when the evolutionary relationships of numerous dinoflagellates
remain unresolved yet. With the exception of some groups (Gymnodiniales sensu stricto,
Thoracosphaerales, Gonyaulacales), the words -incertae sedis- are everywhere, and we
cannot propose a new family or order for each independent lineage of dinoflagellates. A
principle that I follow in the classifications is to avoid adding taxonomical innovations, or
suprageneric new names and using the existing published names (Fensome et al. 1993). New
terminology can be found in other classifications (Hoppenrath 2017). The next classification
is an updated version of that in Gómez (2012b), but in this case from genus to class because
the citation of all species names needs more than 100 pages. A tentative scheme that
summarises the dinoflagellate evolution is proposed in the Figure 14.
Figure 14. Tentative evolutionary relationships of dinoflagellates.

Infraregnum Alveolata, Phyllum Dinoflagellata

Class Ellobiopsea / Ellobiophyceae
Order Thalassomycetales: Ellobiopsidae / Thalassomycetaceae: Ellobiocystis,
Ellobiopsis, Parallobiopsis, Rhizellobiopsis, Thalassomyces
Class Oxyrrhea
Order Oxyrrhida / Oxyrrhinales
Oxyrrhinaceae: Oxyrrhis
Class of Pronoctiluca, incertae sedis. The affinity with the dinoflagellates needs molecular
data.
Protodiniferaceae: Pronoctiluca
Class of Coccinidiales (Marine Alveolate Group I)
Order Coccinidiales: Coccidinium, Dogelodinium, Euduboscquella, Ichthyodinium,
Keppenodinium
Class Syndinea/Syndiniophyceae (Marine Alveolate Group II)
Order Syndiniales
Syndiniaceae: Actinodinium, Caryotoma, Merodinium, Syndinium,
Hematodinium
Sphaeriparaceae: Atlanticellodinium, Sphaeripara
Amoebophryidae / Amoebophryaceae: Amoebophrya
Class Noctilucea / Noctiluciphyceae (Dinokaryota)
Order Noctilucales
Noctilucaceae: Noctiluca, Pomatodinium, Spatulodinium
Kofoidiniaceae: Kofoidinium
Order of Leptodiscaceae
Leptodiscaceae: Abedinium, Cachonodinium, Craspedotella, Leptodiscus,

Petalodinium, Scaphodinium
Class Dinoflagellata / Dinophyceae (Dinokaryota)
Subclass Gymnodiniphycidae
Order Amphidiniales
Amphidiniaceae: Amphidinium s.s., Schillingia, Trochodinium
Order Brachidiniales
Brachidiniaceae: Asterodinium, Brachidinium, Gertia, Karenia,
Karlodinium, Microceratium, Takayama
Order Ptychodiscales
Ptychodiscaceae: Ptychodiscus

28 Fernando Gómez
Order Haplozooidea / Haplozoonales

Haplozoonaceae: Haplozoon
Order Gymnodiniales
Gymnodiniaceae: Barrufeta, Gymnodinium, Gymnoxantella, Lepidodinium,
Paragymnodinium, Polykrikos, Spiniferodinium, Nussuttodinium,
Pellucidodinium, Wangodinium
Chytriodiniaceae: Chytriodinium, Dissodinium, Myxodinium,
Schizochytriodinium, Syltodinium, Gymnodinium s.l.
Warnowiaceae: Erythropsidinium, Nematodinium, Nematopsides,
Proterythropsis, Warnowia
Gymnodiniales sensu stricto, incertae familiae: Gyrodiniellum,
Pheopolykrikos
Torodiniales
Torodiniaceae: Torodinium
Order Amphilothales
Amphilothaceae: Monaster
Order Actiniscales
Actiniscaceae: Actiniscus
Subclass Gymnodiniphycidae, incerti ordinis.
Dicroerismataceae: Dicroerisma
Apodiniaceae: Apodinium, Parapodinium
Ceratoperidiniaceae: Ceratoperidinium, Gynogonadinium, Kirithra, Pseliodinium
Kapelodiniaceae: Kapelodinium
Gyrodiniaceae: Ceratodinium, Gyrodinium s.s., Plectodinium, Sclerodinium
Gymnodiniphycidae, incerti ordinis, incertae familiae: Akashiwo, Ankistrodinium,
Apicoporus, Balechina, Bispinodinium, Cachonella, Cochlodinium, Cucumeridinium,
Filodinium, Grammatodinium, Lebouridinium, Levanderina, Katodinium, Margalefidinium,
Moestrupia, Testudodinium, Togula
Subclass Peridiniphycidae
Order Prorocentrales
Haplodiniaceae: Haplodinium
Prorocentraceae: Prorocentrum s.s., Mesoporos
Family of Prorocentrum lima: Prorocentrum s.l., Exuviaella
Family of Prorocentrum panamense: Genus of Prorocentrum panamense
Order Dinophysales sensu stricto
Amphisoleniaceae: Amphisolenia, Triposolenia

Oxyphysaceae: Dinofurcula, Latifascia, Phalacroma s.s., Proheteroschisma

Dinophysaceae: Citharistes, Dinophysis, Histioneis, Histiophysis,
Metadinophysis, Ornithocercus, Parahistioneis
Order Dinophysales sensu lato
Family of Pseudophalacroma: Metaphalacroma, Pseudophalacroma
Family of Sinophysis: Sinophysis
Order Gonyaulacales / Pyrocystales
Ostreopsidaceae: Alexandrium, Centrodinium, Coolia, Episemicolon,
Gambierdiscus, Gessnerium, Fukuyoa, Goniodinium, Ostreopsis,
Pachydinium, Protogonyaulax, Psammodinium, Pyrodinium,
Pyrrhotriadinium.
Pyrocystaceae: Fragilidium, Pyrocystis, Pyrophacus
Gonyaulacaceae: Gonyaulax, Spiraulax
Lingulodiniaceae: Amylax, Lingulodinium
Ceratiaceae: Ceratium, Tripos
Protoceratidaceae: Ceratocorys, Pentaplacodinium, Protoceratium,
Schuettiella
Thecadiniaceae: Thecadinium
Order Gonyaulacales, incertae familiae: Dapsilidinium
Order Peridiniales sensu stricto
Peridiniaceae: Peridinium, Bagredinium, Glochidinium, Palatinus,

Parvodinium, Staszicella, Thompsodinium
Order Peridiniales sensu lato
Perinidiniopsidae: Peridiniopsis
Glenodiniopsidaceae: Glenodiniopsis
Protoperidiniaceae: Kolkwitziella, Matvienkodinium, Protoperidinium sensu

stricto
Diplopsaliaceae: Boreadinium, Diplopelta, Diplopsalis, Diplopsalopsis,

Dissodium, Gotoius, Huia, Lebouraia, Niea, Qia, Preperidinium,
Protoperidinium depressum-group
Amphidiniopsidaceae: Amphidiniopsis, Archaeperidinium, Herdmania,
Protoperidinium sensu lato.
Podolampadaceae: Blepharocysta, Gaarderiella, Heterobractum,
Lissodinium, Mysticella, Podolampas, Roscoffia. The genera Cabra,
Chrysodinium, Plagiodinium and Planodinium are related, but the placement
in this family needs further research.

30 Fernando Gómez
Lessardiaceae: Lessardia
Heterodiniaceae: Dolichodinium, Heterodinium
Oodiniaceae: Oodinium
Heterocapsaceae: Heterocapsa
Oxytoxaceae: Oxytoxum, Corythodinium
Amphidomataceae: Amphidoma s.s.
Cladopyxidaceae: Cladopyxis, Micracanthodinium, Palaeophalacroma
Endodiniaceae: Endodinium
Family of Azadinium: Azadinium, Amphidoma s.l.
Crypthecodiniaceae: Crypthecodinium
Order Blastodiniales
Blastodiniaceae: Blastodinium
Order Thoracosphaerales or Duboscquellales?
Apocalathium, Amyloodinium, Caladoa, Cachonella, Calcigonellum,

Chalubinskia, Chimonodinium, Crepidoodinium, Cryptoperidiniopsis,
Cystodinedria, Duboscquodinium, Duboscquella, Ensiculifera,
Fusiperidinium, Lebessphaera, Leonella, Luciella, Naiadinium, Oodinioides,
Paulsenella, Pentapharsodinium, Pernambugia, Pfiesteria, Protoodinium,
Pseudopfiesteria, Scrippsiella, Theleodinium, Tyrannodinium, Speroidinium,
Staszicella, Stylodinium, Stoeckeria, Tintinnophagus, Thoracosphaera
Order Dinotrichales
Dinotrichaceae/Kryptoperidiaceae: Blixaea, Dinothrix, Durinskia,
Galeidinium, Kryptoperidinium, Unruhdinium
Symbiodiniales/Dinococcales: Ansanella, Asulcocephallum, Aureodinium,
Biecheleria, Biecheleriopsis, Breviolum, Dactylodinium, Durusdinium,
Effrenium, Fugacium, Gerakladium, Haidadinium, Leiocephalium,
Pelagodinium, Piscinoodinium, Polarella, Protodinium, Symbiodinium, Yihiella
Phytodiniales: Baldinia, Borghiella, Cystodinium, Dinamoebidium,
Dinastridium, Dinoclonium, Dinococcus, Hypnodinium,
Manchudinium, Phytodinium, Prosoaulax, Sphaerodinium,
Tetradinium
Woloszynskiales/Tovelliaceae: Bernardinium, Esoptrodinium, Jadwigia,
Opisthoaulax, Tovellia, Woloszynskia
Peridiniphycidae, incerti ordinis
Dinosphaeraceae: Dinosphaera
Hemidiniaceae: Hemidinium, Nottbeckia

Glenodiniaceae: Glenodiniopsis, Nephrodinium
Peridiniphycidae, incerti ordinis, incertae familiae: Adenoides, Amphidiniella,

Archaeosphaerodiniopsis, Berghiella, Bysmatrum, Grammatodinium, Halophilodinium,
Halostylodinium, Laciniporus, Madanidinium, Peridiniella, Pileidinium, Pseudoactiniscus,
Pseudadenoides, Pseudothecadinium, Pyramidodinium, Rhinodinium, Sabulodinium,
Stylodinium, Vulcanodinium, Thaumatodinium, Thecadiniopsis
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Diversity and classiﬁcation of dinoﬂagellates

Chapter · August 2020

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DIVERSITY AND CLASSIFICATION

Keywords: dinoflagellata biodiversity, Dinophyta classification, Dinophyceae systematics,

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Figure 2. Light micrographs of basal dinoflagellates. A. Parvilucifera in Podolampas. B. Ellobiopsis on

UNARMORED DINOFLAGELLATES (GYMNODINIPHYCIDAE)

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There is an important gap in the knowledge between unarmored and armored

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proposed based on characters such as the degree of cingular displacement (Gyrodinium),

Figure 4. Light micrographs of unarmored dinoflagellates: Amphidinioids and Gymnodiniales sensu

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Figure 5. Light micrographs of unarmored dinoflagellates. A. Asterodinium. B. Karenia. C–D.

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THECATE DINOFLAGELLATES (PERIDINIPHYCIDAE)

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The dinophysoid dinoflagellates possess prorocentroid organization because the theca is

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Figure 7. Light micrographs of thecate dinoflagellates: prorocentroids and dinophysoids. A.

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Figure 9. Light micrographs of gonyaulacoid dinoflagellates. A. Centrodinium. B. Protogonyaulax. C.

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Figure 11. Light micrographs of peridinioid dinoflagellates. A. Peridinium. B–D. Protoperidinium. B.

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Figure 14. Tentative evolutionary relationships of dinoflagellates.

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Infraregnum Alveolata, Phyllum Dinoflagellata

Leptodiscaceae: Abedinium, Cachonodinium, Craspedotella, Leptodiscus,

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Order Haplozooidea / Haplozoonales

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Oxyphysaceae: Dinofurcula, Latifascia, Phalacroma s.s., Proheteroschisma

Order Gonyaulacales, incertae familiae: Dapsilidinium

Order Peridiniales sensu stricto

Peridiniaceae: Peridinium, Bagredinium, Glochidinium, Palatinus,

Order Peridiniales sensu lato

Protoperidiniaceae: Kolkwitziella, Matvienkodinium, Protoperidinium sensu

Diplopsaliaceae: Boreadinium, Diplopelta, Diplopsalis, Diplopsalopsis,

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Apocalathium, Amyloodinium, Caladoa, Cachonella, Calcigonellum,

Peridiniphycidae, incerti ordinis

Hemidiniaceae: Hemidinium, Nottbeckia

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