SEASONAL VARIABILITY OF THE ORGANIC‐WALLED DINOFLAGELLATE CYST PRODUCTION IN THE COASTAL UPWELLING REGION OFF CAPE BLANC (MAURITANIA): A FIVE‐YEAR SURVEY1

A 5‐year sediment trap survey in the upwelling area off Cape Blanc (NW Africa) provides information on the seasonal and annual resting cyst production of dinoflagellates, their sinking characteristics and preservation potential. Strong annual variation in cyst production characterizes the region. Cyst production of generally all investigated species, including Alexandrium pseudogonyaulax (Biecheler) T. Horig. ex T. Kita et Fukuyo (cyst genus Impagidinium) and Gonyaulax spinifera (Clap. et J. Lachm.) Diesing (cyst genus Nematosphaeropsis) was enhanced with increasing upper water nutrient and trace‐element concentrations. Cyst production of Lingulodinium polyedrum (F. Stein) J. D. Dodge was the highest at the transition between upwelling and upwelling‐relaxation. Cyst production of Protoperidinium americanum (Gran et Braarud) Balech, Protoperidinium monospinum (Paulsen) K. A. F. Zonn. et B. Dale, and Protoperidinium stellatum (D. Wall) Balech, and heterotrophic dinoflagellates forming Brigantedinium spp. and Echinidinium aculeatum Zonn., increased most pronouncedly during upwelling episodes. Production of Protoperidinium conicum (Gran) Balech and Protoperidinium pentagonum (Gran) Balech cysts and total diatom valves were related, providing evidence of a predator–prey relationship. The export cyst‐flux of E. aculeatum, P. americanum, P. monospinum, and P. stellatum was strongly linked to the flux of total diatom valves and CaCO₃, whereas the export production of Echinidinium granulatum Zonn. and Protoperidinium subinerme (Paulsen) A. R. Loebl. correlated with total organic carbon, suggesting potential consumption of diatoms, prymnesiophytes, and organic matter, respectively. Sinking velocities were at least 274 m · d^?1, which is in range of the diatom‐ and coccolith‐based phytoplankton aggregates and “slower” fecal pellets. Species‐selective degradation did not occur in the water column, but on the ocean floor.     

Dinoflagellate cyst distribution in marine surface sediments off West Africa (17–6°N) in relation to sea-surface conditions, freshwater input and seasonal coastal upwelling

An organic-walled dinoflagellate cyst analysis was carried out on 53 surface sediment samples from West Africa (17–6°N) to obtain insight in the relationship between their spatial distribution and hydrological conditions in the upper water column as well as marine productivity in the study area.Multivariate analysis of the dinoflagellate cyst relative abundances and environmental parameters of the water column shows that sea-surface temperature, salinity, marine productivity and bottom water oxygen are the factors that relate significantly to the distribution patterns of individual species in the region.The composition of cyst assemblages and dinoflagellate cyst concentrations allows the identification of four hydrographic regimes; 1) the northern regime between 17 and 14°N characterized by high productivity associated with seasonal coastal upwelling, 2) the southern regime between 12 and 6°N associated with high-nutrient waters influenced by river discharge 3) the intermediate regime between 14 and 12°N influenced mainly by seasonal coastal upwelling additionally associated with fluvial input of terrestrial nutrients and 4) the offshore regime characterized by low chlorophyll-a concentrations in upper waters and high bottom water oxygen concentrations.Our data show that cysts of Polykrikos kofoidii, Selenopemphix quanta, Dubridinium spp., Echinidinium species, cysts of Protoperidinium monospinum and Spiniferites pachydermus are the best proxies to reconstruct the boundary between the NE trade winds and the monsoon winds in the subtropical eastern Atlantic Ocean. The association of Bitectatodinium spongium, Lejeunecysta oliva, Quinquecuspis concreta, Selenopemphix nephroides, Trinovantedinium applanatum can be used to reconstruct past river outflow variations within this region.     

Preservation of organic-walled dinoflagellate cysts in different oxygen regimes: a 10,000 year natural experiment

The occurrence of organic-walled dinoflagellate cysts in (fossil) sediments depends on several factors, including as the ecological preferences of the cyst-forming dinoflagellates, cyst production, transport and preservation. Although laboratory experiments have shown that several cyst species are sensitive to chemical treatment, no information about the selective preservation of dinoflagellate cyst species in natural environments has previously been presented. Here, we present data on the effects of oxygen availability in bottom sediments on a cyst assemblage from the ungraded Madeira Abyssal Plain f-turbidite of which only the upper layer has been oxidized. Based on differences in species composition between the oxidized and underlying, unoxidized layers of this turbidite, the influence of oxygen availability on the preservation of individual species has been estimated. Cyst species have been classified in ascending order of resistance to oxygen availability in sediments as: (1) highly sensitive (cysts formed by Protoperidinium species), (2) moderately sensitive (e.g. Spiniferites species), (3) moderately resistant (e.g. Impagidinium paradoxum and Nematosphaeropsis labyrinthus) and (4) resistant (e.g. Impagidinium aculeatum).     

Cyst‐Theca Relationship and Phylogenetic Position of Impagidinium caspienense Incubated from Caspian Sea Surface Sediments: Relation to Gonyaulax baltica and Evidence for Heterospory within Gonyaulacoid Dinoflagellates

We investigate the cyst‐theca relationship of Impagidinium caspienense. Through an incubation experiment, we succeeded in examining the motile stage. Additional molecular analysis of single‐cyst PCR (LSU and SSU rDNA) reveal that the cyst is related to the species Gonyaulax baltica Ellegaard et al. ( 2002 ). The ability of this species to belong to two types of cyst‐based genera (spiniferate and impagidinioid) suggests that environmental (particularly salinity) and not genetic factors explain the formation of both morphotypes by G. baltica, which provides evidence for heterospory in this species. The affiliation to G. baltica demonstrates that I. caspienense is not endemic to the Caspian Sea. The phylogenetic position of several other gonyaulacoid species is also documented: Impagidinium pallidum, Ataxiodinium choane, Pyxidinopsis psilata, Spiniferites belerius, and Spiniferites ramosus. The LSU and SSU rDNA based phylogenies suggest that the genera Impagidinium and Spiniferites are not monophyletic, and that P. psilata and A. choane are close to Gonyaulax verior and Gonyaulax polygramma, respectively. In addition, this study accentuates the importance of cyst morphology in the classification of the Gonyaulacales.     

Horizontal dinoflage11ate cyst distribution, sediment characteristics and benthic flux in Manila Bay, Philippines

The lateral variation of sediment properties and associated cyst content of sediment in Manila Bay were determined and their possible role/s in the occurrences of Pyrodinium bahamense Plate var. compressum (Bohm) Steidinger, Tester et Taylor toxic blooms were assessed. Manila Bay's surface sediment was determined to be silt dominated. Clay generally increased towards the coast, probably as a result of flocculation and rapid deposition upon entry of sediments from the rivers. High sand content characterized the southeastern part of the bay attributed to the greater sand inputs and relatively strong currents in this area. Bulk densities were lower in the eastern side of the bay from dilution by high organic load from sewage and urban areas. Benthic flux calculations, particularly NH3, suggest more than 50% nutrient contribution comes from sediments. In general, dinoflagellate cyst density increased from the center of the bay towards the coast, except in Pampanga Bay where it deceased near the coasts. A maximum of 23 dinoflagellate species were identified: 5 were autotrophic (Lingulodinium polyedrum (Stein) Dodge, Gonyaulax spp., Pyrophacus steinii (Schiller) Wall et Dale, Protoceratium reticulatum (Claparede et Lachmann) Butschli, and Pyrodinium bahamense var. compressum), and the rest were predominantly composed of Protoperidinium spp. and Diplopsalis spp. Heterotrophs comprised about 70% of the total cyst counts. Pyrodinium counts increased towards the northwestern part of the bay where it was the dominant autotroph species. Negative correlations were observed for live Pyrodinium cyst density and N flux, P flux, ratio of N to P and total organic carbon (TOC) content. However, areas with high N:P ratio contain abundant Pyrodinium live cysts.     

A New Heterotrophic Dinoflagellate from the North‐eastern Pacific,Protoperidinium fukuyoi: Cyst–Theca Relationship,Phylogeny, Distribution and Ecology

The cyst–theca relationship of Protoperidinium fukuyoi n. sp. (Dinoflagellata, Protoperidiniaceae) is established by incubating resting cysts from estuarine sediments off southern Vancouver Island, British Columbia, Canada, and San Pedro Harbor, California, USA. The cysts have a brown‐coloured wall, and are characterized by a saphopylic archeopyle comprising three apical plates, the apical pore plate and canal plate; and acuminate processes typically arranged in linear clusters. We elucidate the phylogenetic relationship of P. fukuyoi through large and small subunit (LSU and SSU) rDNA sequences, and also report the SSU of the cyst‐defined species Islandinium minutum (Harland & Reid) Head et al. 2001. Molecular phylogenetic analysis by SSU rDNA shows that both species are closely related to Protoperidinium americanum (Gran & Braarud 1935) Balech 1974. Large subunit rDNA phylogeny also supports a close relationship between P. fukuyoi and P. americanum. Three subgroups in total are further characterized within the Monovela group. The cyst of P. fukuyoi shows a wide geographical range along the coastal tropical to temperate areas of the North‐east Pacific, its distribution reflecting optimal summer sea‐surface temperatures of ~14–18 °C and salinities of 22–34 psu.     

Recent Dinoflagellate cyst distribution in the North Canary Basin,NW Africa

The North Canary Basin (NW Africa) falls within a major eastern boundary upwelling system. This part of the coastal upwelling system is seasonal and is characterised by the development of large filaments migrating seawards. Hence, 16 samples from this location were selected to identify an “upwelling signal” in the composition of the dinoflagellate cyst assemblages.

Samples closest to the most intense upwelling cells are dominated by L. machaerophorum and G. catenatum and Protoperidinium spp. These make up the “upwelling signal” characteristic for the system. Moreover, the “upwelling signal” can be advected offshore, with filaments that may extend as far as 300 km. Finally, the finding of cysts from G. catenatum, a toxic dinoflagellate, raises the need for a better understanding of the relationship between its presence and distribution in the region, and the coastal upwelling system.     

Dinoflagellate cysts as indicators of water quality and productivity in British Columbia estuarine environments

Palynological analyses of 60 surface sediment samples from estuarine environments near Vancouver Island, including the Georgia Strait (GS), the Effingham (EFF) and the Seymour–Belize (SB) Inlets were performed in order to document the distribution of dinoflagellate cyst assemblages and their relationship to hydrographic conditions, productivity and nutrient concentrations. We tested transfer functions using the analogue method, and suggest that dinoflagellate cyst assemblages can be used to reconstruct primary productivity, temperature and salinity. The EFF and SB Inlets are characterized by a dominance of autotrophic taxa, particularly Operculodinium centrocarpum, whereas the Protoperidinioid and gymnodinial heterotrophic taxa such as Quinquecuspis concreta and Brigantedinium spp. dominate the assemblages of the GS. Multivariate analysis shows that this distribution is closely linked to primary productivity, sea-surface temperature (SST) and spring silica concentration. The abundance of autotrophic taxa in the EFF and SB Inlets is associated with high primary productivity and low summer SST, indicating summer upwelling of coastal British Columbia, whereas the heterotrophic taxa that characterizes the GS assemblages are related to low productivity, high summer SST and high silica concentration during spring. Multivariate analysis shows that the most important environmental parameters related to dinocyst distribution in the restricted embayment of the GS, are distance to the shore, distance to Vancouver Harbor, spring sea surface salinity (SSS), spring phosphate concentration and spring productivity. The autotrophic taxa are generally more common in coastal and shallow waters, but Spiniferites ramosus and Pentapharsodinium dalei show an opposite correlation to spring productivity and salinity. P. dalei is particularly abundant around Vancouver Harbor, near highly urbanized shores and within the Fraser River plume, where salinity is low and spring productivity and continental runoff are high. S. ramosus shows its highest abundance on the western coast of GS. Protoperidinioid and gymnodinial cysts characterize distal zones within the central and southern GS that are associated with a mixture of brackish waters coming from the Fraser River and deep upwelling waters entering the GS via Juan de Fuca Strait. The relationship between dinoflagellate cyst assemblages and primary productivity in these estuarine systems differs from that in oceanic and outer neritic zones, where the abundance of heterotrophic taxa is commonly associated with upwelling and high productivity.     

Protoperidinium tricingulatum sp. nov. (Dinophyceae), a new motile form of a round,brown, and spiny dinoflagellate cyst

A small, broadly ovoidal and heterotrophic dinoflagellate containing round, brownish, and spiny cyst was found in the water column of Huibertsplaat in the Wadden Sea off the coast of the Netherlands. This dinoflagellate had these conspicuous morphological characters: a five‐sided first apical plate (1′), only three cingular plates, and an extremely small first antapical plate. Based on these morphological features, Protoperidinium tricingulatum Kawami, vanWezel, Koeman et Matsuoka is described as a new species. The flagellar pore of P. tricingulatum is covered with a small fin, which rises from the left side of the right sulcal plate to the large V‐shaped posterior sulcal plate. This feature suggests that P. tricingulatum is assigned to the Abé's Monovela Group. The cyst stage of P. tricingulatum was positively linked to the vegetative stage by comparison of the ribosomal 5.8S rDNA, internal transcribed spacers (ITS1 and ITS2). Living cysts of P. tricingulatum are round, brownish, and covered with many slender spines bearing capitate or cauliforate distal ends. The cyst also possesses a theropylic archeopyle formed by a slit corresponding to parasutures between three apical and two apical intercaraly plates. These morphological characters indicate that this species is morphologically related to two dinoflagellate cyst‐genera Islandinium and Echinidinium.     

Control of modern dinoflagellate cyst distribution in the Irish and Celtic seas by seasonal stratification dynamics

Surface sediments from seven stations located in the seasonally stratified, frontal and mixed water regions in the Celtic and Irish seas have been analysed for their dinoflagellate cyst assemblages and dinosterol content. A total of 45 dinoflagellate cyst taxa have been identified and the assemblages related to surface and sediment conditions. Sediments from the mixed water region, at 30 m water depth, are characterised by a relatively low cyst concentration (∼2300 cysts/g dry weight) and high relative abundances of Lingulodinium machaerophorum accompanied by Spiniferites membranaceus, Brigantedinium spp. and Dubridinium caperatum. Assemblages from stratified and frontal water stations are dominated by Spiniferites ramosus associated with Operculodinium centrocarpum, Brigantedinium spp., cysts of Polykrikos schwartzii and Selenopemphix quanta. Ordination techniques performed on a restricted number of 35 taxa from the assemblages differentiated the stratified and frontal assemblages based on the abundance of the less abundant species Bitectatodinium tepikiense and Spiniferites elongatus. Among the environmental parameters (sea-surface temperature and salinity, stratification index, chlorophyll concentration and sediment grain-size classes), the seasonal stratification and sedimentological context, itself a function of tidal dynamics, explain most of the variance in the environmental conditions. These results indicate that dinoflagellate cyst analyses of shelf sediment records can be used to document the planktonic signal of seasonal stratification dynamics.     

Molecular phylogenetic study of the heterotrophic dinoflagellate genus Protoperidinium (Dinophyceae) inferred from small subunit rRNA gene sequences

In the present study, we investigated the intrageneric and intergeneric phylogenetic relationships of the heterotrophic marine dinoflagellate genus Protoperidinium. Using single‐cell polymerase chain reaction methods, we determined small subunit ribosomal RNA gene sequences for 10 Protoperidinium species belonging to four sections and two subgenera. Phylogenetic trees were constructed using maximum parsimony, neighbor joining and maximum likelihood methods. We found intraspecific variability of small subunit rDNA sequences in Protoperidinium conicum (Gran) Balech, Protoperidinium crassipes (Kofoid) Balech and Protoperidinium denticulatum (Gran et Braarud) Balech, but not in other species. The small subunit rDNA phylogeny revealed that the genus is monophyletic, but its phylogenetic position within the Dinophyceae could not be determined because of ambiguous basal topologies. Within the genus Protoperidinium, species of the subgenus Archaeperidinium with two anterior intercalary plates (2a) were shown to be monophyletic, but species of the subgenus Protoperidinium with three anterior intercalary plates (3a) were resolved as paraphyletic. The sections Avellana, Divergentia and Protoperidinium were shown to be monophyletic, while the section Conica was paraphyletic. Based on the trees obtained in the present study, most of the traditionally defined sections are supported by molecular phylogeny. It was also indicated that the section Avellana evolved from one of the Conica‐type dinoflagellates.     

Spatial and seasonal changes in the species composition of armored dinoflagellates in the Southwestern Atlantic Ocean

Summary To compare the spatial and temporal (seasonal) distribution of dinoflagellates, vertical net hauls were taken along similar cruise tracks in the Scotia Sea, Weddell Sea and across the Polar Front Zone in the austral spring and the austral fall. Sixty-three species of armored dinoflagellates were identified and enumerated. Chisquare and hierarchical cluster analyses were performed to define spatial and seasonal patterns in genera and species assemblages. The dominant genera were Protoperidinium, Dinophysis and Ceratium. The Polar Front Zone was an important biogeographical barrier with Blepharocysta, Gonyaulax, Heteroschisma, Oxytoxum and Podolampas occurring mainly north of the Front. Species found primarily in the austral spring were Ceratium fusus, Ceratium lineatum, Dinophysis antarctica, Dinophysis simplex, Gonyaulax digitale, Protoperidinium pyriforme and Protoperidinium variegatum. Austral fall species included Dinophysis tuberculata and Protoperidinium elegantissum. Distribution of armored dinoflagellates in the Southwestern Atlantic Ocean is influenced at the generic level by spatial considerations, particular with relation to the Polar Front Zone, whereas species composition can be effected by both region and season.     

Dinoflagellate resting cysts as factors in phytoplankton ecology of the North Sea

The occurrence and distribution of dinoflagellate resting cysts were investigated at 11 locations in the south-eastern part of the North Sea. Twenty-six known cyst species and 7 unknown cyst types, which may act as seed population for planktonic dinoflagellate blooms, have been recorded for the first time in the area. The most common cysts in recent sediments were those ofScrippsiella trochoidea, Zygabikodinium lenticulatum, Peridinium dalei, Scrippsiella lachrymosa, Protoceratium reticulatum, Protoperidinium denticulatum, andP. conicum. At all stations,S. trochoidea dominated the cyst assemblages with a maximal abundance of 1303 living cysts/cm³ in the uppermost half centimetre. Cysts of the potentially toxic dinoflagellatesAlexandrium cf.excavatum andA. cf.tamarense were scarce. In the upper 2-cm layer of sediment, dinoflagellate cysts were found in concentrations of 1.8 up to 682 living cysts/cm³. Empty cysts constituted 22–56% of total cyst abundance. The comparative distribution of the cysts showed a general increase in abundance from inshore sites to the offshore area, whereby sandy stations exhibited the lowest cyst abundance and diversity. The wide distribution of living and empty cysts ofScrippsiella lachrymosa suggests that its motile form, which has not been officially recorded in the area until now, is a common plankton organism in German coastal waters. The relatively high abundance of cysts in recent sediments demonstrates the potential importance of benthic resting stages for the initiation of dinoflagellate blooms in the study area.     

Late Pliocene dinoflagellate cyst and diatom analysis from a high resolution sequence in DSDP Site 594, Chatham Rise, south west Pacific

A high resolution mixed carbonate and siliciclastic sequence from DSDP Site 594 contains a detailed record of climate change in the late Pliocene. The sequence can be accurately dated by the LAD of Nitzschia weaveri, the LAD of Thalassiosira insigna, the LAD of T. vulnifica and the LAD of T. kolbei diatom datums. Carbonate content and δ¹⁸O signatures provide added resolution and place the sequence between isotope stages 100 and 92.The sequence contains well-preserved and diverse dinoflagellate cyst floras. Use of principal component (PCA) and canonical correspondence analyses (CCA) identifies changes in the assemblages that principally reflect warming and cooling trends. Species associated with warmer climates included Impagidinium patulum, I. paradoxum and I. sp. cf. paradoxum while those from cooler climates include Invertecysta tabulata and I. velorum. CCA is shown to be a valuable method of determining the past environmental preferences of extinct species such as I. tabulata.     

Phytoplankton distribution in the upwelling area off NW Africa

In spring 1968, the centre of the upwelling region off NW Africa was investigated using R. V. Meteor. The hydrographic structure in this area is characterized by irregular upwelling in space and time. The complicated distribution of the biological components (phytoplankton and dissolved plus particulate organic substances) is expressed only within the limits given by the resolving power of the system. Therefore, the basic values have been smoothed statistically to suppress accidental irregularities. The problematics of such manipulation are discussed. The phytoplankton distribution shows a pronounced maximum in the Cap Blanc region with extreme values in the range of > 50µg C · l^–1 in the surface layer. A decrease was observed not only in the direction of the open sea, but also along the coast. This distribution pattern is repeated (1) at the depth of the vertical phytoplankton maximum, which is near the surface in the Cap Blanc region; (2) at the large proportion of diatoms characteristic for upwelling water; (3) at the phytoplankton stock in the euphotic zone with maximum values up to > 0.5 g C · m^–2. It is calculated that (minimum) daily production is almost equal to the stock. Processes of decomposition demonstrate the upwelling by regionally different relations between O₂ consumption and PO₄ liberation. An anchor station situated near the centre of the upwelling area indicates another small-scale development of phytoplankton as demonstrated by distribution charts of the total area. Pronounced daily rhythms are revealed after extensive smoothing procedures.     

Cyst‐theca relationship of a new dinoflagellate with a spiny round brown cyst,Protoperidinium lewisiae sp. nov., and its comparison to the cyst of Oblea acanthocysta

Round spiny brown cysts with apiculocavate processes were isolated from sediments of Lake Saroma, Japan, Changle Harbor, East China Sea, China, Jinzhou Harbor, Bohai Sea, China, and San Pedro Harbor, California, USA. Superficially similar round spiny brown cysts of the species, Oblea acanthocysta were, for comparison, restudied through light microscopy and scanning electron microscopy (SEM) and by sequencing of small subunit (SSU) and large subunit (LSU) rDNA obtained through a single cyst from Lake Saroma. These morphological measurements and SEM observations showed that the new cysts can be discriminated from O. acanthocysta by the archeopyle, number of processes, shape of process bases and its apiculocavate processes. Based on LSU sequences, the most closely related species was Protoperidinium monovelum, for which no cyst stage has been described so far. However, the thecal morphology of the specimens found in this study differed from P. monovelum in details of the sulcal plates and shape of apical pore and 2a plate. We therefore describe Protoperidinium lewisiae sp. nov., which can be found in estuarine subtropical to temperate waters of the Pacific Ocean.     

Phenology of Dryopteris affinis ssp. affinis and Polystichum aculeatum: modeling relationships to the climatic variables in a Mediterranean area

The phenology of leaves and stages from immature sori to spore release were studied in natural populations of two perennial herbaceous ferns, Dryopteris affinis ssp. affinis and Polystichum aculeatum, for 2 years in Italy. The Generalized Additive Model for Location, Scale and Shape (GAMLSS) was used to predict a particular phenological event from the climatic variables. Both fern species are evergreen with leaf lifespan of 13–14 months in D. affinis ssp. affinis and 15–24 months in P. aculeatum. Their leaf production is seasonal with most flushed in spring. In D. affinis ssp. affinis the decaying of old leaves is sudden whereas in P. aculeatum it is gradual, and in both types the decaying is accelerated just as the new leaves emerge. Temperature is the best predictor for the development of sori and spore release. The end of spore release and leaf emergence are positively affected by temperature and negatively affected by rainfall and snow cover for P. aculeatum. An almost similar response to climatic factors of emergent and senescent leaves and their phenology supportsthe hypothesis that old leaves serve as nutrient storage organs for new leaf growth. Comparison the phenological patterns between the 2 years indicated that the time lapses between each phenological event were the same within seasons for D. affinis ssp. affinis but show some differences for P. aculeatum. We also hypothesize that endogenous factors may play an important role in the phenology of P. aculeatum.     

A further phylogenetic study of the heterotrophic dinoflagellate genus, Protoperidinium (Dinophyceae) based on small and large subunit ribosomal RNA gene sequences

The heterotrophic marine dinoflagellate genus Protoperidinium is the largest genus in the Dinophyceae. Previously, we reported on the intrageneric and intergeneric phylogenetic relationships of 10 species of Protoperidinium, from four sections, based on small subunit (SSU) rDNA sequences. The present paper reports on the impact of data from an additional 5 species and, therefore, an additional two sections, using the SSU rDNA data, but now also incorporating sequence data from the large subunit (LSU) rDNA. These sequences, in isolation and in combination, were used to reconstruct the evolutionary history of the genus. The LSU rDNA trees support a monophyletic genus, but the phylogenetic position within the Dinophyceae remains ambiguous. The SSU, LSU and SSU + LSU rDNA phylogenies support monophyly in the sections Avellana, Divergentia, Oceanica and Protoperidinium, but the section Conica is paraphyletic. Therefore, the concept of discrete taxonomic sections based on the shape of 1′ plate and 2a plate is upheld by molecular phylogeny. Furthermore, the section Oceanica is indicated as having an early divergence from other groups within the genus. The sections Avellana and Excentrica and a clade combining the sections Divergentia/Protoperidinium derived from Conica‐type dinoflagellates independently. Analysis of the LSU rDNA data resulted in the same phylogeny as that obtained using SSU rDNA data and, with increased taxon sampling, including members of new sections, a clearer idea of the evolution of morphological features within the genus Protoperidinium was obtained. Intraspecific variation was found in Protoperidinium conicum (Gran) Balech, Protoperidinium excentricum (Paulsen) Balech and Protoperidinium pellucidum Bergh based on SSU rDNA data and also in Protoperidinium claudicans (Paulsen) Balech, P. conicum and Protoperidinium denticulatum (Gran et Braarud) Balech based on LSU rDNA sequences. The common occurrence of base pair substitutions in P. conicum is indicative of the presence of cryptic species.