Molecular data and the evolutionary history of dinoflagellates

Saldarriaga, Juan F.; Taylor, F. J. R.; Cavalier‐Smith, Thomas; Menden‐Deuer, Susanne; Keeling, Patrick J.

doi:10.1016/j.ejop.2003.11.003

Cited by 203 publications

(252 citation statements)

References 128 publications

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“…The branching order of these groups is highly congruent with recent classification of the alveolates (Cavalier-Smith, 2004), but whether the MA should be included among the dinoflagellates or as sisters to them is still unclear (see Massana et al, 2008). This unresolved branching order between the dinoflagellates and the MA (Figure 1) could be due to a rapid radiation, early in the evolution of dinoflagellates (Saldarriaga et al, 2004;ShalchianTabrizi et al, 2006); multiple gene phylogenies are needed to help determine the relationships between these groups. The apicomplexans were retrieved as monophyletic (75%, 0.98 pp), whereas Colpodella sp.…”

Section: Resultssupporting

confidence: 62%

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

et al. 2010

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Protist parasites are ecologically important, as they can have great impact on host population dynamics and functioning of entire ecosystems. Nevertheless, little is known about their prevalence in aquatic habitats. Here, we investigate the diversity and distributional patterns of the protist parasites Perkinsus and Parvilucifera (Perkinsea). Our approach included 454 pyrosequencing of the 18S rDNA gene obtained from a high-altitude lake (Lake Finsevatn, Norway) and phylogenetic analyses of all publicly available sequences related to Perkinsea. The applied PCR primers target a 450 bp region that encompass the variable V4 region of the 18S rDNA gene and have been optimized for the Titanium upgrade of the 454 technology. Nearly 5000 sequences longer than 150 bp were recovered from nearly all eukaryotic supergroups, and of those, 13 unique sequences were affiliated to Perkinsea. Thus, our new strategy for 454 amplicon sequencing was able to recover a large diversity of distantly related eukaryotes and previously unknown species of Perkinsea. In addition, we identified 40 Perkinsea sequences in GenBank generated by other recent diversity surveys. Importantly, phylogenetic analyses of these sequences identified 17 habitat-specific marine and freshwater clades . Hence, only a few successful transitions between these habitats have taken place over the entire history of Perkinsea, suggesting that the boundary between marine and fresh waters may constitute a barrier to cross-colonizations for intracellular parasites.

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Section: Resultssupporting

confidence: 62%

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

et al. 2010

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“…Early position of Noctilucales and athecate paraphyly. Athecate dinoflagellates have long confounded dinoflagellate molecular phylogenies as a result of their intermixing with thecate taxa, for example within the so-called Gymnodiniales-Peridiniales-Prorocentrales (GPP) complex (21), or as a result of the unstable position of certain outliers like the Noctilucales, which have at times been placed as basal or nested deeply inside the group (12,16,22). Our analyses resolve these issues and help reconcile dinoflagellate morphological and molecular data in several important ways.…”

Section: Resultsmentioning

confidence: 77%

“…Dinoflagellates have left a fossil record that is one of the richest among protists, and many preserve a detailed record of tabulation through reflection of thecal plates that provide insights into the history of some modern taxa, as well as extinct groups. They have also left an extensive biogeochemical record (i.e., sterols), but reconciling this evidence with poorly resolved gene phylogenies has been difficult (15,16).…”

Section: Significancementioning

confidence: 99%

Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics

Janouškovec

Gavelis

Burki

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an earlybranching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group's cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.dinoflagellates | phylogeny | theca | plastids | dinosterol D inoflagellates comprise approximately 2,400 named extant species, of which approximately half are photosynthetic (1). However, this represents a fraction of their estimated diversity: in surface marine waters, dinoflagellates are some of the most abundant and diverse eukaryotes known (2). Dinoflagellates' ecological significance befits their abundance: photosynthetic species are dominant marine primary producers, and phagotrophic species play an important role in the microbial loop through predation and nutrient recycling. Approximately 75-80% of the toxic eukaryotic phytoplankton species are dinoflagellates, and they cause shellfish poisoning and harmful algal blooms of global importance. Symbiotic genera like Symbiodinium participate in interactions with metazoans and are essential for the formation of reef ecosystems, and parasitic forms play a central role in the collapse of harmful algal blooms, including those caused by dinoflagellates themselves (3). Dinoflagellates synthesize important secondary metabolites including sterols, polyketides, toxins, and dimethylsulfide, and several of them have evolved bioluminescence. They ...

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“…It has been suggested that this species is a misnamed member of the peridinialean genus Amphidiniopsis, which is a heterotrophic sanddwelling genus with diverse cell morphologies and tabulation (Table 1; Hoppenrath et al, 2004;Saldarriaga et al, 2004). The type species of Amphidiniopsis, A. kofoidii, shares features with Archaeperidinium minutum, H. litoralis and T. dragescoi, viz.…”

Section: Molecular Phylogenetic Inferencesmentioning

confidence: 99%