Dinoflagellates are among the most important organisms in the ocean, forming a major part of the plankton and, in the case of heterotrophic species such as those in the genus Protoperidinium, feeding voraciously on other planktonic cells. Like many protists, they alternate between a swimming, armoured motile stage and a dormant cyst stage that sinks to the seafloor and can survive in sediments for years before germinating. Because the cysts are made of highly resistant organic material, many of them fossilise, leaving a continuous record stretching back hundreds of millions of years. This dual life cycle has forced scientists to maintain two parallel naming systems, one for the living cell and one for the cyst, a convention sanctioned by the International Code of Nomenclature for algae, fungi, and plants. The trouble is that linking a particular cyst to the motile cell that produced it is fiendishly difficult, and misassignments have cascaded through the literature for decades.

The heart of the controversy lay with two cyst-based genera, Selenopemphix and Multispinula. Selenopemphix was erected in 1972 on the basis of an Oligocene specimen of Selenopemphix nephroides from Germany, characterised by thin brown walls, a kidney-shaped outline when viewed from the pole, a deeply incised groove called the parasulcus, and a flattened body with two rounded antapical protrusions. Multispinula, described in 1975 from recent sediments of the Persian Gulf with its type species Multispinula quanta, comprised similar-looking cysts but with distinctive rows of solid spines. Over the years, successive authors shuffled Multispinula into Selenopemphix as a junior synonym, then argued it back out, then merged it again, largely because the position of the archeopyle, the opening through which the motile cell escapes the cyst, could not be reliably determined in all specimens. Whether that opening sat symmetrically on the mid-dorsal line or was offset to one side became the pivotal, and bitterly contested, diagnostic character.

David and her colleagues attacked the problem with an unusually comprehensive toolkit. They collected surface sediments from the Atlantic and Pacific Oceans, concentrated the living cysts using density separation with sodium polytungstate, and then performed the most direct experiment imaginable: they picked out individual cysts under an inverted microscope, placed each one in a microwell with culture medium, and waited for them to germinate at 16 degrees Celsius under a controlled light cycle. Thirty-nine cysts hatched into motile cells, allowing the researchers to observe, for the first time with modern methods, exactly which swimming species emerges from which cyst type. The germinated cells were then stained with a fluorescent dye to reveal the intricate geometry of their cellulose plates, photographed under light microscopy, and examined in exquisite detail with a field-emission scanning electron microscope at the marine biology station in Concarneau.

The results were revelatory. Cysts of Selenopemphix nephroides from the Irish Sea hatched into cells matching Protoperidinium subinerme, confirming a link long suspected but never verified with molecular data. Cysts of Multispinula quanta produced cells resembling Protoperidinium conicum. Most excitingly, twenty-nine cells that emerged from a third, smaller cyst type proved to belong to an entirely unknown species, which the team named Protoperidinium parvivariplatum, a nod to its small size and its remarkably variable second anterior intercalary plate. Its cyst counterpart received the name Multispinula varispinosa, honouring the striking variability in spine length, with some specimens bearing long spines of 5 to 14 micrometres, others short spines of 2 to 4 micrometres, and still others a mixture of both. A fourth cyst, large and strongly compressed, with solid spines and fused bases, was recovered from Lake Saroma in Hokkaido and christened Multispinula robusta, its motile equivalent being the classic Protoperidinium conicum described from Norwegian waters.

To place these organisms on the tree of life, the team extracted and sequenced partial large-subunit ribosomal DNA from single germinated cells and from individual cysts, generating twelve new sequences. Bayesian and maximum-likelihood phylogenetic analyses produced a clear and consequential picture: the type species of the two contested genera sit in entirely different branches of the Protoperidinium sensu stricto clade. Selenopemphix nephroides and its relatives cluster within the section Tabulata, while Multispinula varispinosa, together with previously published sequences of Protoperidinium conicum and Protoperidinium cf. conicum, belongs to the section Conica. The two cyst-based genera are therefore polyphyletic if lumped together, meaning that treating them as one genus would group organisms that are not each other’s closest relatives. The sequence divergence was substantial, with Protoperidinium parvivariplatum showing only 85 to 89 percent similarity to its supposed congener Protoperidinium conicum, and the new species formed a well-supported clade with 100 percent bootstrap support.

Morphology told the same story from a different angle. Scanning electron microscopy confirmed that the archeopyle of Selenopemphix nephroides is genuinely offset from the mid-dorsal line, while that of Multispinula varispinosa sits squarely in the centre. Even more strikingly, the electron micrographs revealed, for the first time, a paratabulation on Multispinula cysts, a ghostly map of the plates of the ancestral motile cell traced by rows of spines connected by parasutural ridges across the precingular and postcingular zones. Selenopemphix, by contrast, restricts its ornamentation to the raised margins of the paracingulum. Armed with this convergence of molecular and morphological evidence, the authors formally emended both genera: Selenopemphix now includes only cysts with an offset archeopyle and ornamentation confined to the paracingular margins, while Multispinula is re-established for cysts with a mid-dorsal archeopyle and paratabulation outlined by spines and ridges. Multispinula quanta was transferred back to its original name, and the genus now comprises three species, each tied to a different motile cell and each occupying a distinct thermal niche, from the cold-water Multispinula robusta of Hokkaido and the North Sea to the warm-temperate Multispinula quanta of the Persian Gulf, the Yellow Sea, and the Bay of Biscay, with the broadly tolerant Multispinula varispinosa spanning cold to temperate waters in between.

Perhaps the most forward-looking part of the study went beyond shape and sequence altogether. Using attenuated total reflection Fourier transform infrared microspectroscopy, or ATR µ-FTIR, the team analysed the biomacromolecular composition of individual cyst walls, collecting eighteen spectra from modern and fossil specimens, including six fossil Selenopemphix nephroides dating back to the Rupelian stage of the Oligocene. The spectra revealed that both genera build their walls from a mixture of proteins and melanin-like pigments, the aromatic rings of the latter being responsible for the characteristic brown colouration. But the proportions differ fundamentally: Multispinula cysts are relatively enriched in proteins and poorer in melanin compared with Selenopemphix. This chemical distinction is not merely a curiosity. Proteins are labile molecules that microbes typically hydrolyse within roughly one hundred thousand years of burial, whereas melanin is extraordinarily resistant, having been documented in deposits as old as the Carboniferous. Fossil Selenopemphix nephroides specimens showed exactly the expected maturation signature, retaining their aromatic pigment bands while progressively losing carbohydrate features, a pattern mirroring the thermal evolution of sporopollenin in plant spores.

The implications ripple outward through the fossil record. Multispinula cysts first appear, tentatively, in the upper Oligocene around 23 million years ago, and Multispinula varispinosa is confirmed only from the Pleistocene onward, whereas Selenopemphix nephroides reaches back to the lower Eocene, more than 47 million years before the present. The authors argue that the protein-rich, less melanised walls of Multispinula impose a genuine stratigraphic preservation limit, biasing the apparent evolutionary history of the group and shortening its fossil record relative to its more chemically robust relatives. They caution that palaeoenvironmental studies relying on poorly fossilisable cyst taxa should interpret stratigraphic occurrences with care, and they note that cysts germinated in the laboratory carry chemical contaminants, from lipids and nucleic acids to extracellular polymeric substances, that naturally germinated specimens shed in the sediment, likely through the activity of microbial communities that metabolise labile components while leaving the resistant dinosporin layers intact.

In an era when biodiversity is being inventoried at every scale, from whales to microbes, this study is a reminder that even the tiniest organisms can hold big surprises, and that resolving their identities requires patience, ingenuity, and a willingness to grow them in a dish. By hatching cysts one by one, sequencing their genes, imaging their architecture at nanometre scales, and reading their molecular fingerprints with infrared light, David and her colleagues have not only settled a fifty-year argument but also demonstrated a template for future taxonomy: morphology, molecules, and chemistry, integrated, can reveal hidden species, correct old mistakes, and even explain why some creatures vanish from the rock record while others endure. For the humble dinoflagellate cyst, a grain of organic matter smaller than a speck of dust, the fossil record will never look quite the same again.

Subject of Research: Taxonomic revision of the dinoflagellate cyst genera Selenopemphix and Multispinula using morphology, molecular phylogenetics, and cyst wall chemistry

Article Title: Emendation of the genera Selenopemphix and Multispinula (Peridiniales, Dinophyceae), with the description of Multispinula varispinosa sp. nov. and Multispinula robusta sp. nov.

Article References: David, O., Meyvisch, P., Gu, H., Bilien, G., Clarke, D., Marret, F., & Mertens, K. N. (2026). Emendation of the genera Selenopemphix and Multispinula (Peridiniales, Dinophyceae), with the description of Multispinula varispinosa sp. nov. and Multispinula robusta sp. nov.. Journal of Micropalaeontology, 45(2), 547-576. https://doi.org/10.5194/jm-45-547-2026

Image Credits: AI Generated

DOI: 10.5194/jm-45-547-2026

Keywords: dinoflagellate cysts, Selenopemphix, Multispinula, Protoperidinium, taxonomy, LSU rDNA phylogeny, ATR FTIR spectroscopy, cyst wall composition, micropalaeontology, new species, fossil preservation, marine plankton