Linking biological and geological data on dinoflagellates using the genus <i>Spiniferites</i> as an example: the implications of species concepts, taxonomy and dual nomenclature
Bibliographic record
Abstract
Dinoflagellates encompass two taxonomic systems (dual taxonomy) reflected by separate traditions of nomenclature: one based mainly on living motile stages, and the other mainly on fossil cysts (dual nomenclature). Modern cysts may therefore bear two names if their life cycle is known. There have been attempts to rationalize this duality, but at species and genus level this has been largely unfruitful. New and continuing developments call for a renewed evaluation of this duality: (1) the elucidation of multiple new cyst–motile stage relationships creating overlaps between cyst-based and motile-based systems, and (2) the advent of DNA sequence-based phylogenies, revealing evolutionary patterns (underlying the phenotypic differences) that disagree with trees obtained from the study of fossil cysts. We examine the background of dual nomenclature and discuss the implications of new advances in molecular phylogeny for dual taxonomy as well as briefly review earlier attempts to unite cyst/fossil and motile-/living-based nomenclatures. From this basis, we explore routes for bringing the separate taxonomic systems closer together. Our rationale for doing this lies in the challenges facing communication between the biologists and geologists who work on these different life cycle stages. These challenges encompass taxonomic issues, nomenclature, evolutionary interpretations, and the nature of what we perceive as a species. We use the motile/cyst pair Gonyaulax/Spiniferites as our example, as these, and related genera, provide a useful model for illustrating the difficulties in bridging the gap between biology and palaeontology because they are numerous, with regard to both species and specimens, and are ubiquitous in both time and space.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.009 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.012 | 0.011 |
| Science and technology studies | 0.001 | 0.003 |
| Scholarly communication | 0.002 | 0.004 |
| Open science | 0.001 | 0.004 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".