Multiple protein phylogenies show that Oxyrrhis marina and Perkinsus marinus are early branches of the dinoflagellate lineage
Bibliographic record
Abstract
Oxyrrhis marina and Perkinsus marinus are two alveolate species of key taxonomic position with respect to the divergence of apicomplexans and dinoflagellates. New sequences from Oxyrrhis, Perkinsus and a number of dinoflagellates were added to datasets of small-subunit (SSU) rRNA, actin, alpha-tubulin and beta-tubulin sequences, as well as to a combined dataset of all three protein-coding genes, and phylogenetic trees were inferred. The parasitic Perkinsus marinus branches at the base of the dinoflagellate clade with high support in most of the individual gene trees and in the combined analysis, strongly confirming the position originally suggested in previous SSU rRNA and actin phylogenies. The SSU rRNA from Oxyrrhis marina is extremely divergent, and it typically branches with members of the Gonyaulacales, a dinoflagellate order where SSU rRNA sequences are also divergent. Conversely, none of the three protein-coding genes of Oxyrrhis is noticeably divergent and, in trees based on all three proteins individually and in combination, Oxyrrhis branches at the base of the dinoflagellate clade, typically with high bootstrap support. In some trees, Oxyrrhis and Perkinsus are sisters, but most analyses indicate that Perkinsus diverged prior to Oxyrrhis. Morphological characters have previously pointed to Oxyrrhis as an early branch in the dinoflagellate lineage; our data support this suggestion and significantly bolster the molecular data that support a relationship between Perkinsus and dinoflagellates. Together, these two organisms can be instrumental in reconstructing the early evolution of dinoflagellates and apicomplexans by helping to reveal aspects of the ancestors of both groups.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".