Phylogenetic position and mitochondrial genome evolution of “orphan” eukaryotic lineages
Bibliographic record
Abstract
The phylogenetic tree of eukaryotes is divided into a handful of highly diverse "'supergroups"; only a few so-called "orphan" lineages branch in uncertain positions outside of these large clades. We found that the mitochondrial genome of one such lineage, the telonemids, is considerably gene-rich, a feature observed in other "orphans" as well, raising the possibility that these organisms share a common history. On the contrary, our phylogenomic analyses show that "orphans" with gene-rich mitochondria branch into two different positions: telonemids actually belong to the established supergroup Haptista, while provorans and meteorids form a strongly supported clade with hemimastigophorans, in a previously unrecognized ancient supergroup that we dub here Promethea. Comparative genomics shows that this split reflects differences between mitochondrial gene sets. Thanks to the increased number of available representatives analyzed together, our results further simplify and illuminate the evolutionary relationships between eukaryotes.
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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 | 0.000 | 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 | 0.000 | 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) | 0.001 | 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".