Additional file 1 of A new lineage of non-photosynthetic green algae with extreme organellar genomes
Bibliographic record
Abstract
Additional file 1: Fig. S1. Maximum likelihood phylogenetic tree ((IQ-TREE, TIM2+F+I+G4 substitution model) of 18S rRNA gene sequences from Chlorophyceae. Fig. S2. Predicted secondary structure of the ITS2 region of Leontynka pallida, with differences in the corresponding region of Leontynka elongata mapped onto it. Fig. S3. Maximum likelihood phylogenetic tree of Chlorophyceae, including Leontynka pallida, inferred from a concatenated set of seven conserved mitogenome-encoded proteins (2,608 amino acid positions). Fig. S4. Light micrographs of Leontynka pallida. Fig. S5. Light micrographs of Leontynka elongata. Fig. S6. Ultrastructure of Leontynka elongata (a–f) and Leontynka pallida (g–i). Fig. S7. Occurrence of the “variant 8” repeat (see Fig. 4) in the FtsH protein of Leontynka pallida mapped onto its predicted structure. Fig. S8. Alignment of the highly similar terminal regions of the originally assembled linear mitogenome contig. Fig. S9. Occurrence of the “variant 8” repeat (translated in reading frame +0 as KDKPANLTS and -0 as KEVSFAGLSL; both boxed in colour) in a variable region of protein sequence of the ribosomal protein Rps8 from Leontynka pallida (full protein alignment together with representatives of other chlamydomonadalean algae). Fig. S10. Phylogenetic analysis of a concatenated dataset of 24 conserved plastome-encoded proteins (5020 amino acid positions) from Chlamydomonadales, including Leontynka pallida, and the sister order Sphaeropleales (sensu lato).
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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 | 0.002 | 0.014 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.006 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.822 | 0.221 |
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".