Molecular evolution of eukaryotes using structural genomic data
Bibliographic record
Abstract
One of the most challenging evolutionary problems is locating the root of the eukaryote tree. We know that the root lies somewhere within the kingdom Protozoa, but the widespread view that early eukaryotes were amitochondrial has recently been dramatically overturned. Systematic biases in sequence evolution prevent the reliable inference of the eukaryote root from single‐gene trees. Concatenated sequence trees should be more reliable, but leave many possibilities open. In principle deletions/insertions or gene fusions should be superior for this purpose whenever ancestral and derived states are clearly distinguishable. Using a derived gene fusion between dihydrofolate reductase (DHFR) and thymidylate synthase (TS), genes we were able to greatly narrow down the position of the root. This gene fusion clearly divides eukaryotes into two clades: Amoebozoa plus opisthokonts (unikonts, which are ancestrally uniciliate) and bikonts, which are ancestrally biciliate. Another gene fusion between the first three enzymes of the six enzyme pyrimidine synthesis pathway supports this division. This derived three gene fusion is seen in Amoebozoa and opisthokonts (unikonts) but not in bikonts. A third gene fusion in the phosphofructokinse gene which is so far only found in opisthokonts and Amoebozoa further lends support to the eukaryote unikont/bikont divide. Independent support comes from sequence trees based on concatenated protein alignments. Our results show that the primary divergence of eukaryotes was probably between unikonts (animals, Fungi, Choanozoa and Amoebozoa) and bikonts (plants, chromists, all other Protozoa: alveolates, excavates, Rhizaria, Apusozoa) and that the root of the eukaryote tree lies between these two groups.
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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 | 0.007 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.006 | 0.006 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| 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".