The evolutionary relationships amongst excavates: a concatened protein analysis
Bibliographic record
Abstract
Morphological studies and phylogenies of ribosomal RNA, taken together, suggest that excavate protists may be related to each other, but many of the deepest level relationships amongt these organisms remain poorly understood. We have assembled a data set of six slowly evolving nuclear‐encoded protein genes that include nine of the 10 recognized excavate groups. Maximum likelihood analyses demonstrate that diplomonads and Carpediemonas than parabasalids are related to each other. They also confirm that Trimastix is specifically related to oxymonads, forming the taxon Preaxostyla. There is strong support for a clade of Euglenozoa, Heterolobsea and jakobids, but, unexpectedly, jakobids and Heterolobosea are robustly recovered as sister taxa. Malawimonas is placed either as sister to Preaxostyla or as sister to the (Euglenozoa, Heterolobosea, jakobid) clade. The original data set strongly supports an association between the (diplomonad, Carpediemonas, parabasalid) clade and Opisthokonts. However, this grouping is not recovered when α‐tubulin is excluded from the analysis, suggesting that the signal for this relationship lies within this one protein and might be suspect. All other important nodes in the tree are, by contrast, robust to the removal of any one gene. With α‐tubulin excluded, excavates tend to form just two clades, with no strong nodes separating them. Jakobids, with their apparently ancestral bacterial‐type mitrochondrial RNA polymerase are nonetheless nested within a clade with normal phage‐type RNA polymerases, complicating any understanding of deep‐level mitochondrial evolution The position of jakobids also seriously challenges the now well‐accepted concept of a taxon Discicristata.
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
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".