Filling in the gaps: EST surveys of under‐represented chromalveolates
Bibliographic record
Abstract
The “chromalveolate hypothesis” posits the monophyly of alveolates (apicomplexans, dinoflagellates and ciliates), heterokonts, haptophytes and cryptomonads. One implication of the monophyly of chromalveolates is that the plastids in this group could share a common ancestor—derived from a single endosymbiosis. Members of all chromalveolate groups, with the exception of ciliates, possess a secondary plastid originating from a rhodophytic symbiont (although the rhodophytic origin of the apicomplexan plastid remains contentious). A single origin of this chromalveolate plastid represents the most parsimonious hypothesis for plastid acquisition. Growing support for the “chromalveolate hypothesis” has relied on a relatively small number of molecular studies to date, and a more thorough examination of this alliance has been undermined by a paucity of broad molecular data from several of its members, despite complete genome sequences from apicomplexans and ciliates. To address this deficit we have undertaken EST (Expressed Sequence Tag) surveys of several taxa, representing dinoflagellates, haptophytes and cryptomonads. Using EST data we are undertaking broad molecular comparisons of these groups through molecular phylogenies, analyses of common biochemical pathways, and studies of organelle evolution. This genome‐based approach provides a more complete view of the major chromalveolate groups, and a chance to more thoroughly test the chromalveolate hypothesis.
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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) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".