EARLY EVOLUTIONARY HISTORY OF DINOFLAGELLATES AND APICOMPLEXANS (ALVEOLATA) AS INFERRED FROM HSP90 AND ACTIN PHYLOGENIES<sup>1</sup>
Bibliographic record
Abstract
Three extremely diverse groups of unicellular eukaryotes comprise the Alveolata: ciliates, dinoflagellates, and apicomplexans. The vast phenotypic distances between the three groups along with the enigmatic distribution of plastids and the economic and medical importance of several representative species (e.g. Plasmodium , Toxoplasma , Perkinsus , and Pfiesteria ) have stimulated a great deal of speculation on the early evolutionary history of alveolates. A robust phylogenetic framework for alveolate diversity will provide the context necessary for understanding the basic biological properties of the group and for developing appropriate strategies for management. We addressed the earliest stages of alveolate evolution by sequencing heat shock protein 90 (hsp90) genes from several ciliates, apicomplexans, and dinoflagellates, including key species thought to represent early diverging lineages: Oxyrrhis marina , Perkinsus marinus , Cryptosporidium parvum , and the eugregarine Monocystis agilis . Moreover, by sequencing the actin gene from Monocystis , we were able to examine the sister relationship between gregarines and cryptosporidians with a three‐protein concatenated data set (hsp90, actin, and β‐tubulin). Phylogenetic analyses of the hsp90 data set provided a robust topology for alveolate relationships: Alveolates were monophyletic and apicomplexans and dinoflagellates formed sister groups to the exclusion of ciliates. Oxyrrhis formed the earliest diverging sister lineage to the “core” dinoflagellates, and Perkinsus formed the earliest diverging sister lineage to the Oxyrrhis –dinoflagellate clade. This topology was strongly supported inall analyses and by a unique indel shared by Oxyrrhis and dinoflagellates. A sister relationship between Cryptosporidium and Monocystis was weakly supported by the hsp90 data set but strongly supported by the three‐protein concatenated data set.
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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 | 0.001 | 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".