A floristic survey of marine tube-forming diatoms reveals unexpected diversity and extensive co-habitation among genetic lines of the<i>Berkeleya rutilans</i>complex (Bacillariophyceae)
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Bibliographic record
Abstract
Limited molecular data for marine tube-forming diatoms are available currently and this study provides the first molecular survey of these taxa. To conduct this survey, we used a molecular-assisted alpha taxonomy (MAAT) approach that utilizes DNA barcode data. We used three DNA barcode markers: the 3´ end of the large subunit of RUBISCO (rbcL-3P); the variable D2/D3 region of the nuclear large subunit ribosomal DNA (LSU D2/D3); and the internal transcribed spacer 2 (ITS2) to assign marine tube-forming diatoms from Canada to genetic species groups. The rbcL-3P analysis uncovered 29 genetic groups including representatives of Haslea crucigera, Navicula bottnica, N. brunelii, N. ramosissima, Nitzschia fontifuga, N. tubicola, Parlibellus berkeleya and P. delognei f. elliptica, as well as a complex of 14 closely related groups morphologically consistent with Berkeleya rutilans. We sequenced ITS2 for representatives of the B. rutilans complex; these data were consistent with the rbcL-3P genetic clusters for 86% of the colonies tested. The remaining 14% were in conflict, possibly indicating that more than a single Berkeleya genetic species was present in each colony. To investigate this hypothesis further, we developed 'species-specific' ITS2 primers and confirmed heterogeneity of Berkeleya genetic species in 64% of the colonies tested (N = 91). Therefore, a taxonomic assessment of tube-forming species that were originally described on the basis of colony morphology (e.g. Berkeleya rutilans) can only proceed using clonal cultures or single-cell analysis.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 it