STRUCTURAL AND SEQUENCE SIGNATURES OF NUCLEAR SSU RRNA DEFINE TAXONOMIC LEVELS WITHIN THE RHODOPHYTA
Bibliographic record
Abstract
Over 400 nuclear SSU rRNA sequences representing all orders of the Rhodophyta were aligned and analyzed using comparative sequence analysis. Numerous nucleotide positions and structural elements were found that delineated various taxonomic groups. The 1245 region (E. coli numbering) contained a loop that differed in size between two conserved helices and clearly separated the Florideophyceae [3 nt (>95% of 268 sequences)], Bangiales [13 to 14 nt (100% of 116 sequences)] and remaining Bangiophyceae including the Cryptophyta nucleomorphs [four to eight nt (100% of 32 sequences)]. In addition, members of the Thoreaceae were found to have additional helices in the 650 and 1139 region of which a corresponding structure was not present in any other red algal SSU rRNA gene sequence. Base‐pair and nucleotide signatures differentiated the Bangiales, Florideophyceae, Bangiophyceae (not including Bangiales) and Hildenbrandiales at three levels of comparison: within the Rhodophyta (>400 sequences), the Eukaryota (not including Rhodophyta;> 1300 sequences) and three kingdom (Archaea, Bacteria, 2 organelles, Eukaryota;> 7000 sequences). For example, all members of the Hildenbrandiales have a change in the base‐pair 512:539 that is a region of functional importance. Sequences from the Eukaryota, Archaea, Bacteria and two organelles have a C:G or a U:A in this position whereas the Hildenbrandiales have a C:A pair. This analysis raises the possibility of utilizing structural features of nuclear SSU rRNA and sequence signatures to support and delineate phylogenetic clades within the Rhodophyta.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| 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".