Resolving species diversity in the red algal genus <i>Callophyllis</i> (Kallymeniaceae, Gigartinales) in Canada using molecular assisted alpha taxonomy
Bibliographic record
Abstract
The COI-5P DNA barcode (the 5′ region of the mitochondrial cytochrome c oxidase I gene) has proven an effective tool for quickly screening large numbers of biological specimens and assigning them to genetic species groups for subsequent examination in an approach known as molecular-assisted alpha taxonomy (MAAT). In the present study, we applied MAAT to Canadian species of the red algal genus Callophyllis in order to resolve confusion surrounding this taxonomically perplexing group. A total of 563 Callophyllis specimens were examined (either molecularly, morphologically or both) – 504 from British Columbia along the Pacific coast of Canada and 59 from the U.S.A., Australia and Chile. In total, 16 genetic species groups were resolved including 12 in Canada although only nine species are reported in the flora. Here we report range extensions of C. beringensis and C. radula from the NW Pacific, C. dissecta from California, U.S.A. and the Chilean species C. variegata (the type species) into the Canadian flora. Our results also uncovered cryptic diversity in the genus necessitating the description of C. schneideri Clarkston & G.W. Saunders sp. nov. Subsequent analyses of a subset of specimens using the internal transcribed spacer of the ribosomal cistron (ITS) resolved the same groups as COI-5P while the universal plastid amplicon (UPA, domain V of theplastid 23S rRNA gene) had poor resolution at the species level and in one case underestimated species diversity. Finally, large-subunit ribosomal DNA (LSU), nuclear elongation factor 2 (EF2), COI-5P and a combined LSU, EF2 and COI-5P alignment were subjected to phylogenetic analyses in order to investigate relationships among Canadian species of Callophyllis. A significant outcome was the resolution of two well-supported lineages for the monocarpogonial versus polycarpogonial species of this genus, as had been posited in the literature.
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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 | 0.003 | 0.003 |
| Science and technology studies | 0.003 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 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 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".