Additional file 1 of Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation
Bibliographic record
Abstract
Additional file 1: Table S1. Nutrient measures across sampled points. Table S2. Ratio of nutrients concentrations. Table S3. RDP classification of partial 16S rRNA. Table S5. General information of the 42 Vibrionaceae genomes and 5 references used in this study. Table S6. Results of the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis (see methods) using 452 BUSCOS of 721 species of the Gamma-proteobacteria database. Table S9. GO terms enriched at the unique genes of each clade. Figure S1. Phylogenetic reconstruction of 16S RNA sequences. Figure S2. AdaptML analysis. Figure S3. Random analysis of alpha values within each clade. Figure S4. Analysis of structure of Clade II. Figure S5. Frequency of recombination events. Figure S6. Recombination events across a whole genome alignment. Figure S7. UPGMA and membership of the CCB strains.
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 | 0.001 | 0.012 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.833 | 0.154 |
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".