In search of lost ergots: phylogenetic re-evaluation of Claviceps species in Japan and their biogeographic patterns revealed-SUPP files
Bibliographic record
Abstract
Supplementary files. Fig. S1. Cultures of Claviceps spp. Three-point inoculation on petri dishes (52 mm diam) with 5 mL T2 agar (sucrose 100 g, l-asparagine 10 g, yeast extract 0.1 g, KH2PO4 0.25 g, MgSO4·7H2O 0.25 g, FeSO4·7H2O 0.02 g, ZnSO4·7H20 0.015 g, KCI 0.12 g, Ca(NO3)2·4H2O 1.0 g, agar 20 g; pH 5.2, 1000 mL). The plates were incubated in dark at 20 °C for 20 days. The morphology of ergot colonies is an unstable feature as it often changes with age. The colonies of the same isolates were shown with a light blue background. T = ex-type, NT = ex-neotype, ET = ex-epitype. Fig. S2. Maximum likelihood phylogenetic tree based on each gene (LSU, TEF-1α, Mcm7, TUB2 and RPB2). Bootstrap (BS) support values from ML and MP analyses are shown at branch (MLBS/MPBS). MLBS < 50 are not shown. Culture collection number or specimen numbers, country code and host genus name are presented after the species name. Ergots analysed in this study are in bold. Ergots collected in Japan are marked by the yellow boxes. The scale represents the number of nucleotide substitutions per site. T = ex-type, NT = ex-neotype, ET = ex-epitype. Abbreviated country code; ARG = Argentina, AU = Australia, BELG = Belgium, BOTSW = Botswana, BRA = Brazil, CA = Canada, CZ = Czech Republic, FRA = France, GER = Germany, IND = India, JA = Japan, KAZ = Republic of Kazakhstan, LIT = Lithuania, MEX = Mexico, SA = South Africa, SWI = Switzerland, THAI = Thailand, UK = United Kingdom, USA = United States of America, ZW = Zimbabwe. Table S1. Nucleotide sequences of primers used in this study.
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.004 | 0.007 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.010 | 0.004 |
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".