Additional file 1 of A novel distribution of supergene genotypes is present in the socially polymorphic ant Formica neoclara
Bibliographic record
Abstract
Additional file 1: FigureS1. A Results of GEMMA analysis utilizing workers from colonies fromall regions, visualized via Manhattan plot. We used a linear mixed model withcolony social form as the independent variable. Each point represents anindividual SNP, with the corresponding chromosome on the x-axis and thenegative logarithm of the SNP p-value on the y-axis. Only one SNP, from chromosome 3, exceeds the significance level (Bonferroni corrected significance threshold: 1.52E−04;p-value: 7.26E−06). B Results of GEMMA analysis onworkers from colonies in Alberta only, to reduce the effect of underlyingpopulation structure on the GWAS, visualized via Manhattan plot. We used alinear mixed model with colony social form as the independent variable. Eachpoint represents an individual SNP, with the corresponding chromosome on thex-axis and the negative logarithm of the SNP p-value on the y-axis. Five SNPs,all from chromosome 3, are above the significance threshold (Bonferroni corrected significance threshold: 1.89E−04; p-values: 7.79E−07, three at 4.43E−07, and 3.79E−07). Figure S2. Stacked bar plot displaying genotypes of samples from colonies labeled as ambiguous in social form (three from Alberta, one from southern British Columbia). Each bar represents all samples from an individual colony. Genotype in relation to each individual worker, is indicated by color: green = Sm/Sm andbrown = Sm/Sp. Figure S3. Line graph showing the effects of missingness on the Huang estimator. Individual (red) and whole sample (black) relatedness values are represented as lines. Figure S4. Density plot showing pairwise relatedness (determined by PolyRelatedness) among all sequencedworkers of colonies from the Evan Thomas trailhead in Alberta, Canada. On average, workers from monogyne colonies are the most related, whereas intermediate colonies (“ambiguous” in Fig. 1) have a bimodal distribution offull siblings and individuals with intermediate relatedness values, andpolygyne colonies have the lowest overall pairwise relatedness. Figure S5. A principal component analysis utilizing all markers except those on chromosome 3 in individuals fromcolony samples, with the year of the respective batches color coded. Table S1. Overview of consensus social form variables. Table S2. Sampling regions and their associated coordinate values. Table S3. PC axis weightings of variants on chromosome 3 (see also Fig. 2). Weightings greater than 1 or less than − 1 are highlighted in grey for each PC axis. The outliers from GWAS analyses are highlighted in green (Alberta only) and orange (GWAS of the full dataset).
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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 | 0.014 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.794 | 0.113 |
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".