Additional file 1: of Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels
Bibliographic record
Abstract
Figure S1. Principal coordinate analysis (PCoA) of red squirrel gut microbial communities in grid KL based on Bray-Curtis distance. Samples are colored by sampling season. The percentage of the variation explained by the first three coordinates is indicated on the axes. Figure S2. Time-decay of the red squirrel gut microbial communities. Each dot represents a comparison between two samples of the same individual collected at different time points. The colors of dots represent the combination of seasons when the two samples were collected. Y-axis represents the microbiota similarity. The similarity decay as a function of time best fits a power law (blue line). The shade shows the 95% confidence bounds. Figure S3. The composition of red squirrel diet across 3 years aggregated by month. Each color represents a different dietary item. Figure S4. Seasonal rhythm in the alpha diversity of red squirrel gut microbiota. Species richness is estimated by Chao1 index. Figure S5. Key hub species in OTU co-occurrence network vary by season. The co-occurrence network is displayed using Cytoscape with the Prefuse Force Directed (edge betweenness) layout. Negative correlations are represented by red edges and positive correlations by green. Each node represents an OTU with > 0.1% relative abundance and is colored by bacterial family to which it belongs. Key hub OTUs are labeled with their IDs, genus names, and the numbers of positive and negative edges. Figure S6. Principal coordinate analysis (PCoA) of red squirrel gut microbial communities across six grids based on Jaccard distance. Samples are colored by food supplement status. The percentage of the variation explained by the first three coordinates are indicated on the axes. Figure S7. Locations of study grids along the Alaska Highway in the southwest Yukon (61°N, 138°W) near Kluane National Park. (Adopted from 73) Each grid is labeled with the number of samples collected and the food supplement status. Table S1. Properties of OTU networks in three seasons. (PDF 903 kb)
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 | 0.002 | 0.019 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.847 | 0.093 |
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".