Selective histories of poplar protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates
Bibliographic record
Abstract
To further our understanding of plant defense evolution and the consistency of selection at the nucleotide level we analysed polymorphism data from five protease inhibitor (PI) genes in Populus balsamifera. We compared diversity at the five PI genes to diversity at nondefense loci in both range-wide samples as well as in two subpopulations, one from the northern edge of the species range and one from the southern edge of the range. We also compared our data with previously reported diversity in Populus tremula, a European species with similar ecology to North American P. balsamifera. The PIs show diverse histories, including repeated bouts of positive selection and excess diversity. These genes also exhibit diverse histories in P. tremula but the signatures of selection acting at the specific loci differed between the species. One locus, KTI3, segregates several recent duplicates that show evidence of either positive selection or relaxed selective constraints. The patterns of diversity at the PIs varied within P. balsamifera and between two closely related species. The lack of consistent patterns suggests that evolution of host defense genes, including adaptations to enemy-imposed selection, may often be lineage- and gene-specific.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 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".