Darwin's "Abominable Mystery": The Role of RNA Interference in the Evolution of Flowering Plants
Bibliographic record
Abstract
Darwin was famously concerned that the sudden appearance and rapid diversification of flowering plants in the mid-Cretaceous could not have occurred by gradual change. Here, we review our attempts to resolve the relationships among the major seed plant groups, i.e., cycads, ginkgo, conifers, gnetophytes, and flowering plants, and to provide a pipeline in which these relationships can be used as a platform for identifying genes of functional importance in plant diversification. Using complete gene sets and unigenes from 16 plant species, genes with positive partitioned Bremer support at major nodes were used to identify overrepresented gene ontology (GO) terms. Posttranscriptional silencing via RNA interference (RNAi) was overrepresented at several major nodes, including between monocots and dicots during early angiosperm divergence. One of these genes, RNA-dependent RNA polymerase 6, is required for the biogenesis of trans-acting small interfering RNA (tasiRNA), confers heteroblasty and organ polarity, and restricts maternal specification of the germline. Processing of small RNA and transfer between neighboring cells underlies these roles and may have contributed to distinct mutant phenotypes in plants, and in particular in the early split of the monocots and eudicots.
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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 | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".