Distinguishing successive ancient polyploidy levels based on genome-internal syntenic alignment
Bibliographic record
Abstract
BACKGROUND: A basic tool for studying the polyploidization history of a genome, especially in plants, is the distribution of duplicate gene similarities in syntenically aligned regions of a genome. This distribution can usually be decomposed into two or more components identifiable by peaks, or local maxima, each representing a different polyploidization event. The distributions may be generated by means of a discrete time branching process, followed by a sequence divergence model. The branching process, as well as the inference of fractionation rates based on it, requires knowledge of the ploidy level of each event, which cannot be directly inferred from the pair similarity distribution. RESULTS: For a sequence of two events of unknown ploidy, either tetraploid, giving rise to whole genome doubling (WGD), or hexaploid, giving rise to whole genome tripling (WGT), we base our analysis on triples of similar genes. We calculate the probability of the four triplet types with origins in one or the other event, or both, and impose a mutational model so that the distribution resembles the original data. Using a ML transition point in the similarities between the two events as a discriminator for the hypothesized origin of each similarity, we calculate the predicted number of triplets of each type for each model combining WGT and/or WGD. This yields a predicted profile of triplet types for each model. We compare the observed and predicted triplet profiles for each model to confirm the polyploidization history of durian, poplar and cabbage. CONCLUSIONS: We have developed a way of inferring the ploidy of up to three successive WGD and/or WGT events by estimating the time of origin of each of the similarities in triples of genes. This may be generalized to a larger number of events and to higher ploidies.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 teacher head, 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".