The evolution of retrotransposon sequences in four asexual plant species /
Bibliographic record
Abstract
Since their discovery, transposable elements (TEs) have been regarded either as useful building blocks of genomes, or as "selfish DNA": genetic parasites that exploit the sexual cycle to spread in copy number within populations to the detriment of their hosts. If the "selfish DNA" hypothesis is correct, TEs are expected to deteriorate and be lost from asexual populations. This thesis tests the predictions of the "selfish DNA" hypothesis in four asexual plant species, focusing on patterns of nucleotide diversity and nucleotide substitution. Sequences bearing strong resemblance to known TE families including Ty1/copia, Ty3/gypsy, and LINE-like elements were successfully isolated from all four plant species, and showed patterns of nucleotide substitution consistent with a long history of purifying selection. Stochastic simulations were also conducted, and suggested that this result is expected if the host species has been asexual for less than tens of thousands of generations.
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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) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 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) | 0.001 | 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".