Impact of ploidy level on the distribution of Pokey element insertions in the Daphnia pulex complex
Bibliographic record
Abstract
BACKGROUND: Transposable elements (TEs) play a major role in genome evolution. Their capacity to move and/or multiply in the genome of their host may have profound impacts on phenotypes and dramatic consequences on genome structure. The population dynamics and distribution of TEs are influenced by their mode of transposition, the availability of niches in host genomes, and host population dynamics. Theories predict an increase in the number of TE insertions following hybridization or polyploidization. Evolution of TEs in hybrids and polyploids has mostly been studied in plants; few studies have examined the impacts of hybridization and/or polyploidization on TEs in animals. Hybrids and polyploids have arisen multiple times in the Daphnia pulex complex and are thought to reproduce by obligate parthenogenesis. Our study examines the effects of ploidy level on polymorphism and number of Pokey element insertions in diploid and polyploid hybrid isolates from the Daphnia pulex complex. RESULTS: The polymorphism of Pokey insertion sites did not depend solely on either the ploidy level or the genetic background of their host; therefore, it may be the result of interactions between these parameters and other parameters such as Pokey activity, selection and/or drift. No significant effect of ploidy level was found on the number of Pokey insertions using TE display and qPCR. However, the load of Pokey insertion sites and the number of unique insertion sites were slightly (but not significantly) higher in polyploids than in diploids. CONCLUSIONS: These results suggest a lack of increase in the number of Pokey insertions following polyploidization but higher availability of Pokey insertion sites in polyploids than in diploids. Compared to previous TE display and qPCR results, the load of Pokey insertions in hybrid diploids was higher than in non-hybrid sexual and asexual diploids, which suggests an increase in the density of Pokey insertions following hybridization.
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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 | 0.000 | 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) | 0.002 | 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".