The two sub-genomes of the allotetraploid frog Xenopus laevis are evolving under similar selective pressure in extant populations
Bibliographic record
Abstract
The model species Xenopus laevis is an allotetraploid species, whose genome consists of two sub-genomes (the L and S sub-genomes) that were inherited from its parental species. Previous studies comparing the genome of X. laevis with other species of the genus revealed that the L sub-genome was more conserved than the S sub-genome suggesting it has been evolving under stronger purifying selection. However, it remains unclear if this difference reflects evolutionary processes that are still at play in extant populations. To answer this question, we conducted the first genome-wide survey of variation in this species by re-sequencing 44 individuals from its native South African range at ~ 10 × coverage. We generated a dataset of ~ 260M SNPs, which constitutes a valuable resource for the Xenopus community. We found that the South African populations of X. laevis are highly structured and differentiated, reflecting ancient divergence followed by more recent admixture at contact zones. We also determined that the landscapes of variation of the L and S sub-genomes do not show any significant differences suggesting that the two sub-genomes are responding to evolutionary forces in a similar manner. In particular we showed that purifying selection and positive selection are acting identically on the two sub-genomes, suggesting that the sub-genomes of X. laevis are evolving under similar selective pressure. Since 60% of the ancestral homeologous genes have been retained in X. laevis, this result suggests that the function of those genes is conserved on both sub-genomes or that a large number of genes has experienced neo- or sub-functionalization.
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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 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 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".