Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)
Bibliographic record
Abstract
All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Theory suggests that non-recombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole genome scans that the sex-associated region in P. trichocarpa is small and much younger than the age of the genus. This indicates that sex-determination is highly labile in poplar, consistent with recent evidence of “turnover” of sex determination regions in animals. We performed whole genome resequencing of 52 Populus trichocarpa (black cottonwood) and 34 P. balsamifera (balsam poplar) individuals of known sex. Genome-wide association studies (GWAS) in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ∼100 Kbp. All significant SNPs were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex associated SNPs revealed this to be an XY sex determining system. Estimated divergence times of X and Y haplotype sequences (6-7 MYA) are much more recent than the divergence of P. trichocarpa (poplar) and P. tremuloides (aspen). Consistent with this, in P. tremuloides we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.
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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 | 0.000 |
| 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".