Disentangling serial chloroplast captures in willows
Bibliographic record
Abstract
PREMISE: Chloroplast capture is a process through which the chloroplast of a focal species is replaced by the chloroplast from another species during repeated backcrossing of an initial hybrid. Here we investigated serial chloroplast capture from Salix nigra in willows during sequential hybridization events that led to the capture of the same chloroplast lineage across multiple Salix species. METHODS: Previously generated sequences of nuclear and chloroplast regions from several Salix species were used to identify cases of cytonuclear phylogenetic discordance, a pattern indicating chloroplast capture. Serial chloroplast captures were identified by comparing phylogenetic topologies of the chloroplast trees to discriminate among (1) a single chloroplast capture and subsequent speciation of the lineage with the captured chloroplast, (2) multiple chloroplast captures from the same parent species, and (3) serial chloroplast captures. We also looked for hybridization in genes involved in cytonuclear interactions and in photosynthesis. RESULTS: We identified cases of serial chloroplast capture and speciation after chloroplast capture in Salix. Although these chloroplast capture events were accompanied by signals of hybridization in the nuclear genomes, nuclear genes that functionally interact with chloroplast genes and nuclear genes involved in photosynthesis were no more likely to introgress in species with chloroplast captures than in species without chloroplast captures. CONCLUSIONS: This study illuminates the complex evolution of the chloroplast genomes in Salix and the potential for hybridization and introgression to influence genomic evolution.
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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 | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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".