Coalescent-Based Analysis Distinguishes between Allo- and Autopolyploid Origin in Shepherd's Purse (Capsella bursa-pastoris)
Bibliographic record
Abstract
Polyploidization plays an important role in plant speciation. The most recent estimates report that up to 15% of angiosperm speciation events and 31% in ferns are accompanied by changes in ploidy level. Polyploids can arise either through autopolyploidy, when the sets of chromosomes originate from a single species, or through allopolyploidy, when they originate from different species. In this study, we used two different coalescent-based methods to determine the date and mode of the polyploidization event that led to the tetraploid cosmopolitan weed, Capsella bursa-pastoris. We sampled 78 C. bursa-pastoris accessions, and 53 and 43 accessions from the only two other members of this genus, C. grandiflora and C. rubella, respectively, and sequenced these accessions at 14 unlinked nuclear loci with locus-specific primers in order to be able to distinguish the two homeologues in the tetraploid. A large fraction of fixed differences between homeologous genes in C. bursa-pastoris are segregating as polymorphisms in C. grandiflora, consistent with an autopolyploid origin followed by disomic inheritance. To test this, we first estimated the demographic parameters of an isolation-with-migration model in a pairwise fashion between C. grandiflora and both genomes of C. bursa-pastoris and used these parameters in coalescent simulations to test the mode of origin of C. bursa-pastoris. Second, we used Approximate Bayesian Computation to compare an allopolyploid and an autopolyploid model. Both analyses led to the conclusion that C. bursa-pastoris originated less than 1 Ma by doubling of the C. grandiflora genome.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| 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) | 0.000 | 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 teacher head, 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".