Ancient differentiation of the H and I haplomes in diploid <i>Hordeum</i> species based on 5S rDNA
Bibliographic record
Abstract
5S rDNA clones from 12 South American diploid Hordeum species containing the HH genome and 3 Eurasian diploid Hordeum species containing the II genome, including the cultivated barley Hordeum vulgare, were sequenced and their sequence diversity was analyzed. The 374 sequenced clones were assigned to "unit classes", which were further assigned to haplomes. Each haplome contained 2 unit classes. The naming of the unit classes reflected the haplomes, viz. both the long H1 and short I1 unit classes were identified with II genome diploids, and both the long H2 and long Y2 unit classes were recognized in South American HH genome diploids. Based upon an alignment of all sequences or alignments of representative sequences, we tested several evolutionary models, and then subjected the parameters of the models to a series of maximum likelihood (ML) analyses and various tests, including the molecular clock, and to a Bayesian evolutionary inference analysis using Markov chain Monte Carlo (MCMC). The best fitting model of nucleotide substitution was the HKY+G (Hasegawa, Kishino, Yano 1985 model with the Gamma distribution rates of nucleotide substitutions). Results from both ML and MCMC imply that the long H1 and short I unit classes found in the II genome diploids diverged from each other at the same rate as the long H2 and long Y2 unit classes found in the HH genome diploids. The divergence among the unit classes, estimated to be circa 7 million years, suggests that the genus Hordeum may be a paleopolyploid.
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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".