Analysis of diversity of natural populations and commercial lines of<i>Echinacea</i>using AFLP
Bibliographic record
Abstract
An analysis of diversity of Echinacea native to North America, using amplified fragment length polymorphism (AFLP ® ), was carried out to complement a previously undertaken taxonomic revision of Echinacea that employed multivariate morphometrics. A total of 53 940 AFLP fragments, of which 40 455 were polymorphic, were scored on 435 individual plants from 58 populations consisting of ±10 individuals per population. The resulting polymorphism was sufficient to distinguish each plant. A monomorphic AFLP band and a polymorphic AFLP band that migrated at the same position, taken from samples of four species and eight varieties, were cloned, and multiple clones were sequenced. The polymorphic band at the same position across fragments was not identical, with identity as low as 23% compared with 50% identity of the monomorphic band, both of which were at the 100% threshold of sequence similarity. Thus, the AFLP banding profiles, irrespective of their sequence identity, were treated as phenotypes for population genetic, discriminant, and phylogenetic analyses. Variance components within populations and among populations within species were of equal magnitude, but the partitioned variation was slightly higher among varieties than among populations within varieties. Since no species-specific or variety-specific AFLP fingerprints were found, canonical discriminant analysis was conducted, resulting in support for four species but not for the varieties. Similar results were obtained with cluster and principal coordinate analyses, based on genetic distances. To achieve identification using AFLP fingerprints, various classificatory analyses were performed, followed by bootstrapping for validation. An example to identify an unknown plant at the species level with a minimum of 10 AFLP fragments, with greater than 82% overall correct classification, is provided. Phylogenetic analysis of all 435 individuals supported only Echinacea purpurea (L.) Moench and Echinacea laevigata (C.L. Boynton & Beadle) as separate entities, and only the three Echinacea atrorubens varieties and Echinacea pallida var. tennesseensis (Beadle) Binns, B.R. Baum & Arnason.Key words: Echinacea, population genetic analysis, multivariate analysis, AFLP band homologies.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| 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".