Identification of possible evolutionary pathways of <i>Plum pox virus</i> and predicting amino acid residues of importance to host adaptation
Bibliographic record
Abstract
Plum pox virus (PPV) displays significant genetic diversity that has resulted in the identification of several different strains, some that differ in their biological properties and in their geographic distribution. Some strains are limited in their distribution to a single country, while isolates of PPV strain D are found in every country where the virus has been detected. Many questions remain regarding the evolutionary history of PPV: its genetic (strain) diversification, its origin, its dispersal and the distribution of isolates and/or strains. To explore the evolution of PPV, inferred ancestral sequences were reconstructed at various phylogenetic nodes using PAML. Evidence was obtained that indicates that the strains PPV D and PPV M were likely the earliest strains of PPV to evolve. Specifically considered also was the point at which adaptation occurred that allowed infection of Prunus avium and/or Prunus cerasus, sweet cherry and sour cherry, respectively. Eight amino acid sites were identified that appear to have undergone positive selection during this adaptation process. These amino acid sites cluster into two areas, P1 and VPg. These areas of the genome are known to be important for functions such as the control of viral replication rate. In combination with other data, this information sheds light on functionally significant points along the PPV genome and perhaps even characteristics of ancient PPV populations.
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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 | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 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".