Genetic mixed-stock analysis reveals evidence of adverse effects on fall Chum Salmon tagged in the Yukon River
Bibliographic record
Abstract
ABSTRACT Objective In 1999, radiotelemetry data suggested that 25% of the fall Chum Salmon Oncorhynchus keta migration in the Yukon River above the confluence with the Tanana River remained in the Yukon Flats, an extensive, highly braided main-stem area of the Yukon River. Our objective was to determine whether this represents Chum Salmon spawning within main-stem reaches of the Yukon Flats or a handling effect impacting fish from stocks destined for spawning areas farther upstream. Methods To assess the validity of the radiotelemetry-based stock composition estimates, we conducted genetic mixed-stock analysis on tissue samples collected from radio-tagged fish. Results Nonoverlapping CIs provided evidence that radiotelemetry and genetic stock composition estimates were different for upper Yukon River stocks. The genetic-based composition estimate (42%) for upper Yukon River stocks was greater than the radiotelemetry estimate (18%). Overlapping CIs provided no evidence that the estimates from the two methods were different for the U.S. border and upper Porcupine River. For fish last located by radiotelemetry in the Yukon Flats, genetic stock composition estimates classified most (86%) as upper Yukon River stocks. The likelihood ratio test revealed strong evidence that genetic stock composition estimates were different between fish tracked to terminal locations and those not tracked to terminal locations. A greater proportion of fish from the upper Yukon River was present in the mixture of fish that did not reach terminal locations, whereas a greater proportion of fish from the U.S. border was present in the terminal mixture. The assignment test revealed strong evidence that radiotelemetry samples had a higher proportion of misassignments than known-origin samples. Most (64%) misassignments involved fish that were genetically assigned to the upper Yukon River. Conclusions These results indicate that upper Yukon River fish in the radiotelemetry study suffered from residual handling effects and were less likely to reach their natal spawning grounds.
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 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 | 0.001 |
| 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".