Exploring control region variability in Striped Bass (Morone saxatilis) mitochondrial DNA for use in characterizing populations
Bibliographic record
Abstract
In the past 30 years Striped Bass populations have declined along the eastern coast of North America, and Canadian populations are considered threatened (COSEWIC, 2004). Historically, there were at least five separate spawning populations. Currently only two populations remain in Atlantic Canada located in the Shubenacadie (NS) and Miramichi (NB) Rivers. For this study the U.S.A. is considered a single population. Distinguishing among populations is important so that changes in population size can be monitored through catch data and to help management practices that are generally population specific. To differentiate populations of Striped Bass, the use of meristics, morphometrics and, more recently, DNA analysis have been used. This study was undertaken to determine if Atlantic Canada Striped Bass populations could be differentiated using the mitochondrial control region, and to characterize control region variability. During May and June of 2008 and 2010, fin clip tissue samples were taken from Striped Bass spawning on the Shubenacadie River by local anglers. Using 5AS and R2RC primers, a portion of the mitochondrial control region was sequenced. These sequences are representative of the Shubenacadie River population. During July and August, Striped Bass fin clips were taken from the Gaspereau River, the Guzzle, and Five Islands in Nova Scotia. These fish probably represent a mixed population (Canada and U.S.A.). Samples were analyzed using neighbour joining and maximum parsimony phylogenetic trees. Variability within the mitochondrial control region was very low. Therefore, populations within the Bay of Fundy could not be differentiated using this genomic region. More research is needed to conclude that mitochondrial control region sequences are not useful in differentiating populations.
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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) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.001 |
| 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".