Biodiversity genomics for species at risk: patterns of DNA sequence variation within and among complete mitochondrial genomes of three species of wolffish (Anarhichas spp.)
Bibliographic record
Abstract
The first marine fish species to be listed under the Canadian Species At Risk Act as Threatened with extinction are the spotted wolffish ( Anarhichas minor Olafsen, 1774) and the broadhead wolffish ( Anarhichas denticulatus Krøyer, 1844); a third species, the striped wolffish ( Anarhichas lupus L., 1758), is listed as a species of special concern. As part of the recovery plan for wolffish, we determined the complete mitochondrial DNA (mtDNA) genome sequences of all three species to identify the most variable gene regions for population analysis. Anarhichas genomes comprise either 16 519 or 16 520 base pairs (bp), among which there are 449 single nucleotide polymorphisms (SNPs). The most variable protein-coding loci are ND4, CYTB, and ND2, with 4.40, 4.22, and 4.19 SNPs / 100 bp, respectively. Comparisons of rates of synonymous and nonsynonymous nucleotide substitutions indicate no evidence of selection. The control region, characterized in many species as hypervariable, was less variable than 9 of 13 protein-coding loci (2.45 SNPs / 100 bp). Phylogenetic analysis shows that A. lupus and A. minor are more closely related to each other than either is to A. denticulatus. Amplification and sequence analysis of a contiguous block of 6392 bp that spans the ND4, ND5, ND6, and CYTB loci is an efficient strategy for evaluating patterns of intraspecific mtDNA variability.
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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 | 0.000 |
| 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 | 0.000 | 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".