The potential role of chromosomal inversions in the persistence of small, isolated populations of Brook Trout (Salvelinus fontinalis)
Bibliographic record
Abstract
Understanding the role of structural variants such as chromosomal inversions in local adaptation among small, isolated populations is an important addition to robust conservation strategies, as most studies investigating inversions to date have been conducted on high gene flow systems. Brook Trout (Salvelinus fontinalis), an economically important top sportfish, is extremely vulnerable to thermal stress. Local adaptation with respect to this trait warrants investigation as climate change accelerates the loss of cold-stream ecosystems. We performed low-coverage whole genome sequencing (lcWGS) on N=192 Brook Trout from nine small, isolated streams in Nova Scotia, Canada. Using the indirect structural variant detection framework, we detected four potential chromosomal inversions in the three westernmost populations which differ from all other streams in water temperature, streamflow, and surficial geology. These genomic regions exhibited high linkage disequilibrium (LD) and principal component analyses (PCA) revealed the presence of three karyotypes (inverted and non-inverted homokaryotype, and heterokaryotype). Heterozygosity was lowest among inverted homokaryotypes, providing further support of the presence of inversions. Mitogenome analyses suggest that a single glacial lineage recolonized the region. The mtDNA haplotypes of individuals carrying potential inversions were shared among individuals with two copies of non-inverted chromosomal regions, suggesting these inversions were derived post-recolonization. These novel inversions comprised genes involved in different biological processes including thermal adaptations.
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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 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| 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 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".