Genome-wide characterization of upper Fraser River sockeye salmon identifies a region of major differentiation between run timing groups in the Stuart River Watershed
Bibliographic record
Abstract
Abstract Effective wildlife conservation and management depends on a thorough understanding of both neutral and adaptive intraspecific genomic variation. Although population structure is often well understood for many ecologically or economically important species, the extensive population genomic resources required to characterize putatively adaptive variation, for example in punctuated genomic regions, is typically only recently available in many species, if at all. Here we explore recently published whole-genome resequencing data in the upper Fraser River and identify a large island of divergence separating populations with different run timings in the Nechako Watershed. The island of divergence at approximately 56.3-58.0 Mbp of Chr18 has extended homozygosity and reduced Tajima’s D in specific populations of the upper Fraser River. These include the Nadina and Stellako River sockeye, as well as the Stuart-Summer run timing group, but not the geographically proximal Early Stuart sockeye. In the populations without the Stuart-Summer haploblock, genetic variation looks more similar to elsewhere throughout the chromosome. When investigating the gene content of this region, importantly it was determined to contain the leucine rich-repeat containing 9-like ( lrrc9-like ) gene and surrounding homeologous region to the lrrc9 region of Chr12, known to contain a conserved and selected island of divergence that has been associated with life history traits and run timing throughout the species range. By also inspecting the samples in the present work at the Chr12 haploblock, three genotypic states were observed throughout the region, although the Stuart River run timing groups contained mainly the reference haplotype. Using similar methods, no other regions of major differentiation were observed in the available samples for the Chilcotin or Quesnel River systems. These results provide additional evidence for the importance of both homeologous regions holding lrrc9 and lrrc9-like in different geographic regions and underscore the uniqueness of upper Fraser River sockeye in this potentially adaptive island of divergence.
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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 | 0.001 | 0.001 |
| 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) | 0.001 | 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".