Comparative Genomic Analyses and a Novel Linkage Map for Cisco ( <i>Coregonus artedi)</i> Provide Insights into Chromosomal Evolution and Rediploidization Across Salmonids
Bibliographic record
Abstract
Abstract Whole-genome duplication (WGD) is hypothesized to be an important evolutionary mechanism that can facilitate adaptation and speciation. Genomes that exist in states of both diploidy and residual tetraploidy are of particular interest, as mechanisms that maintain the ploidy mosaic after WGD may provide important insights into evolutionary processes. The Salmonidae family exhibits residual tetraploidy, and this, combined with the evolutionary diversity formed after an ancestral autotetraploidization event, makes this group a useful study system. In this study, we generate a novel linkage map for cisco (Coregonus artedi), an economically and culturally important fish in North America and a member of the subfamily Coregoninae, which previously lacked a high-density haploid linkage map. We also conduct comparative genomic analyses to refine our understanding of chromosomal fusion/fission history across salmonids. To facilitate this comparative approach, we use the naming strategy of protokaryotype identifiers (PKs) to associate duplicated chromosomes to their putative ancestral state. The female linkage map for cisco contains 20,292 loci, 3,225 of which are likely within residually tetraploid regions. Comparative genomic analyses revealed that patterns of residual tetrasomy are generally conserved across species, although interspecific variation persists. To determine the broad-scale retention of residual tetrasomy across the salmonids, we analyze sequence similarity of currently available genomes and find evidence of residual tetrasomy in seven of the eight chromosomes that have been previously hypothesized to show this pattern. This interspecific variation in extent of rediploidization may have important implications for understanding salmonid evolutionary histories and informing future conservation efforts.
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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 | 0.001 | 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".