Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps
Bibliographic record
Abstract
Abstract Whole genome duplication (WGD) can provide material for evolutionary innovation. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for non-model species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, around 65 million years ago, then rediploidized and diversified. Extensive synteny between orthologous chromosomes occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Here we generate a high-density linkage map (3826 markers) for the Salvelinus genera (Brook Charr S. fontinalis ), and then identify orthologous chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus , and one species for each of Salmo and Coregonus , as well as the sister group for the salmonids, Esox lucius for homeolog designation. To this end, we developed MapComp , a program that identifies identical and proximal markers between linkage maps using a reference genome of a related species as an intermediate. This approach increases the number of comparable markers between linkage maps by 5-fold, enabling a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and identifying several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp , available at: https://github.com/enormandeau/mapcomp/
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 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".