Adaptation to seasonal reproduction and temperature-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow
Bibliographic record
Abstract
Abstract Natural selection can maintain local adaptation despite the presence of gene flow. However, the genomic basis and environmental factors involved in adaptation at fine-spatial scales are not well understood. Here, we address these questions using Atlantic herring ( Clupea harengus ), an abundant, migratory, and widely distributed marine species with substantial genomic resources including a chromosome-level genome assembly and genomic data from the eastern Atlantic and Baltic populations. We analysed whole-genome sequence and oceanographic data to examine the genetic variation of 15 spawning aggregations across the northwest Atlantic Ocean (∼1,600 km of coastline) and the association of this variation with environmental variables. We found that population structure lies in a small fraction of the genome involving adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Two of these loci appear to be private to the northwest, four loci share a large number of adaptive variants between northwest and northeast Atlantic, and four shared loci exhibit an outstanding diversity in haplotype composition, including a novel putative inversion on chromosome 8. Another inversion on chromosome 12 underlies a latitudinal genetic pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Our genome-environment association analysis indicates that sea water temperature during winter is the environmental factor that best correlates with the latitudinal pattern of this inversion. We conclude that the timing and geographic location of spawning and early development are under diverse selective pressures related to environmental gradients. Natural selection appears to act on early-life performance traits with differential fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes, and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
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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".