A complex copy number variant underlies differences in both colour plumage and cold adaptation in a dimorphic seabird
Bibliographic record
Abstract
SUMMARY Colour morphs associated with different physiological adaptations offer unique opportunities to study the genomic basis of otherwise elusive adaptive traits. These complex balanced polymorphisms are often controlled by groups of tightly linked genes, and understanding how these ‘supergenes’ evolve and are maintained is an active area of research in evolutionary biology (Schwander et al . 2014, Thompson and Jiggins 2014). Within the Atlantic, the common murre ( Uria aalge , a colonial seabird) displays a plumage colour dimorphism (‘bridled’ and ‘unbridled’) that seems to be associated with differences in thermal adaptation (Birkhead 1984; Reiertsen et al . 2012). The genes associated with bridling and how these genes affect thermal adaptation are unknown. Using whole genome resequencing, we investigate the genomic basis of differences in colouration and thermal adaptation between the two morphs, and how the association between the two traits is maintained despite random mating. We identify a 60 kb genomic region of high differentiation laying in the intergenic area amongst three candidate genes for colouration and thermal adaptation: retinoic acid receptor beta ( RARB ), thyroid hormone receptor beta ( THRB ), and nuclear receptor subfamily 1 group D member 2 ( NR1D2 or Rev-erbβ ). Differentiation is due to a complex copy number variant (CNV) that suppresses recombination locally. We show that this CNV acts as a ‘supergene’ and maintain association between regulatory elements likely affecting gene expression of one or more of the identified candidate genes. Our analyses also provide insights into the origin of the dimorphism: while copy number proliferation in the unbridled haplotype was potentially mediated by transposable elements (TEs), the bridled haplotype seems to have introgressed from the more cold-adapted sister species, the thick-billed murre ( U. lomvia ). Our results highlight the role of copy number variants in adaptation, especially when association among traits is maintained in the face of gene flow. They also shed light into the molecular mechanisms of adaptive thermogenesis in birds, which is poorly understood. Highlights Differences in plumage colour in Atlantic common murres are associated with different thermal adaptations A single region is highly differentiated between bridled and unbridled morphs A complex copy number variant in a non-coding region underlies the dimorphism Transposable elements and adaptive introgression from the thick-billed murre seem to explain the origin of the dimorphism
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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 | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 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".