Phylogenomics Reveals that Mitochondrial Capture and Nuclear Introgression Characterize Skua Species Proposed to be of Hybrid Origin
Bibliographic record
Abstract
The skuas and jaegers (Stercorariidae) are an enigmatic family of seven seabird species that breed at Arctic and Antarctic latitudes. The phylogenetic relationships amongst the species have been controversial, with one of the biggest enigmas involving the Pomarine Jaeger (Stercorarius pomarinus), which has been proposed to represent a hybrid species originating from the merging of distant lineages within the complex. We inferred a phylogeny for the family using multispecies coalescent methods with whole-genome sequencing for all seven species of Stercorariidae, and document an evolutionary history rich in introgression. We uncover evidence for mitochondrial capture and nuclear introgression between S. pomarinus and Stercorarius skua, providing a potential avenue for adaptive introgression. One candidate for adaptive introgression is the MC1R plumage gene which appears to have introgressed from one of the large skuas into S. pomarinus, where it now forms the basis of the dark-morph color polymorphism of that species. We further highlight a complex biogeographical history of interchange between the Arctic and Antarctic, with unexpected close ancestry between S. skua of the northern hemisphere and Stercorarius antarcticus of the southern hemisphere. These results highlight the dynamic history of introgression during pelagic seabird radiation. [Incomplete lineage sorting; introgression; mitochondrial capture; phylogenomics; skua; species tree; stercorariidae; whole-genome resequencing.].
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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 | 0.001 |
| 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 | 0.001 |
| 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".