Genomic mechanisms underlying migration timing and population differentiation across North America in a long-distance migratory songbird
Bibliographic record
Abstract
Understanding adaptive potential in migratory animals is important for anticipating population responses to rapid environmental changes. Because shifts in spring phenology can disrupt synchrony between individuals’ movements and seasonal resources, it is crucial to examine mechanisms underlying migration timing and population genomics in vulnerable migratory species. In this thesis, I used the purple martin (Progne subis), a long-distance migratory songbird, as a model species to address the following objectives: 1) identify genomic regions underlying migration timing and corresponding to spring phenology, and 2) examine population structure across four North American breeding colonies and relate patterns of differentiation to natal dispersal. Using next-generation sequencing, I assembled a new draft reference genome and whole-genome data for 93 individuals. I then integrated genomic variation, direct migration timing data, first bloom dates, and continent-wide band encounter records. I recorded a high heritability in migration timing, demonstrating a strong genetic basis in this trait. I also identified loci associated with spring and fall migration near multiple genes, such as MEF2D and CRY1, which could play an important role in photoreception and circadian rhythms. Additionally, I found that timing of first bloom was associated with a high proportion of genomic variance and loci of polygenic effect. Although overall population differentiation was low, I documented isolation-by-distance and greatest distinction between the most northern (Alberta) and more southern colonies. Patterns of differentiation were consistent with observations of greater longitudinal than latitudinal movement in natal dispersal. Overall, my results advance our understanding of migration genomics by demonstrating a novel connection between genomic variation and direct migration timing phenotypes in a long-distance migratory songbird, while the new reference genome provides a foundation for purple martin genomic research. The population structure and latitudinal patterns of differentiation I identified can inform conservation management of this species through delineation of distinct groups between northern and more southern breeding populations. Together, the strong genomic influences on migration timing and spatial limitations on latitudinal gene flow in the purple martin can be used as a framework to describe potential constraints on adaptability in changing climates.
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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 | 0.000 | 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".