Genomic data support interspecific divergence but reveal limited population structure and cryptic hybridization in <i>Rallus elegans</i> (King Rail) and <i>R. crepitans</i> (Clapper Rail)
Bibliographic record
Abstract
Abstract Coastal ecosystems across the globe are threatened due to anthropogenic activities and human-mediated climate change. Sea level rise and altered hydrology may lead to increased secondary contact between closely related freshwater and saltwater species, such as Rallus elegans (King Rail) and R. crepitans (Clapper Rail). The 2 rallid species are secretive marsh birds with declining populations and largely uncharacterized population structure. Rallus elegans and R. crepitans are known to hybridize, but the extent of hybridization and introgression have not been studied using modern genomics. Hence, to increase our understanding of the connectivity of R. crepitans populations and their hybridization with R. elegans, we adopted a genomic approach using restriction site-associated DNA sequencing (RAD-seq) to examine intra- and interspecific variation in single nucleotide polymorphisms (SNPs) from populations along the east coast of North America. We obtained 154 R. crepitans samples from Connecticut, Delaware, North Carolina, South Carolina, and Louisiana and 50 R. elegans samples from North Carolina and Louisiana. In addition, we included 15 putative hybrids collected in Louisiana. Using 8,834 SNPs across the genome, we found that some individuals had been misidentified in the field, including 5 cryptic hybrids from Delaware salt marshes classified as R. crepitans and 16 individuals from Louisiana. There was evidence of hybridization across all sampled populations with more than 20% of sampled individuals having some degree of introgression based on 142 SNPs found to be fixed between the parental species. Our results suggest that R. crepitans is panmictic, and we found no support for the currently described subspecies in the sampling regions. The 2 R. elegans populations show some evidence of differentiation, albeit with weak support.
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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 | 0.000 | 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".