Patterns of genetic diversity and structure in Pressodonta viridis, Slippershell Mussel, in streams of the U.S. Midwest - data
Bibliographic record
Abstract
Data derived from restriction-site associated (RAD) sequencing of Pressodonta viridis (Slippershell Mussel) of the U.S. Midwest. Included is the VCF file, R script/metadata file, and river distances calculated for isolation-by-distance models. All files used for downstream analyses found in the manuscript. ABSTRACT: Pressodonta viridis (Bivalvia: Unionida) is a species of freshwater mussel considered rare and imperiled in 14 U.S. states and Ontario, Canada. Limited population-level genetic information is available for P. viridis despite the species’ imperilment status. We used 13,661 single nucleotide polymorphisms (SNPs) derived from double digest restriction site-associated sequencing (ddRAD-seq) to examine patterns in population genetic diversity, structure, and differentiation among P. viridis populations in the Upper Mississippi River, Ohio and Wabash rivers, and Great Lakes watersheds. Structure analyses revealed significant differentiation related to major drainage among groups of P. viridis populations. Evidence of founder effects in Great Lakes populations by colonization routes from Upper Mississippi River and Ohio/Wabash River systems was found in admixture analyses. Limited evidence of isolation-by-distance effects was found, suggesting that multiple colonization routes and glacial refugia are responsible for current P. viridis genetic structure. A combination of ancient river hydrological patterns and more recent headwater stream capture events following the last glacial retreat likely correspond to considerable admixture found among populations of P. viridis in the Upper Mississippi, Wabash, and Ohio Rivers. Population genetic variation, structure, and differentiation described in this study should be used to inform conservation efforts of P. viridis in the future, particularly if recovery actions include population augmentation from translocations or hatchery propagation.
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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 | 0.000 |
| 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".