Development of a 96 SNP panel for fecal genotyping and individual identification of bobcats (Lynx rufus) in California
Bibliographic record
Abstract
Spatial mark-recapture abundance estimates obtained from fecal genotyping are becoming an essential component of conservation of carnivores. The bobcat ( Lynx rufus ) is a widespread carnivore in California, USA, that until recently lacked robust demographic data. To facilitate a statewide abundance study, we created a single nucleotide polymorphism (SNP) genotyping panel for individual identification. For SNP discovery, we performed restriction site-associated DNA sequencing (RADseq) on 78 samples collected throughout California and subsequently designed a panel of 96 SNPs for sequencing on a microfluidic platform. This panel includes loci to identify sex and differentiate bobcats from other common carnivores. The panel reliably differentiates individuals when using DNA extracted from feces, with 89% of samples amplifying at > 90% of SNPs. Importantly, we found autosomal SNPs were monomorphic in the closely related Canada lynx ( L. canadensis ) suggesting the panel would still be effective for bobcat study in areas of sympatry. Fecal genotyping provides a cost-effective, noninvasive method for population monitoring and detecting individual movement. Our panel generates standardized genotypes that can be analyzed across laboratories and used for continued bobcat monitoring in California and other western states.
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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".