Replication Data for: A comparison of protocols for isolating and extracting host DNA from caribou (Rangifer tarandus) fecal pellets
Bibliographic record
Abstract
These datasets contain the data and code required to replicate analyses in Barrette et. al. (2026), testing multiple fecal DNA extraction protocols to determine the most effective method for obtaining high-quality caribou DNA for genotyping-by-sequencing. Our experiment was split into 2 sections, the first being an initial comparison of DNA extraction protocols on samples from one caribou population in British Columbia to determine the best-performing methods. We tested five mucosal layer isolation methods combined with three QIAGEN extraction kits (15 combinations total; see Methods and Supplementary Data). Each sample was processed using a specific combination of isolation and extraction method, allowing us to evaluate the relative performance of both components across extractions. Methods were selected based on use and success in previous studies. We compared methods in terms of total DNA recovered, PCR amplification success, and the amount and proportion of host DNA. The latter was assessed using a new qPCR assay designed using the caribou F2 sequence to target ungulate host DNA. Once the 4 best protocol combinations were identified, these were used in a post-hoc validation (the second section of our study) to extract samples from 7 additional caribou populations spanning 3 ecotypes across BC. For each sample processed in both study sections, the isolation and extraction method was recorded, total DNA was measured using a Quant-It fluorometer, target DNA was measured using a new qPCR assay, and the ratio of target DNA to total DNA was calculated using these values (later converted to a percentage for analyses). Sample collection locations span caribou ranges across BC, although exact locations are not provided as caribou are a species-at-risk, and exact locations were not relevant for this study. Caribou population and ecotype are provided for each sample in the post-hoc validation, as well as the date collected. The R script provided contains all the code used in the paper for analysis and figure generation. We found that all methods yielded at least 10 ng of caribou DNA per pellet, sufficient for most PCR-based genotyping protocols. In boreal caribou, the incubation isolation and QIAamp DNA Mini kit yielded the highest DNA quantities, while the wash isolation with Fast DNA Stool and PowerSoil kits yielded the highest host DNA proportions. Post-hoc validation, however, revealed that the wash isolation in combination with the QIAamp DNA Mini kit was more reliable for minimizing PCR inhibitors across populations while maximizing DNA yield.
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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 | 0.030 | 0.088 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.004 | 0.004 |
| Science and technology studies | 0.004 | 0.002 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.003 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.051 | 0.026 |
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".