Incidence and attributes of chimeric COI and 18S sequences derived from nematode-infected arthropods
Bibliographic record
Abstract
Abstract High-throughput sequencing is speeding the discovery of new species and making it possible to quantify the species richness of bulk samples. However, chimeric sequences can lead to both type I errors (true species mistakenly rejected) and type II errors (chimeras incorrectly viewed as valid species). This study employed nanopore sequencing to examine the incidence and nature of chimeric sequences recovered from 531 arthropod specimens infected with nematodes. Specifically, it examined chimera formation in two gene regions: the 658 bp segment of mitochondrial COI employed as the barcode region for the animal kingdom, and a 900 bp segment of nuclear 18S often employed to discriminate lineages of nematodes. This work revealed chimeras for both gene regions despite the deep sequence divergences between members of these two phyla. However, the incidence of chimeric molecules was higher for 18S than COI, with chimera formation correlating with local variation in DNA stability and conserved regions between parent sequences. Aside from demonstrating that chimeras can arise from distantly related organisms, this study provides insights into the mechanisms underlying their formation.
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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 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 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".