Inter- and Intraspecific Venom Variation in the Reclusive Rear-Fanged Black-Striped Snakes (Coniophanes).
Part of the results reproduced; minor but material deviations remained.
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- 🔴Could not use the authors’ exact input data
- 🔴Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🔴A deviation was attributed to the published material
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The deviation was non-trivial in magnitude
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
This paper has a computational component, but its primary data is legally or ethically access-restricted — identifiable patient cohorts, rare-disease genomes, or controlled-access biobanks that cannot be openly shared. The reproduction therefore could not be attempted. That is a neutral verdict: it does not mean the result is wrong or that the authors fell short — only that, for legitimate privacy reasons, it cannot be independently checked from public data. We deliberately do NOT assign a 0–100 score here, because a low number would wrongly read as a failed reproduction.
▸Reproduction agent’s raw note
DROP (data_restricted). Coniophanes Duvernoy's-gland transcriptomics paper; the entire reported pipeline (Trim Galore 0.6.7 -> PEAR -> Extender+Trinity -> ToxCodAn+BLAST+Geneious[manual]+ChimeraKiller -> BWA-MEM+RSEM -> DESeq2) takes as its sole input the raw RNA-seq under PRJNA88989 (runs SRR36021064-SRR36021070, exp SRX31070228-SRX31070234). All 7 runs are REGISTERED but NOT RELEASED: NCBI SDL HTTP 403 'object has not been published', efetch 'is not public', ENA 404 (verified control-plane 2026-06-16). No assembled transcripts / TPM tables deposited as a fallback (GenBank/TSA nuccore 'Coniophanes venom transcriptome' Count=0). Code repos (Trim Galore, ChimeraKiller) are public (HTTP 200) but useless without input data. Therefore NO pipeline-derived value (17 reported numbers pre-recorded in claims.tsv) is reproducible and NO «our HPC» compute was spent. NOT ATTEMPTED beyond screening: read trimming/assembly/quantification (blocked by embargo); the manual Geneious toxin-curation step would in any case break 1:1 reproducibility of transcript counts. Re-attemptable once the SRA embargo lifts. This is the politically-important 'published paper, data not actually accessible yet' attrition class.
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Assessment versions
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v1 current initial assessmentassessed: 2026-06-16 ⛓ 07c15fc28fad
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When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-16
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-16no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: opusRear-fanged snakes of the genus Coniophanes have never had their venom characterized despite documented human envenomations; this study tests what toxin families compose Coniophanes venom and characterizes inter- and intraspecific venom variation and the venom delivery system.
- ★ This is the first characterization of the venom profiles (transcriptomic and proteomic) of the genus Coniophanes. resource
- ★ Toxins account for 38.8% to 66% of total Duvernoy's gland transcriptomes, with 18 toxin families represented across the genus. finding
- ★ CRiSPs are prominently expressed in three species and SVMPs (SVMPIII) in all four species; species produce either SVMP- or CRiSP-dominated venoms. finding
- ★ Coniophanes shows significant interspecific and intraspecific venom variation, notably geographic variation in 3FTx expression within C. imperialis (high in Texas, virtually absent in Honduras). finding
- ★ diceCT imaging reveals C. fissidens possesses enlarged grooved rear maxillary teeth in close proximity to a prominent Duvernoy's gland, indicating a specialized venom delivery system. finding
- ★ De novo Duvernoy's gland transcriptomes were assembled and annotated for seven individuals across four Coniophanes species. method
- Kunitz-type proteins are highly expressed in the Honduran C. imperialis and may functionally substitute for 3FTx in prey subjugation. mechanism
- 15 of 60 unique toxin transcripts were differentially expressed between northern (Texas) and southern (Honduras) C. imperialis samples. finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| de novo RNA-seq transcriptomics | Duvernoy's gland; seven individuals across four Coniophanes species (C. imperialis, C. fissidens, C. lateritius, C. schmidti) | none | toxin family transcript expression (TPM), unique toxin transcript counts | — |
| differential expression analysis | C. imperialis Duvernoy's gland transcriptomes from two localities (Texas vs. Honduras) | none (geographic comparison) | differentially expressed toxin transcripts between northern and southern samples | — |
| quantitative mass spectrometry (qMS) proteomics | whole venom of two C. imperialis individuals (DRR0034 and DRR0035) | none | proteomic confirmation of toxin families present in venom | — |
| diffusible iodine-based contrast-enhanced computed tomography (diceCT) | C. fissidens specimen (UMMZ Herps 87643), Chiapas, Mexico | none | venom delivery system morphology (rear fangs, grooves, Duvernoy's gland) | — |
- – Toxins constitute 38.8% to 66% of total DVG transcriptomes across the four species 38.8–66%
- ▲ C. fissidens venom is most strongly CRiSP-dominated CRiSPs 63.6%, SVMPIII 25.7%
- ▲ C. schmidti venom is SVMP-dominated SVMPIII 62.7%
- ▲ C. imperialis consensus transcriptome dominated by CRiSPs, CTLs, and 3FTx CRiSP 30.1%, CTL 23.5%, 3FTx 20.4%
- ▲ C. lateritius venom is CRiSP-dominated with notable Kunitz-type peptides CRiSP 51%, SVMPIII 21.5%, KUN 16.6%
- – 3FTx virtually absent in Honduran C. imperialis but substantial in Texas individuals; KUN higher in Honduran sample 3FTx avg ~24% of toxins in Texas; Waprin 9.3% in Honduran individual
- – 15 of 60 unique toxin transcripts differentially expressed between northern and southern C. imperialis, including five 3FTx and two KUN 15/60
- – diceCT shows C. fissidens has enlarged maxillary teeth with deep anterior longitudinal grooves near a large Duvernoy's gland
- other 38.8% to 66% (toxin proportion of total DVG transcriptomes across genus)
- count 18 toxin families (toxin families represented in genus Coniophanes)
- count 16 to 56 unique toxin transcripts (range from C. schmidti (16) to a C. imperialis individual (56))
- other SVMPIII 62.7% (highest toxin family in C. schmidti)
- other CRiSP 63.6% (highest toxin family in C. fissidens)
- count 15 of 60 (differentially expressed toxin transcripts between northern/southern C. imperialis (four individuals))
- count 9 to 14 million assembled reads per sample (transcriptome sequencing output per individual)
- other 8.1–62.7% (SVMPIII proportion across every individual's DVG transcriptome)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
The study sequenced and annotated de novo Duvernoy's gland transcriptomes from seven Coniophanes individuals across four species, quantifying toxin expression as percent of total toxin TPM for interspecific comparisons. Intraspecific variation in C. imperialis was assessed via differential expression analysis between three northern (Texas) and one southern (Honduras) individuals. Quantitative mass spectrometry (qMS) cross-referenced with transcriptome data proteomically confirmed toxin presence in two individuals. Results were reported primarily as percentage contributions of toxin families to total toxin TPM, with counts of differentially expressed transcripts for the population comparison.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| differential expression analysis (specific test or software tool not stated in provided text) | comparison of C. imperialis toxin transcripts between northern (Texas, n=3) and southern (Honduras, n=1) populations; 15 of 60 unique toxin transcripts reported as differentially expressed | 4 individuals total (3 northern, 1 southern) | not stated |
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Most species were represented by a single individual (C. fissidens, C. lateritius, C. schmidti each n=1), and the intraspecific DE analysis used an unbalanced design of 3 northern vs. 1 southern C. imperialis↳ Could also: increasing biological replication to n≥3 per group per species is standard practice for transcriptomic venom studies — larger within-group n enables variance estimation, improves power for detecting DE transcripts, and allows individual variation to be distinguished from species-level or population-level signal
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No multiple-testing correction method was stated for the 15 differentially expressed transcripts identified among 60 toxin transcripts tested↳ Could also: Benjamini-Hochberg FDR control is the standard correction for transcriptome-wide DE testing — with 60 simultaneous tests, an FDR-adjusted threshold (e.g., FDR < 0.05 or 0.10) would clarify the expected proportion of false discoveries among the reported hits and is widely expected in DE reporting
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Toxin family expression levels were summarized as percentage of total toxin TPM without reporting within-group dispersion for groups with multiple individuals (C. imperialis, n=4)↳ Could also: reporting mean ± SD or range alongside percentages for groups with multiple individuals is also standard — dispersion metrics convey inter-individual variability, which is particularly informative for intraspecific comparisons and helps readers assess whether observed differences exceed typical within-group spread
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Interspecific differences in toxin composition were described narratively using TPM percentages, including from single-individual representatives of three species↳ Could also: a compositional data analysis framework (e.g., Aitchison log-ratio transforms with permutational MANOVA, or Bray-Curtis dissimilarity-based ordination) is also used for multi-species venom composition comparisons — compositional methods explicitly account for the constrained-sum nature of percentage data (proportions are not independent), which can prevent spurious correlations inherent in treating relative abundances as ordinary continuous variables
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The specific differential expression software and test (e.g., DESeq2 Wald test, edgeR likelihood-ratio test, limma-voom) were not stated in the provided text↳ Could also: DESeq2 or edgeR are widely used count-based DE methods for low-replicate RNA-seq designs and produce explicit fold-change estimates with standard error and adjusted p-values — reporting the specific tool, version, and statistical model used allows readers to assess how overdispersion was handled and to reproduce the analysis; fold-change estimates also convey effect magnitude alongside significance
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Proteomic cross-referencing with qMS was reported as presence/absence of toxin families rather than quantitative abundance↳ Could also: iBAQ-based or spectral-count-based relative protein abundance normalization is standard for comparing protein-level contributions across samples — quantitative proteomic metrics would enable direct comparison between transcript-level (TPM) and protein-level relative contributions and could reveal post-transcriptional regulation not captured by transcript abundance alone
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Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
This is a clean data-unavailability drop, not a discrepancy. The reported pipeline (Trim Galore→PEAR→Trinity→ToxCodAn→RSEM→DESeq2) takes only the raw Duvernoy's-gland RNA-seq under PRJNA88989, and all 7 runs are registered but embargoed (NCBI SDL 403, efetch 'not public', ENA 404), with no assembled transcripts/TPM tables deposited as fallback. Therefore 0/17 reported values (e.g. CRiSP 30.1% TPM, 18 toxin families, 15 DE genes) are reproducible and no compute was spent. The fault sits on the data-availability/authors-journal side (published claims over inaccessible data), with no fabrication signal — q5/q7/q8 are held at yellow (undetermined, re-attemptable when the embargo lifts) rather than red.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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