The evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- Every checked point held up.
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
Described well enough to reproduce 1:1. The authors' own repo (pbrec/popgen-popchem @ 2ca05c9) ships the derived data matrices, so the downstream pipeline-derived results run directly without re-deriving from SRA reads. All 4 in-scope claims reproduced on «our HPC» (conda R 4.5.3 + SNPRelate/vegan/ecodist): moments AIC weight=1 (exact), GBS PCA PC1+PC2=3.81% which is <4% (exact bound), perfume ANOSIM R=0.7751~0.8 & p=0.001 (within-tol), and the 306-individual perfume filter (exact). NOT attempted: (1) genome-wide FST/pi/Tajima's D sliding-window scan (genome_analysis.R) because its VCFs are not in the repo and the script says to request them by email -> data_restricted; (2) Or41 functional electrophysiology (or41_functional_plotting.R, Fig 4) which reads Fig-4 Source Data not in the repo and is wet-lab -> non_pipeline. Minor honesty flags: a shipped-code typo in gbs_analysis.R's filename (double .txt) had to be corrected to run; the paper cites 16,369 SNPs while the shipped PCA matrix has 5428 (MAF>=0.05 set); the shipped ANOSIM code filters to 270 individuals (top-50 compounds) vs the paper's headline 306 (looser filter) but both give R=0.8,p=0.001. No fabrication detected -- all reproduced values derive from shipped data+code.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
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v1 current initial assessment Score 93assessed: 2026-06-16 ⛓ f2f3347434dc
✎ I am an author of this paper
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Provenance — full disclosure
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 2026-06-18no 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: opusDo specific odorant receptor (OR) genes facilitate the divergence of sexual chemical signaling (perfume communication) and reproductive isolation during the early speciation of the orchid bee lineages Euglossa dilemma and E. viridissima?
- ★ E. dilemma and E. viridissima are reproductively isolated genetically distinct lineages despite low genome-wide differentiation. finding
- ★ Perfume chemistry is species-specific, driven mainly by lineage-specific major compounds HNDB (E. dilemma) and L97 (E. viridissima). finding
- ★ Perfume differentiation coincides with two species-specific selective sweeps harboring tandem arrays of odorant receptor genes (43 ORs total). finding
- ★ The odorant receptor Or41 evolved under positive selection in E. dilemma (selective sweep) but purifying selection in E. viridissima. mechanism
- ★ The derived Or41 variant in E. dilemma is specifically tuned to its major perfume compound, while the ancestral E. viridissima variant is broadly tuned to multiple odorants. finding
- ★ OR evolution likely contributed to the divergence of sexual communication and pre-mating reproductive barriers in natural populations. mechanism
- Functional in vitro assays of OR variants link OR genotype to odorant tuning phenotype. method
- Net interspecific differentiation (∆FST') leveraging intraspecific population structure identifies islands of divergence. method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| SNP genotyping / population genetics (PCA, ADMIXTURE, f4-test, demographic modeling) | 232 male orchid bees (E. dilemma and E. viridissima) across Central America | none | genetic differentiation, population structure, admixture (16,369 SNPs) | — |
| Whole-genome resequencing / genome-wide divergence scan | 30 males from three genetic lineages (n=10 each Ed north, Ed south, Ev) | none | FST, ∆FST', Dxy, nucleotide diversity (π), LD, selective sweeps (CLR) | E. dilemma reference genome |
| Gas chromatography–mass spectrometry (GC–MS) of perfume chemistry | 384 male orchid bees (hind tibial perfume extracts) | none | perfume chemical composition / relative compound abundance (nMDS, ANOSIM, SIMPER) | GC–MS |
| Morphometric analysis of mandible dentation | E. dilemma and E. viridissima males (sympatric and allopatric) | none | number of mandibular teeth | — |
| Maximum likelihood phylogeny and dN/dS molecular evolution analysis | Or41 sequences from 47 individuals plus five outgroup species | none | genotype species-specificity, dN/dS, selection signature | — |
| Functional odorant receptor assay (heterologous expression) | Or41 derived (E. dilemma) and ancestral (E. viridissima) variants | OR variant comparison | odorant tuning / response specificity to perfume compounds | — |
- – PCA of 16,369 SNPs separated E. dilemma and E. viridissima in allopatry and sympatry, with first two PCs explaining <4% of variation. <4% variance on PC1+PC2
- – Perfume composition differentiated into two distinct lineage-specific chemical phenotypes independent of geography. ANOSIM R=0.8, p=0.001
- – HNDB (E. dilemma) and L97 (E. viridissima) are diagnostic compounds accounting for the largest perfume proportions and a large share of chemical differentiation. HNDB 55%, L97 37%; together 46.3% of differentiation
- – Two species-specific selective sweeps identified, harboring tandem OR arrays totaling 43 OR genes. 39 ORs (Ed sweep) + 4 ORs (Ev sweep)
- – Or41 shows positive selection on the E. dilemma branch but purifying selection in E. viridissima. dN/dS=3.6 (E. dilemma) vs 0.3 (E. viridissima)
- ▼ Nucleotide diversity (π) at Or41 was much lower in E. dilemma than E. viridissima, consistent with a sweep. 5-fold lower π in E. dilemma
- – Of 19 substitutions mapped on Or41 membrane topology, 17 were non-synonymous and 2 synonymous. 17/19 non-synonymous
- ▲ In sympatry 26% of E. viridissima males had three mandibular teeth vs 3% in allopatry, consistent with introgression. 26% vs 3%; Fisher p=0.0009
- correlation ANOSIM R=0.8 (perfume composition differentiation between lineages, p=0.001)
- fold_change dN/dS=3.6 (positive selection on Or41 E. dilemma branch)
- fold_change dN/dS=0.3 (purifying selection on Or41 E. viridissima branch)
- pvalue p=0.0009 (Fisher's exact test, three-tooth frequency sympatry vs allopatry)
- other f4=0.001, z=2.7, p=0.007 (f4-test rejecting simple bifurcating phylogeny)
- correlation r=−0.13, p=0 (Dxy negatively correlated with ∆FST')
- other pairwise FST: 0.04–0.18 (low differentiation among three genetic lineages)
- count 43 OR genes (39 + 4) (ORs in the two selective sweep tandem arrays)
Statistical methods review
Model: opusA 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 combines population-genomic, chemical-ecology, and molecular-evolution analyses across distribution-wide samples (232 genotyped males, 384 perfume samples, 30 re-sequenced genomes). Genetic structure was assessed with PCA, ADMIXTURE clustering, F_ST, an f4-test, and AIC-based demographic model selection; perfume chemistry was compared with nMDS plus ANOSIM and SIMPER; genome divergence used a net-F_ST (ΔF_ST') window scan with correlation analyses, a Mann–Whitney U comparison of D_xy, selective-sweep (CLR) detection, and dN/dS and maximum-likelihood phylogenetics on Or41. A categorical trait was tested with Fisher's exact test. Results were reported with test statistics and p-values, with dispersion shown as SEM and box-plot quartiles/IQR.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Principal components analysis (PCA) of genetic variance | Genetic differentiation of E. dilemma vs E. viridissima, Fig. 1b | 232 males / 16,369 SNPs | not stated |
| ADMIXTURE genetic clustering analysis | Population/species structure, Fig. 1c | 232 males | not stated |
| Pairwise F_ST estimation | Differentiation among Ev, Ed-south, Ed-north (0.04–0.18) | — | na |
| f4-test (four-population test) | Test of bifurcating phylogeny among lineages (z = 2.7, p = 0.007) | — | not stated |
| Demographic model selection via Akaike Information Criterion (AIC) | Species differentiation model (AIC weight = 1), Supplementary Table 5 | 30 re-sequenced genomes | not stated |
| Fisher's exact test | Three-tooth frequency in sympatric vs allopatric E. viridissima males (p = 0.0009) | — | na |
| Non-metric multidimensional scaling (nMDS) with ANOSIM | Perfume composition differentiation (R = 0.8, p = 0.001), Fig. 1d | 384 individuals | not stated |
| Similarity Percentage (SIMPER) analysis | Contribution of HNDB and L97 to chemical differentiation (46.3%) | — | na |
| Net interspecific F_ST (ΔF_ST') window scan | Genome-wide divergence in 50 kb windows (>99th percentile outliers), Fig. 2 | 30 genomes (n = 10 per lineage) | na |
| Pearson's correlation | ΔF_ST' vs gene density (r = 0.17), π (r < −0.24), D_xy (r = −0.13), LD (r ≥ 0.1), all p = 0 | — | not stated |
| Mann–Whitney U-test | D_xy in outlier vs non-outlier regions (p = 0.001), Fig. 2b | — | na |
| Composite likelihood ratio (CLR) selective-sweep test | Sweep detection in outlier windows / Or41, Fig. 3a | n = 10 per lineage | na |
| Maximum likelihood phylogeny with bootstrap support | Or41 genotype phylogeny, Fig. 3b | 47 individuals | na |
| dN/dS analysis | Selection on Or41 branches (E. dilemma dN/dS = 3.6; E. viridissima = 0.3), Fig. 3b | 5 outgroup species | na |
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Genome-wide divergence outliers were identified using a fixed 99th-percentile threshold on ΔF_ST' windows.↳ Could also: A model-based or empirical-null approach (e.g., simulation under demography, or a formal false-discovery-rate control across windows) could ALSO be used to flag outliers. — An explicit FDR or null-model calibration would attach a quantified error rate to each candidate region, complementing the percentile cutoff.
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Several p-values from correlation tests are reported as 'p = 0'.↳ Could also: Reporting exact small p-values (e.g., p < 1e-16) or the test statistic with degrees of freedom would ALSO convey the result. — Precise small-value reporting communicates the strength of evidence and aids reproducibility and meta-analysis.
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Dispersion for D_xy was shown as 1 SEM, alongside IQR-based box plots elsewhere.↳ Could also: Standard deviation or a 95% confidence interval could ALSO be reported. — SD or a CI conveys the spread or estimation uncertainty directly and is often preferred for describing variability, providing consistent dispersion reporting across panels.
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Perfume composition was compared using ANOSIM following nMDS ordination.↳ Could also: PERMANOVA (e.g., adonis on the dissimilarity matrix) could ALSO be used to test group differences. — PERMANOVA partitions variance, accommodates covariates such as geography, and is less sensitive to within-group dispersion differences than ANOSIM.
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A categorical tooth-count difference between population types was tested with Fisher's exact test.↳ Could also: A logistic regression or generalized linear model could ALSO model the trait while incorporating site or population as a covariate. — A regression framework would allow adjustment for additional factors and yield an effect size (e.g., odds ratio) with a confidence interval.
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Branch-wise selection on Or41 was summarized with a single dN/dS ratio per branch.↳ Could also: A branch-site likelihood test with a formal null comparison (e.g., LRT) could ALSO be applied. — A branch-site test provides a statistical significance assessment for positive selection at specific codons, complementing the descriptive dN/dS values.
Result convergence & founder nodes
Findings this paper shares with others that ran a comparable experiment. A node’s strength is how many independent papers report it (replication breadth) — not how often it is cited, so a heavily-replicated but under-cited founder still stands out.
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Three-toothed mandible phenotype is more frequent in sympatric E. viridissima males (26%) than allopatric individuals (3%), consistent with introgression of E. dilemma morphologyimaging eulaema-viridissima up 2020×1papers★ This paper is the founder (earliest)
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HNDB is the species-diagnostic perfume compound of E. dilemma males (55% of bouquet) and L97 of E. viridissima (37%), together explaining 46% of inter-species chemical differentiationmetabolomics eulaema-dilemma-eulaema-viridissima tibial-gland 2020×1papers★ This paper is the founder (earliest)
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Male orchid bee tibial perfume composition differentiates into two distinct lineage-specific chemical phenotypes independent of geographic overlap (ANOSIM R=0.8, p=0.001)metabolomics eulaema-dilemma-eulaema-viridissima tibial-gland 2020×1papers★ This paper is the founder (earliest)
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Or41 underwent positive selection in E. dilemma (dN/dS=3.6) but purifying selection in E. viridissima (dN/dS=0.3), linking odorant receptor divergence to species-specific perfume signalingother eulaema-dilemma-eulaema-viridissima mixed 2020×1papers★ This paper is the founder (earliest)
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17 of 19 inter-species amino acid substitutions in Or41 are non-synonymous, indicating strong functional divergence of this odorant receptor across speciesother eulaema-dilemma-eulaema-viridissima 2020×1papers★ This paper is the founder (earliest)
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PCA of 16,369 SNPs separates E. dilemma and E. viridissima in both allopatry and sympatry, confirming species-level genetic distinctivenessother eulaema-dilemma-eulaema-viridissima 2020×1papers★ This paper is the founder (earliest)
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Two species-specific selective sweeps identified by genome-wide FST scan, each harboring tandem odorant receptor gene arrays (39 OR genes in E. dilemma sweep, 4 in E. viridissima sweep)WGS eulaema-dilemma-eulaema-viridissima 2020×1papers★ This paper is the founder (earliest)
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Or41 nucleotide diversity (π) is ~5-fold lower in E. dilemma than E. viridissima, consistent with a recent selective sweep at this locus in E. dilemmaWGS eulaema-dilemma down 2020×1papers★ This paper is the founder (earliest)
Citation network
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Data lineage
The datasets this paper uses (text-mined from the full text via Europe PMC), and which other assessed papers stand on the same data. A shared dataset is a factual link — not a judgement.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-31932598
Paper: Brand et al. 2020, Nat Commun 11:244. "The evolution of sexual signaling is linked to odorant receptor tuning in perfume-collecting orchid bees." DOI 10.1038/s41467-019-14162-6.
Code: https://github.com/pbrec/popgen-popchem @ commit
2ca05c9c32ddc55b022ec44ae92cd4a01ad64d1d (pushed 2019-12-15). Authors' own code
(R scripts). README is a one-line title only — no run instructions; scripts are
self-documenting and read shipped data files.
Data: SRA PRJNA529235 (WGS + GBS reads). Crucially, the repo ships the derived data matrices used by most downstream analyses, so those analyses can be reproduced 1:1 without re-running the upstream read→alignment→SNP-call pipeline.
In scope (pipeline-derived, reproducible from SHIPPED data)
| # | Result | Script | Shipped input | Pipeline / tool |
|---|---|---|---|---|
| C1 | Demographic model selection by AIC: best moments model has AIC weight = 1 |
moments_AIC.R |
moments_results.txt (16 models, log-likelihoods) |
base R AIC + Akaike weights over moments (Jouganous et al.) fit log-likelihoods |
| C2 | GBS SNP PCA: PC1+PC2 jointly explain <4% of genetic variation | gbs_analysis.R |
GBS_SNPs_MAF0.05_SNPrelate_format.txt (5428 SNPs), pop_ids_gbs.txt |
SNPRelate snpgdsPCA |
| C3 | Perfume chemistry ANOSIM E. dilemma vs E. viridissima: R = 0.8, p = 0.001 | perfume_analysis_and_plotting.R (ANOSIM block) |
peak_area_matrix_Brandetal.txt (384 indiv × 653 compounds), pop_ids_gcms.txt |
vegan/ecodist Bray-Curtis + anosim (999 perms) |
| C4 | Perfume filtering: 384 → 306 individuals after ≥10-peak filter | same | same | data filtering step (deterministic) |
Out of scope (NOT attempted, with reason)
| Result | Script | Why out of scope |
|---|---|---|
| Genome-wide FST / π / Tajima's D sliding-window scan (Fig 2/3) | genome_analysis.R |
Header states: "request VCF files (very large) by emailing Philipp Brand … or Santiago Ramirez." The VCFs are not in the repo and are on-request only → data_restricted. Re-deriving them would require the full WGS read→ref-map→SNP-call pipeline plus the reference genome + GFF (not pointed to), a separate large effort outside the shipped-data reproduction. |
| Or41 functional electrophysiology (Fig 4) | or41_functional_plotting.R |
Reads data.txt / hndb_dilutions.txt = "Source Data file for Figure 4" — not in repo; these are single-sensillum-recording (wet-lab) measurements, non-pipeline. Plotting only. |
Notes
- The shipped GBS matrix is the MAF≥0.05 SNPRelate-format set with 5428 SNPs; the paper text mentions 16,369 SNPs (likely a pre-filter count). The PCA script re-applies maf=0.05 + missing.rate=0.5 on this matrix, so the reproduced variance % is computed on the shipped set. We compare the PC1+PC2 magnitude claim.
- Compute: conda R env built inside a «our HPC» SLURM job (compute nodes have internet); shipped data already on «infra».
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
All four in-scope, pipeline-derived claims reproduce 1:1 from the authors' own deposited matrices and R scripts: moments AIC weight=1 (exact), GBS PCA PC1+PC2=3.81% (<4% as stated), perfume ANOSIM R=0.7751→0.8 with p=0.001, and the 306-individual filter (exact). The only gaps are on our/technical side or harmless packaging — a 1-decimal rounding on R, a filename typo, a 16,369-vs-5428 SNP labelling nuance, and a looser-vs-stricter filter that gives the same ANOSIM result. No fabrication; the genome-wide diversity scan (on-request VCFs) and Or41 electrophysiology (wet-lab) were legitimately out of scope, which is a data-availability/non-pipeline matter, not an authors' defect on the reproduced claims.
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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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.