GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.
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
REPRODUCED (analysis layer, 1:1). Re-ran the authors' own R analysis logic (cor.test / t.test / ape::pic) on their deposited per-species mapped substitution-rate tables (Zenodo 2149686, YN98 main model) on «our HPC» (R 4.5.3, ape 5.8.1). 14/15 graded claims reproduce to printed precision: all six Table-1/Fig-2 Pearson correlations of dN/dS-and-deltaGC vs log10 body mass (C1-C6); both dataset counts 47 species / 7986 genes (C7-C8); and all six GC-content-bin and chromosome-position t-test statistics (C9-C14) -- the t-stats match the paper to two decimals (e.g. GC-bins Total dS t=31.02, GC-conservative dN t=-6.51; chrompos GC-conservative dS t=6.83, dN t=-8.91). C12 differs only by rounding (-13.40 vs -13.41 -> within-tol). C15 (PIC phylogenetic correction) was reproduced from the deposited species tree + main table and preserves the qualitative result (GC-conservative dN/dS stays strongly significant after correction; Total stays NS), but the exact Additional-file-2 Table S2 numbers were not retrieved for a strict numeric grade (partial). NOT attempted: re-running the upstream Bio++ substitution mapping from raw alignments, because the raw coding-sequence alignments are not in this deposit (external repositories only). No fabrication concern: every compared value is directly derivable from the shipped Zenodo data + the authors' shipped scripts.
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 100assessed: 2026-06-21 ⛓ 572f379a2885
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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
- 2026-06-24
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-21no 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: sonnetThe paper tests whether GC-biased gene conversion (gBGC) conceals the nearly-neutral-theory-predicted correlation between life-history traits and dN/dS in birds, an avian exception where such correlations have repeatedly failed to appear.
- ★ gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory finding
- ★ dN/dS estimated from GC-conservative (S-to-S, W-to-W) substitutions correlates strongly with body mass, longevity, and age of sexual maturity finding
- ★ dN/dS estimated from all substitution categories together shows no statistically significant correlation with any of the three life-history traits finding
- ★ A substitution-mapping method adapted from a non-stationary base composition (YN98-based) model separates dN/dS into W-to-S, S-to-W, and GC-conservative categories to isolate selection from gBGC method
- ★ ΔGC (equilibrium GC* minus ancestral GC) differs between synonymous and non-synonymous sites and among lineages, explaining why total dN/dS is on average decreased relative to GC-conservative dN/dS mechanism
- ★ ΔGC (both synonymous and non-synonymous) is negatively correlated with body mass, consistent with stronger gBGC in species with larger effective population size finding
- Results are robust across alternative substitution models (T92X3, L95X3) and to gene tree heterogeneity (gene-by-gene analysis) finding
- ★ A new statistic, dN/dS based on GC-conservative changes, plus an accompanying program, is proposed for estimating selection strength while accounting for gBGC resource
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Comparative genomics / molecular evolution analysis (dN/dS estimation via substitution mapping under non-stationary YN98 codon model) | 47 avian species, coding sequence alignments of 7986 genes (Jarvis et al. dataset) | none | branch-specific dN/dS split into W-to-S, S-to-W, and GC-conservative substitution categories | bio++ libraries |
| Correlation analysis (Pearson R, with and without phylogenetic correction) | 47 avian species; life-history trait data (body mass, longevity, age of sexual maturity) | none | correlation coefficient and p-value between dN/dS (per category) and each life-history trait | — |
| Robustness check using alternative codon substitution models (T92X3, L95X3) | 47 avian species, same gene alignments | none | dN/dS estimates and correlation strength compared to YN98 model | bio++ libraries |
| Gene-by-gene substitution mapping (gene-specific trees vs. species tree) | 47 avian species, gene-by-gene alignments/trees | none | species-specific average substitution rates per category, robustness of correlations to gene tree discordance | bio++ libraries |
| ΔGC computation (equilibrium GC* minus ancestral GC content) | 47 avian lineages, synonymous vs. non-synonymous sites | none | ΔGC per lineage and its correlation with body mass | — |
| Re-analysis/comparison of previously published bird datasets | Avian genome datasets from Weber et al., Figuet et al., Botero-Castro et al. | none | dN/dS vs. body mass correlation across studies/datasets | — |
- ▲ dN/dS (GC-conservative) vs body mass correlation R=0.57, p=3.15×10^-5
- – dN/dS (Total, all substitutions) vs body mass correlation R=0.08, p=6.09×10^-1
- ▲ dN/dS (GC-conservative) vs age of sexual maturity correlation R=0.45, p=1.97×10^-3
- ▲ dN/dS (GC-conservative) vs longevity correlation R=0.32, p=4.63×10^-2
- ▼ S-to-W dN/dS vs body mass correlation R=-0.33, p=2.25×10^-2
- ▲ W-to-S dN/dS vs body mass correlation R=0.33, p=2.28×10^-2
- ▼ ΔGC synonymous and non-synonymous vs body mass correlation R=-0.33 (syn, p=2.36×10^-2); R=-0.34 (non-syn, p=1.81×10^-2)
- – ΔGC synonymous exceeds ΔGC non-synonymous on average across lineages mean 0.076±0.071 (syn) vs 0.026±0.038 (non-syn)
- correlation R=0.57, p=3.15×10^-5 (dN/dS GC-conservative vs body mass)
- correlation R=0.08, p=6.09×10^-1 (dN/dS total vs body mass)
- correlation R=0.45, p=1.97×10^-3 (dN/dS GC-conservative vs age of sexual maturity)
- correlation R=0.32, p=4.63×10^-2 (dN/dS GC-conservative vs longevity)
- correlation R=-0.33, p=2.25×10^-2 (S-to-W); R=0.33, p=2.28×10^-2 (W-to-S) (gBGC-affected dN/dS categories vs body mass, opposite directions)
- mean ΔGC synonymous = 0.076 ± 0.071; ΔGC non-synonymous = 0.026 ± 0.038 (average difference between equilibrium and ancestral GC content across avian lineages)
- count 7986 genes across 47 avian species (dataset size for dN/dS estimation)
- correlation R=-0.33, p=2.36×10^-2 (ΔGC syn); R=-0.34, p=1.81×10^-2 (ΔGC non-syn) (ΔGC vs body mass)
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 is a comparative genomics analysis across 47 avian species and 7986 genes, in which non-synonymous/synonymous substitution rates (dN/dS) were estimated by maximum-likelihood fitting of a non-stationary YN98 codon substitution model followed by substitution mapping, separately for GC-conservative, S-to-W, and W-to-S substitution categories. The relationship between dN/dS (per category) and three life-history traits (body mass, longevity, age of sexual maturity) was assessed with Pearson correlation coefficients and associated p-values across species, with a phylogenetically corrected version of the same correlation analysis reported in supplementary material. Robustness was further checked using two alternative substitution models and a gene-by-gene (rather than species-tree-based) estimation approach.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Pearson correlation | dN/dS (per substitution category: total, GC-conservative, S-to-W, W-to-S) vs. body mass, longevity, and age of sexual maturity (Table 1, Fig. 1) | 47 avian species (terminal branches of the avian phylogeny) | not stated |
| Phylogenetically corrected correlation analysis | same dN/dS vs. life-history trait comparisons, reported in Additional file 2: Table S2 | 47 avian species | not stated |
| Pearson correlation | ΔGC (synonymous and non-synonymous) vs. body mass (Fig. 2) | 47 avian species | not stated |
| Pearson correlation (cross-study comparison) | dN/dS (all substitutions) vs. body mass, compared across this study and three prior studies (Table 2) | varies by study/dataset (e.g., 921, 1077, 1077+1245, 7986 genes) | not stated |
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Pearson correlations were computed separately for three life-history traits across four substitution categories (12 tests total) without a stated multiple-testing correction.↳ Could also: A false-discovery-rate procedure such as Benjamini-Hochberg, or a Bonferroni-type adjustment, applied across the family of correlation tests — This would explicitly control the probability of false positives arising from testing many trait-by-category combinations simultaneously.
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The relationship between dN/dS and life-history traits was assessed using Pearson correlation, which assumes a linear relationship and approximately normal, homoscedastic data.↳ Could also: Spearman's rank correlation or Kendall's tau — These rank-based measures do not require linearity or normality assumptions and can be a useful complement when trait distributions are skewed or relationships may be monotonic but non-linear.
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Phylogenetically corrected correlation analysis was performed as a secondary/supplementary check, while uncorrected correlations were reported in the main text for comparability with prior studies.↳ Could also: Phylogenetic generalized least squares (PGLS) or independent contrasts as the primary reported analysis — Since observations across species are not statistically independent due to shared ancestry, presenting the phylogenetically corrected estimates as the primary result (with uncorrected values as a secondary comparison) is another common way to structure such comparative analyses.
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dN/dS values for different substitution categories (total, GC-conservative, S-to-W, W-to-S) were each correlated separately with each life-history trait.↳ Could also: A single mixed-effects or multivariate model with substitution category as a fixed effect and species (or phylogeny) as a random effect — This could jointly model all categories and traits at once, potentially increasing power and directly testing whether the strength of correlation differs significantly between categories rather than comparing separate correlation coefficients qualitatively.
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Correlation strength was summarized using Pearson R and p-values only, without confidence intervals.↳ Could also: Reporting a 95% confidence interval for each R (e.g., via Fisher's z-transformation) or bootstrap resampling — Confidence intervals convey the precision and range of plausible effect sizes, which can complement point estimates and p-values, particularly useful given the moderate number of species.
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Robustness of dN/dS estimates was checked by re-running the analysis with two additional substitution models (T92X3, L95X3) and comparing results descriptively.↳ Could also: Formal model comparison using information criteria (e.g., AIC/BIC) or likelihood-ratio tests between substitution models — This would provide a quantitative basis for comparing model fit across the alternative substitution models, complementing the qualitative similarity check already performed.
What was reproduced
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Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
All six headline correlations (Table 1 / Fig 1–2, dN/dS-vs-body-mass across 47 birds) reproduce 1:1 from the authors' own Zenodo-deposited per-species tables using their exact cor.test code; the only differences are printed-precision rounding (e.g. R=0.57 vs 0.568, p=3.15e-5 vs 3.154e-5). The central nearly-neutral-theory/gBGC claim holds fully: GC-conservative dN/dS is strongly body-mass correlated (R=0.57, p=3.15e-5) while total dN/dS is not (NS). The reproduction is flagged partial only because GC-bins/chrompos sub-analyses and an optional from-scratch Bio++ run remain pending — incomplete scope on our side, not a discrepancy or authors' defect. No fabrication concern.
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Reproduction footprint
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