Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.
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 and reproduced 1:1. This P16-style reproduction re-ran the authors' OWN post-processing scripts (jackKnife.R, chisq.R) on their OWN shipped intermediate inputs on «our HPC» (SLURM 2176464, R 4.3.3). Claim 1 (the paper's headline introgression result, Z=-3.64 for G. davidsonii->G. aridum Colima admixture via ANGSD ABBA-BABA block jackknife) reproduced EXACTLY: our output is byte-identical to the repo's shipped aridum.txt (same SHA256) and rounds to the paper's -3.64. Claim 2 (Table 4 introgressed-SNP chi-square) reproduced within Monte-Carlo tolerance: all deterministic floor p-values match to the last digit and every significance call is identical; borderline/non-significant rows differ only in Monte-Carlo noise (simulate.p.value=TRUE, unknown seed). NOT attempted (heavy ~20%, needs full raw SRA PRJNA488266 / days of compute): genome assembly+stats (Tables 1-2), BUSCO (Table 3), k-mer/GenomeScope genome sizes, read mapping + SNP/indel calling, dN/dS, TE clustering/dating, RAxML phylogenies. The SNP COUNTS feeding Table 4 are upstream variant-calling output and were used as shipped inputs (graded partial), not regenerated. No fabrication indicators: every checked value is fully derivable from the shipped data + 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
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 87assessed: 2026-06-14 ⛓ 12df57f24901
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Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
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
- 2026-06-14
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-15no 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: opusHow did the New World diploid D-genome cottons (Gossypium subgenus Houzingenia) diversify, and what are the pace and patterns of molecular evolution of their genes and repetitive sequences, including phylogenetic relationships, divergence timing, introgression, and genome-size dynamics?
- ★ Subgenus Houzingenia originated via transoceanic dispersal from Africa ~6.6 Ma, with most biodiversity arising from rapid mid-Pleistocene (0.5–2.0 Ma) diversification plus multiple long-distance dispersals. finding
- ★ Comparison of cpDNA versus nuclear data reveals several clear cases of interspecific introgression in the subgenus. finding
- ★ Repetitive DNA comprises roughly half of the ~880 Mb genome, but most transposable element families are relatively old and stable among species. finding
- ★ A 2-fold bias toward small deletions over insertions counteracts TE-driven genome-size growth, explaining the small genomes restricted to this subgenus. mechanism
- ★ Pairwise synonymous mutation rates average ~1% per Myr, with nonsynonymous changes about seven times less frequent. finding
- The rate of indel occurrence is much lower than nucleotide substitution, averaging ~17 nucleotide substitutions per indel event. finding
- ★ Whole-genome resequencing produced new genome and plastome assemblies for most included species, providing community resources. resource
- Phylogenomic + ancestral-state reconstruction workflow (assembly, mapping, ML phylogeny, divergence dating, indel/SNP and repeat characterization) for closely related plant species. method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Whole-genome resequencing (Illumina, 2×100 bp and 2×150 bp) | Gossypium subgenus Houzingenia D-genome species (leaves), plus outgroup G. longicalyx | none | genomic sequence reads / coverage | Illumina HiSeq2500 (HiSeq PE Rapid v2 / SBS Kit v2); BGI, Novogene, and USDA-ARS GBRU libraries (Nextera, Accel-NGS 2S PCR-Free) |
| De novo genome assembly and annotation | D-genome Gossypium species assemblies | none | assembly size, E-size, % genome covered, gene models, BUSCO recovery | ABySS v2.0.1, Chromosomer v0.1.3, MAKER v2.31.6, BUSCO v2.0 |
| Reference mapping and per-gene assembly for phylogenetics | Houzingenia species mapped to G. raimondii reference | none | gene alignments for ML phylogeny | BWA v0.7.10, samtools, BamBam v1.3, RaxML |
| Divergence time estimation / ancestral state reconstruction | Houzingenia species tree | none | node ages (Ma), ancestral genome sizes | R chronos/ape, phytools fastAnc |
| Indel and SNP characterization and effect analysis | Houzingenia genomes vs G. raimondii reference | none | >1.1 million indels polarized, SNP introgression proportions, indel effects on genes | GATK, ANGSD, SnpEff, SnpSift |
| Gene family / copy number evolution analysis | orthologous gene clusters across species | none | gene family sizes and ancestral states | OrthoFinder, Count (birth-and-death model) |
| Repetitive sequence (graph-based) characterization | 1% genome-size-equivalent read subsamples per accession | none | repeat cluster abundance, genome occupation (Mb) per repeat type | RepeatExplorer, RepeatMasker, custom cotton-enriched repeat library |
| Repeat heterogeneity / relative age estimation | repeat clusters from D-genome accessions | none | pairwise percent identity divergence profiles classifying clusters as young/old | all-vs-all BLASTn, regression models with BIC |
- – Subgenus likely originated from African transoceanic dispersal ~6.6 Ma
- – Rapid mid-Pleistocene diversification accounts for nearly all biodiversity 0.5–2.0 Ma
- – Bias toward small deletions over insertions detected from polarized indels 2-fold
- – Synonymous substitution rate ~1% per Myr
- ▼ Nonsynonymous changes much rarer than synonymous ~7-fold less frequent
- – Substitution events per indel event ~17 substitutions per indel
- – Repetitive DNA fraction of genome ~50% of ~880 Mb
- – Assemblies cover most of each genome 67–85% covered; 585–775 Mbp (avg 643 Mbp)
- other average of 33× genomic coverage (average per-sample sequencing coverage after filtering)
- count over 1.1 million indels (indels detected and phylogenetically polarized)
- fold_change 2-fold bias toward deletions over small insertions (indel deletion vs insertion bias)
- other ~1% per Myr (average pairwise synonymous mutation rate)
- fold_change ~7 times less frequent (nonsynonymous vs synonymous change frequency)
- count genome size 841–934 Mb (~1.11-fold range) (genome sizes across D-genome cottons (Hendrix and Stewart 2005))
- count 169.4 M raw reads/accession; 136.9 M after filtering (range 67.2–260.2 M) (sequencing read counts per accession)
- count 20,522–45,244 gene models per accession (annotation output across assemblies)
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.
This is a phylogenomic and molecular-evolution study based on whole-genome resequencing of New World diploid cottons. The overall approach is model-based and comparative rather than hypothesis-test-driven: phylogeny was inferred by maximum likelihood (RAxML, GTRGAMMA) with rapid bootstrapping, divergence times were estimated via penalized/maximum likelihood, gene-family size and ancestral states were reconstructed with likelihood-based birth-death and continuous-trait models, repeat composition was summarized with Principal Coordinate Analysis, and relative repeat age was classified using regression models selected by Bayesian Information Criterion. Results are reported largely as estimated quantities (coverage, rates, counts, percentages, divergence dates) rather than as p-values or formal significance tests.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Maximum likelihood phylogenetic inference (RAxML, GTRGAMMA model) | concatenated nuclear gene alignment phylogeny of subgenus Houzingenia | genes filtered by coverage/length with >=1 accession per species (exact count not stated) | stated |
| Rapid bootstrapping with consensus tree generation | node support on the ML phylogeny (10,000 alternative runs on distinct starting trees) | — | na |
| Penalized likelihood / maximum likelihood divergence-time estimation (chronos, ape) | species divergence time / temporal framework | — | stated |
| Likelihood-based phylogenetic birth-and-death model (Count) | gene-family copy-number evolution and ancestral state reconstruction | 1,000 resampling-with-replacement permutations | stated |
| Continuous-trait ancestral state reconstruction (fastAnc, phytools; fitContinuous, Geiger) | genome size and per-cluster repeat abundance across the tree | — | not stated |
| Principal Coordinate Analysis (PCoA) | multivariate repeat-cluster abundance patterns per genome (log-normalized or genome-size-normalized) | — | na |
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Node support was assessed with rapid bootstrapping in a maximum likelihood framework.↳ Could also: Bayesian inference (e.g., MrBayes or RevBayes) yielding posterior probabilities, and/or coalescent-based species-tree methods (e.g., ASTRAL) on per-gene trees could also be used. — A coalescent species-tree approach would also accommodate gene-tree discordance from incomplete lineage sorting and introgression, which is relevant given the reported introgression cases, while Bayesian posteriors offer a complementary measure of clade support.
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Genes were concatenated into a single supermatrix for the ML phylogeny.↳ Could also: Partitioned models with per-locus or per-codon-position rate parameters could also be applied to the same alignment. — Allowing substitution parameters to vary among loci/codon positions would also capture among-gene rate heterogeneity and is a widely used complement to a single GTRGAMMA model across all sites.
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Divergence times were estimated with penalized/maximum likelihood (chronos) using calibrated node ages.↳ Could also: A Bayesian relaxed-clock approach (e.g., BEAST or MCMCtree) could also be used. — A Bayesian dating analysis would also propagate calibration and rate uncertainty into credibility intervals around each node age, providing an explicit measure of dating uncertainty.
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Repeat-cluster abundance patterns were summarized and visualized with Principal Coordinate Analysis.↳ Could also: Formal multivariate tests such as PERMANOVA (adonis) or model-based differential-abundance frameworks could also accompany the ordination. — These would also provide a quantitative, testable assessment of how much repeat composition differs among groups, complementing the visual ordination.
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Relative repeat age was classified by selecting regression models with the Bayesian Information Criterion.↳ Could also: Reporting alongside AIC/AICc, or model-averaging across candidate models, could also be used. — Comparing information criteria or averaging would also convey how strongly the data favor the selected trend versus close alternatives.
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Estimated quantities (rates, counts, divergence dates) were generally reported as point values.↳ Could also: Accompanying these with confidence/credible intervals or bootstrap-derived ranges could also be reported. — Reporting interval estimates alongside point estimates would also convey the precision of each estimate, which is often preferred when summarizing evolutionary rates and dates.
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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Polarized indel analysis reveals a approximately 2-fold bias toward small deletions over insertions across Gossypium Houzingenia genomes.WGS gossypium houzingenia 2019×1papers★ This paper is the founder (earliest)
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De novo assemblies of Gossypium Houzingenia accessions cover 67–85% of each genome, yielding 585–775 Mbp assembled sequence (average 643 Mbp).WGS gossypium houzingenia 2019×1papers★ This paper is the founder (earliest)
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Nearly all species diversity in Gossypium subgenus Houzingenia arose through rapid mid-Pleistocene diversification between 0.5 and 2.0 Ma.WGS gossypium houzingenia 2019×1papers★ This paper is the founder (earliest)
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Gossypium subgenus Houzingenia originated via African transoceanic dispersal approximately 6.6 Ma.WGS gossypium houzingenia 2019×1papers★ This paper is the founder (earliest)
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Nonsynonymous substitutions occur approximately 7-fold less frequently than synonymous substitutions in Gossypium Houzingenia, indicating strong purifying selection.WGS gossypium houzingenia down 2019×1papers★ This paper is the founder (earliest)
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Repetitive DNA constitutes approximately 50% of the ~880 Mb Gossypium Houzingenia genome.WGS gossypium houzingenia 2019×1papers★ This paper is the founder (earliest)
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Approximately 17 substitution events occur per indel event in Gossypium Houzingenia genomes.WGS gossypium houzingenia 2019×1papers★ This paper is the founder (earliest)
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The synonymous substitution rate in Gossypium Houzingenia is approximately 1% per million years.WGS gossypium houzingenia 2019×1papers★ 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.md — pmid-30476109
Paper: Grover et al. 2019, "Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing." GBE 11(1):53-71. PMID 30476109 · PMCID PMC6320677 · DOI 10.1093/gbe/evy256 Code: https://github.com/IGBB/D_Cottons_USDA (master, commit f9675740faf21a361d6f33a89ce3665565908e98, pushed 2019-07-18) Data: SRA PRJNA488266 (raw Illumina reads, 13 D-genome cotton species)
Pipeline map (which reported results come from a bioinformatic pipeline)
| Result | Pipeline | In scope? | Why |
|---|---|---|---|
| Genome assemblies (ABySS) + stats (Table 1/2) | trim→ABySS v2.0.1→E-size select | OUT (heavy 20%) | needs all raw SRA reads + many-kmer assemblies; days of compute, not low-hanging |
| BUSCO (Table 3) | MAKER annot → BUSCO v2 | OUT | depends on assemblies above |
| k-mer genome sizes (GenomeScope) | jellyfish→GenomeScope per accession | OUT (heavy) | needs raw reads per accession to build k-mer histograms |
| Read mapping + SNP/indel calling | BWA→samtools→variant calls | OUT (heavy) | needs raw reads + reference; upstream of the stats below |
| ABBA-BABA D-statistic / Z (introgression) | ANGSD abbababa → block-jackknife jackKnife.R |
IN | shipped input (aridum.abbababa) + script + expected output (aridum.txt); deterministic; seconds |
| Introgressed-SNP chi-square (Table 4) | chisq.R on shared.derived.snps |
IN (post-proc) | shipped input + script + expected p-values (Table4 xlsx); Monte-Carlo (within-tol). NOTE: the SNP counts are upstream variant-calling output (out of scope to regenerate); only the chi-square step is reproduced |
| CNV evolution rates | count.bootstrap.R (CAFE-style) |
OUT (optional) | candidate, not attempted (80/20) |
| dN/dS, indel, TE/clustering, phylogeny (RAxML) | various R + RAxML | OUT | heavy / depend on upstream alignments |
What we attempt (IN scope, low-hanging, fully shipped)
- D-statistic introgression test — re-run the authors'
jackKnife.Ron the shippedaridum.abbababa(3 individuals: D4-12.Garid1=aridum Colima, D4-185=aridum Jalisco, D3-D-27.Gdavi1=davidsonii H3) and check the resulting Patterson's D + block-jackknife Z against the shippedaridum.txtAND the paper's reported Z = -3.64. - Introgression chi-square (Table 4) — re-run the authors'
chisq.Ron the shippedshared.derived.snpsand compare Monte-Carlo p-values to the manuscript Table 4 xlsx.
All compute on «our HPC» («infra»). Repo cloned + R env built inside the compute job («infra»).
Assessments & scoring basis
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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.
Re-ran the authors' own scripts (jackKnife.R, chisq.R) on their shipped intermediate inputs. The paper's headline introgression result Z=-3.64 reproduces byte-identical (Z=-3.640015, D=-0.005534797 — same SHA256 as the shipped aridum.txt), the supporting davidsonii-vs-aridum D-stats are byte-identical, and Table 4's chi-square reproduces with all 8 deterministic floor p-values exact (1/2001) and every significance call identical. The only differences are unseeded Monte-Carlo noise on borderline/non-significant rows (genic 1/2001 vs 3/2001, same p<<0.01 conclusion). Upstream variant-calling (the SNP counts) was out of scope and used as shipped inputs, verified == Table 4. No fabrication indicators — a clean 1:1 reproduction.
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.