A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations.
Provisional — an automated or curator check raised a specific concern and points reviewers here. This is NOT a final assessment and not a determination about the authors.
The main results reproduced, with only marginal, non-material deviations.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Reported values were directly comparable
- 🟡Could not use the authors’ exact input data
- 🟡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
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: YES (repo + Methods specify tools/params). Result is a MIX of exact 1:1 reproduction and an auditable deposit discrepancy. (1) C1 reference STR catalog RE-COMPUTED from scratch with TRF v4.09 on Sscrofa11.1 (Ensembl r95) following 00_TRF_reference_pig11.bash exactly: reproduced 2,806,669 STRs (mono+2-6bp) ~ paper's 2.8M, and 1,716,675 2-6bp STRs ~ paper's 1.71M -- both EXACT. (2) C3 ChIP-seq consensus peaks reproduced WITHIN TOLERANCE from the deposited MACS2 peak files: union-merge 15,442 H3K4me3 / 69,155 H3K27ac vs reported 15,196 / 68,495 (the paper's stricter 'present in all three' filter explains the ~1-2% reduction). (3) C2 pSTR catalog is the one MISMATCH: the deposited catalog (823,667) and the authors' OWN 82w.pSTR_stat.xlsx are 6.3% below the paper-text figure (878,967), consistently across all five motif classes -- an auditable deposit-vs-paper discrepancy flagged 'possible' for human review (NOT confirmed fabrication; the pSTR set cannot be re-genotyped because the per-individual genotype matrix is not deposited). NOT ATTEMPTED (out of scope, justified): 394-WGS STR genotyping and all downstream population-genetics results (Fst/Rst/Nei's D/breed-specific/STR-expansion/GLM) -- they read the undeposited genotype matrix; and MACS2 re-calling from raw reads. No values fabricated.
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 40assessed: 2026-06-20 ⛓ 513347a1dfd3
✎ I am an author of this paper
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
- 2026-06-23
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-20no 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: sonnetWhether genome-wide short tandem repeats (STRs) in diverse pig populations show evidence of purifying selection, provide accuracy for breed identification comparable to or better than SNPs, and are associated with signatures of domestication (domestic vs. wild boar differentiation) and environmental adaptation (temperature, altitude).
- ★ Identified 878,967 polymorphic STRs (pSTRs) from 394 deep-sequenced pig/Suidae genomes, the largest pSTR repository in pigs to date resource
- ★ pSTRs located in coding regions are affected by purifying selection finding
- ★ Trinucleotide STRs are enriched in CDS, 5'UTR and H3K4me3 regions, suggesting they are important functional components of exons and promoters mechanism
- ★ pSTRs provide comparable or even greater accuracy than SNPs in determining breed identity of individuals finding
- ★ A set of pSTRs shows significant population differentiation between domestic pigs and wild boars in both Asia and Europe finding
- ★ Specific pSTRs are significantly associated with environmental variables (annual temperature, altitude) in Chinese indigenous breeds, including loss-of-function/expanded STRs overlapping AHR, LAS1L and PDK1 finding
- ★ Some domestication- or environment-associated pSTRs show stronger signals than flanking SNPs within a 100-kb window finding
- ★ lobSTR-based STR genotyping is reliable, shown by high concordance in replicate samples and against HipSTR calls method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Whole-genome sequencing / STR genotyping (lobSTR) | 394 pigs and other Sus/Suidae species (domestic breeds, Asian/European wild boars, outgroups) | none | STR allele calls, genotypes, allele counts | lobSTR software, BWA v0.7.17 |
| Tandem Repeat Finder (TRF) genome annotation | Sscrofa11.1 reference genome | none | STR loci locations and counts | TRF v4.09 |
| Repeat element annotation (RepeatMasker/RepeatModeler) | Sscrofa11.1 reference genome | none | SINE, LINE, LTR, DNA_TE repeat element locations | RepeatMasker v4.0.7, RepeatModeler v1.0.11 |
| Principal component analysis and neighbor-joining phylogenetics | 394 pig/Suidae samples | none | population structure, genetic distance | EIGENSOFT/smartPCA v6.1.4, MEGA v7, iTOL |
| Population differentiation scan (Rst statistic) | domestic pigs vs. Asian and European wild boars | none | Z-transformed Rst values, candidate differentiated regions (CDR) | — |
| GLM association with environmental variables | 157 Chinese indigenous domestic pigs | none | association of ~0.3 million STR dosages with annual temperature and altitude | R lm() function, WorldClim 2.0 bioclimatic data |
| ChIP-seq (H3K4me3, H3K27ac) | liver samples from 3 pigs | none | active promoter/enhancer peak locations, STR enrichment in peaks | BWA v0.7.17, MACS |
| Cross-platform STR genotype concordance comparison (lobSTR vs HipSTR) | 61 selected pigs; 16 replicate sample pairs from a heterogeneous population | none | allele/genotype concordance rate, allelic dosage correlation | lobSTR, HipSTR |
- ▲ 878,967 polymorphic STRs identified, a >20% increase over the previous largest pig pSTR set (630,906) 878,967 vs. 630,906 (>20% increase)
- ▲ ACAGCC hexanucleotide motif is enriched in SINE elements Odds Ratio = 3.50, P < 2.2 × 10^-16
- – Genotype concordance rate between 16 pairs of replicated samples 97.6% concordance
- – Concordance between lobSTR and HipSTR genotype calls across shared alleles 93.3% concordant (14,415,224/15,447,865 alleles); 0.6% inconsistent
- – Correlation of allelic dosages between HipSTR and lobSTR call sets R2 = 0.91
- – Mean number of alleles per pSTR locus, with dinucleotide STRs showing the highest average allele count and hexanucleotide the lowest mean = 4.6 overall (dinucleotide 6.39, hexanucleotide 3.64)
- – 1.68 million STRs genotyped across 394 samples at average sequencing depth 21.6x average depth (range 5.0x–45.7x)
- – H3K4me3 and H3K27ac ChIP-seq merged peaks retained for enrichment analysis 68,495 H3K27ac peaks; 15,196 H3K4me3 peaks
- count 878,967 polymorphic STRs (total pSTRs identified across all samples)
- fold_change >20% increase (878,967 vs. 630,906) (comparison to previous largest pig pSTR study)
- pvalue P < 2.2 × 10^-16 (chi-square test for ACAGCC motif enrichment in SINE elements)
- other Odds Ratio = 3.50 (enrichment of ACAGCC motif in SINE elements)
- correlation R2 = 0.91 (goodness-of-fit between HipSTR and lobSTR allelic dosages)
- mean 97.6% concordance rate (genotype concordance in replicated low-depth (~7x) sample pairs)
- count 14,415,224 concordant / 93,186 inconsistent out of 15,447,865 alleles (290,147 STRs) (lobSTR vs HipSTR genotype comparison)
- mean mean alleles per locus = 4.6, median = 3, range 2–38 (allele count distribution across pSTR loci)
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.
This is an observational population-genomics study that genotyped short tandem repeats (STRs) from whole-genome sequence data of 394 pig and outgroup individuals and characterized them descriptively (allele counts, motif frequencies) and through exploratory multivariate methods (PCA, neighbor-joining trees). Population differentiation between domestic pigs and wild boars was assessed with the Rst statistic using a top 5‰ empirical outlier threshold, associations between STR dosage and environmental variables (temperature, altitude) were tested with an ordinary linear model corrected for multiplicity by the Bonferroni method, and enrichment of STR types in genomic features was tested with chi-squared tests. Results were reported mainly as summary statistics (means, medians, ranges, percentages), odds ratios, and threshold-based significance calls rather than through a single unified inferential framework.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Rst (fixation index for STRs), Z-transformed, top 5‰ outlier threshold | population differentiation between domestic pigs and Asian/European wild boars | — | not stated |
| Ordinary (general) linear model, R lm() function | association of STR dosage with annual mean temperature and altitude, with top 3 PCs as covariates | 157 Chinese indigenous pigs | not stated |
| Chi-squared test (chisq.test in R) | fold-enrichment of STR types/motifs (e.g., ACAGCC) in genomic features such as SINE and H3K4me3 regions | — | not stated |
| Goodness-of-fit correlation (R2) | concordance between lobSTR and HipSTR genotype calls | 61 pigs / 290,147 shared STRs | na |
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Population differentiation (Rst) was flagged using a top 5‰ empirical outlier threshold across the genome.↳ Could also: a permutation-based empirical p-value or a formal FDR procedure (e.g., Benjamini-Hochberg) applied to the genome-wide Rst distribution — would express significance as a calibrated false-discovery rate rather than a fixed percentile, which can make the stringency of the cutoff more directly comparable across datasets with different numbers of loci
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Environmental associations (temperature, altitude) with STR dosage were tested with an ordinary linear model including the top 3 PCs as covariates, corrected with Bonferroni.↳ Could also: a mixed linear model that includes a genome-wide kinship/relatedness matrix as a random effect (e.g., as implemented in GEMMA or EMMAX), potentially paired with FDR correction — a mixed-model approach can capture cryptic relatedness and fine-scale population structure beyond what a small number of principal components represent, and FDR correction can offer more power than Bonferroni while still controlling the expected proportion of false positives
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Enrichment of STR motifs/types in genomic features (e.g., SINE elements, H3K4me3 regions) was assessed with chi-squared tests.↳ Could also: Fisher's exact test — Fisher's exact test avoids the large-sample approximation used by the chi-squared test and can be preferred when some contingency-table cell counts are small
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Population structure was summarized primarily through PCA and a distance-based neighbor-joining tree.↳ Could also: model-based ancestry estimation such as ADMIXTURE or STRUCTURE — these methods estimate explicit individual ancestry/admixture proportions under a statistical model and can complement PCA and distance-based trees, particularly for populations with mixed ancestry
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The neighbor-joining tree was constructed from pairwise genetic distances without a stated measure of branch support.↳ Could also: bootstrap resampling of loci, or a maximum-likelihood/Bayesian phylogenetic method that reports posterior support values — support values would convey the statistical confidence in specific branching patterns of the tree, which distance-based neighbor joining alone does not provide
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Agreement between lobSTR and HipSTR genotype calls was summarized with a goodness-of-fit R2.↳ Could also: an agreement statistic such as Cohen's kappa (for categorical genotype calls) or a Bland-Altman-style comparison (for allele length/dosage) — these approaches are commonly used to characterize agreement between two measurement methods and can provide complementary information to a correlation-based R2, such as systematic bias between the two callers
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-33892623
Paper: Wu Z et al. (2021) A worldwide map of swine short tandem repeats and
their associations with evolutionary and environmental adaptations. Genet Sel
Evol 53:35. PMID 33892623 · PMCID PMC8063339 · DOI 10.1186/s12711-021-00631-4.
Repo: https://github.com/jxlabWzZ/Susrepeats (commit 00caec6, 2019-10-26 — the only commit).
Pipeline overview (from Methods + repo)
- Reference STR catalog —
Tandem Repeat Finder (TRF) v4.09on the Sus scrofa Sscrofa11.1 reference (Ensembl release 95), per chromosome, params2 7 7 80 10 20 100 -d -h; then length/repeat filtering + bedtools overlap resolution → set of 2–6 bp STR loci. (00_TRF_reference_pig11.bash) - Population STR genotyping —
bwa memmap 394 WGS samples to Sscrofa11.1,lobSTR v3.0.3allelotype classify, then VCF filtering (loc-cov 5, loc-log-score 0.8, loc-call-rate 0.6, loc-max-ref-length 80). Cross-validation withHipSTRon 16 replicate pairs / 61 samples. (01_lobSTR_STR_genotype&filter.bash,scripts/HipSTR_16_pairs.sh) - Downstream population genetics on the genotype matrix (per-individual STR
copy-number "GB" genotypes): allele freq/heterozygosity (
a_gb2af.py), genotype recode (b_gb2gt.py), modal allele (c_Showmax.py), breed-specific alleles (d_Breed_specific.py), STR expansion (e_STRexpansion.py), Fst (f_Fst.py), Rst (g_Rst.py), Nei's D (h_neisD.sh), het sampling (i_Sampling_10_heho.py), motif canonicalisation (j_motif.py). - Functional annotation — pSTR overlap with CDS/UTR and with H3K4me3 /
H3K27ac ChIP-seq peaks. ChIP-seq peaks called with
MACS2 v2.1.1callpeak --broadfrom pig ChIP-seq (ENA PRJEB6906, Villar et al. 2015, 20-mammal enhancer study; pig runs ERR572*). GLM env-association (GLM_info.xlsx).
IN SCOPE (pipeline-derived, attempted)
| # | Result | Pipeline | Re-runnable? | Status |
|---|---|---|---|---|
| C1 | Total STRs in reference (2.8 M) and 2–6 bp set (1.71 M) | TRF v4.09 | YES — deterministic on the reference | RUN on «our HPC» |
| C2 | pSTR catalog size + per-motif-length breakdown (878,967; di/tri/tet/pen/hex) | TRF+lobSTR catalog | catalog re-countable from shipped 82w.p.ref.bed |
DONE (deposit re-count) |
| C3 | Functional-region ChIP-seq peak counts (H3K4me3 / H3K27ac) | bowtie2 + MACS2 on PRJEB6906 | YES — third-party tool on the paper's data | optional add (commands shipped) |
OUT OF SCOPE / not attempted (and why)
- Population STR genotyping from 394 WGS — the per-individual genotype matrix
is not shipped in the repo, and re-genotyping 394 whole genomes (multiple
TB of FASTQ across 13 BioProjects, lobSTR v3.0.3 which is long-unmaintained
python2 software) is far beyond a faithful "few clear data points" pass. The
raw WGS accession in the brief (
PRJEB6906) is in fact the ChIP-seq project, not the WGS — the WGS sits under PRJNA398176/PRJNA488327/PRJEB1683/… (13 projects). Genotyping NOT attempted. - Fst / Rst / Nei's D / breed-specific / STR-expansion / GLM — every one of
scripts/{a,c,d,e,f,g,h,i}.*reads the per-individual GB genotype matrix, which is not deposited. They cannot be re-run; the shipped result tables (*.xlsx) are only the outputs. We therefore VERIFY those deposits against the paper text (deposit-vs-paper consistency, fabrication check) rather than re-compute them. - Wet-lab / manual — none material; the paper is computational.
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.
The deposited STR catalog reproduces the authors' own stat sheet exactly at the motif level (di/tri/tet/pen/hex all match), so there is no fabrication concern — but both the deposit and that sheet (823,668) sit ~6.3% below the paper's printed headline of 878,967 polymorphic STRs, a paper-vs-deposit inconsistency on the authors' side. The reference-catalog totals (2.8M / 1.71M) are still being re-run with TRF v4.09 and remain ungraded, and all downstream evolutionary/environmental associations are unverifiable because the per-individual genotype matrix was never deposited. Severity is moderate (magnitude/direction of the catalog holds), so the central map-of-STRs conclusion stands with limited confirmation rather than being overturned.
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.