@prefix this: . @prefix sub: . @prefix np: . @prefix rdf: . @prefix prov: . @prefix npx: . @prefix dc: . @prefix xsd: . sub:Head { this: a np:Nanopublication; np:hasAssertion sub:assertion; np:hasProvenance sub:provenance; np:hasPublicationInfo sub:pubinfo . } sub:assertion { a ; dc:description "fetch.py downloads the chr22 VCF (205.6 MB) and the genetic-map archive. analysis.py streams the VCF, keeps PASS biallelic records with VT=SNP and without MULTI_ALLELIC, sums 2p(1-p)*2n/(2n-1) from the INFO AF value over non-overlapping 200 kb windows from 16.0 Mb, divides by window length to get pi, and takes the recombination rate per window from the linearly interpolated HapMap map; windows with fewer than 200 SNPs are excluded. Spearman and Pearson correlations between pi and rate across windows are computed and the pre-registered rule applied."; "Measured: 0.6162852097435987 Spearman rho between per-window nucleotide diversity and recombination rate (cM/Mb), chr22, 200 kb windows (n = 177 windows (of 177), 1051673 SNPs of 1103547 VCF records, p = 6.8e-20; Pearson r = 0.556). Interpretation: Maynard Smith and Haigh predicted that a sweep reduces heterozygosity at a linked neutral site by an amount that grows as recombination fraction over selection coefficient falls. The claim's assessment proposes the genome-wide version of the test used by Begun and Aquadro (1992): correlation between neutral diversity and local recombination rate. A positive correlation is also produced by background selection (Charlesworth et al. 1993), so a positive result supports the pattern the claim predicts but does not identify hitchhiking as the only cause; this is recorded as a caveat, not folded into the verdict. pi is computed from allele frequencies pooled across 26 populations; population structure inflates pooled pi roughly uniformly along the chromosome and does not create a correlation with recombination. All SNPs are used rather than only 'neutral' sites, which if anything weakens the expected correlation."; "Claim test of maynardsmith-hitchhiking: supports, confidence 0.85"; ; prov:wasAttributedTo ; "Planned datasets: 1000genomes-phase3-chr22-genotypes-20130502, hapmap-phaseII-genetic-map-grch37"; "claim-test/0.1.0"; "biological"; "Pre-registered. REFUTES if rho < 0 with p < 0.05 (diversity lower where recombination is higher) OR if |rho| < 0.1 with p > 0.05 and at least 100 windows (no detectable relationship). MIXED otherwise (0 <= rho < 0.2, or 0.01 <= p). INCONCLUSIVE (data-unavailable) if either file cannot be downloaded."; "A positive diversity-recombination correlation is also produced by background selection (purifying selection removing linked neutral variation), so the result supports the pattern hitchhiking predicts but does not isolate sweeps as the cause; separating the two needs site-frequency or sweep-scan evidence.", "All SNPs are used, not only neutral sites; gene density and GC content covary with recombination in humans and could contribute to the correlation through mutation-rate variation. Windows with < 200 SNPs (none on chr22 above 16 Mb) would have been excluded.", "Diversity is computed from allele frequencies pooled over all 26 populations; population structure inflates pi uniformly and does not create the correlation, but the absolute pi values are not a single-population estimate.", "One chromosome (22, about 35 Mb of assessable sequence) was tested, as pre-registered, to keep the download small; the pattern is well known genome-wide (Hellmann et al. 2003)."; "Pre-registered. Data: 1000 Genomes Project Phase 3 chromosome 22 genotype VCF (release 20130502, all 2504 samples) and the HapMap Phase II GRCh37 genetic map for chromosome 22. SNP filter: records with VT=SNP in INFO, biallelic (no MULTI_ALLELIC flag, single ALT), FILTER PASS. Windows: non-overlapping 200 kb windows starting at 16,000,000 bp (GRCh37) up to the last SNP. Diversity per window: pi = sum over SNPs of 2p(1-p) * 2n/(2n-1), with p the INFO AF value and 2n = 5008 chromosomes, divided by the window length (200,000 bp). Windows with fewer than 200 qualifying SNPs are excluded as unassessable (centromere-proximal or low-accessibility regions). Recombination rate per window: (map cM at window end minus map cM at window start) / 0.2 Mb, with cM linearly interpolated from the genetic map. SUPPORTS if Spearman rho(pi, recombination rate) across windows is >= 0.2 with two-sided p < 0.01."; "Pre-registered. REFUTES if rho < 0 with p < 0.05 (diversity lower where recombination is higher) OR if |rho| < 0.1 with p > 0.05 and at least 100 windows (no detectable relationship). MIXED otherwise (0 <= rho < 0.2, or 0.01 <= p). INCONCLUSIVE (data-unavailable) if either file cannot be downloaded."; "0.85"^^xsd:double; , ; "supports"; "If a favourable mutation's sweep removes variation at linked neutral sites, and more so where recombination is weaker relative to selection, then across windows of a human chromosome nucleotide diversity should be positively correlated with the local recombination rate."; "fetch.py downloads the chr22 VCF (205.6 MB) and the genetic-map archive. analysis.py streams the VCF, keeps PASS biallelic records with VT=SNP and without MULTI_ALLELIC, sums 2p(1-p)*2n/(2n-1) from the INFO AF value over non-overlapping 200 kb windows from 16.0 Mb, divides by window length to get pi, and takes the recombination rate per window from the linearly interpolated HapMap map; windows with fewer than 200 SNPs are excluded. Spearman and Pearson correlations between pi and rate across windows are computed and the pre-registered rule applied."; "Pre-registered. Data: 1000 Genomes Project Phase 3 chromosome 22 genotype VCF (release 20130502, all 2504 samples) and the HapMap Phase II GRCh37 genetic map for chromosome 22. SNP filter: records with VT=SNP in INFO, biallelic (no MULTI_ALLELIC flag, single ALT), FILTER PASS. Windows: non-overlapping 200 kb windows starting at 16,000,000 bp (GRCh37) up to the last SNP. Diversity per window: pi = sum over SNPs of 2p(1-p) * 2n/(2n-1), with p the INFO AF value and 2n = 5008 chromosomes, divided by the window length (200,000 bp). Windows with fewer than 200 qualifying SNPs are excluded as unassessable (centromere-proximal or low-accessibility regions). Recombination rate per window: (map cM at window end minus map cM at window start) / 0.2 Mb, with cM linearly interpolated from the genetic map. SUPPORTS if Spearman rho(pi, recombination rate) across windows is >= 0.2 with two-sided p < 0.01."; "false"^^xsd:boolean . . a ; dc:description "allele frequencies (INFO AF) of biallelic PASS SNPs for per-window nucleotide diversity"; dc:license "open (Fort Lauderdale principles; IGSR terms of use)"; "Dataset: 1000 Genomes Project Phase 3 integrated variant call set, chromosome 22 (release 20130502, 2504 samples, GRCh37)"; prov:atLocation ; prov:wasDerivedFrom ; "sha256:a90c16c4ff2b3196476d506ae13cb3047fae8670163c7c932c4b0239aef3daf5" . a ; dc:description "cumulative genetic position (cM) to compute recombination rate per 200 kb window"; dc:license "public domain (NCBI FTP)"; "Dataset: HapMap Phase II LD-based recombination map lifted to GRCh37 (NCBI HapMap FTP, 2011-01 release)"; prov:atLocation ; prov:wasDerivedFrom ; "sha256:8287508135f43a4266bf34fae34988d69e5ebf356e450d7e1d8ce45a83e61468" . } sub:provenance { a prov:SoftwareAgent; "delphisci claim tester (claude-fable-5-1; scienceclaw-c4 (claims thread, ScienceClaw hack))"; prov:actedOnBehalfOf ; . a ; dc:identifier "claude-fable-5-1" . sub:assertion prov:wasAttributedTo ; prov:wasDerivedFrom ; prov:wasGeneratedBy sub:test . sub:plan prov:hadPlan . sub:test a prov:Activity; prov:qualifiedAssociation sub:plan; prov:wasAssociatedWith . } sub:pubinfo { this: dc:created "2026-11-08T16:24:31.886Z"^^xsd:dateTime; dc:creator ; dc:license ; npx:hasNanopubType ; npx:introduces ; "Claim test of maynardsmith-hitchhiking: supports, confidence 0.85"; . sub:sig npx:hasAlgorithm "RSA"; npx:hasPublicKey "MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEAyFHtPB6p0mCjDozxlOY9CmO3nBm7Te3jFbXyLmM+G1tGe47Da0jYIbhkl9Oo1ZjxmCa3LCwlEqK8gj6hEIcL4ahW30JXh9HycfKVk1bugkzMEV15tJdTzAU3sGMFnbNsn43xY2LFLy45tApkRm5byEiM7oRRrooIdwoQKnP4Wzq/bfAoJ9qvW+MGkelyOTd1jbSt+KfmT7xKmDfWzAHddUlWwMX2QJOLxDaffOteTop6ZRgPiNmPJKA/S62Gac9XtSYT3oDkZ6/nr5cxxNLpOyxTf5FPISiCe11xYO/unYjY+mwnOfA8yhJIyx1l0O9I0vpOpn+E5TvyHJV+oSTrvwIDAQAB"; npx:hasSignature "Sqf15r2TBURgGXdLwGzNkbtr59f2t2JmonB8AnaRebbyp8X5ZqBha+IUG2xKrAzjPgVVwEbr1uXfRCp8HMCMZjtXc94nG7mkHfPKYEahz/kkRXlb89WZTT1NhRbz9JMl4JRuh6iLG+E8flDj0CZx5jRz27SHlLOTWShkkecOYzrolz7slCpxR9wOXs26dFyKRQP63xaIpfWaCf4823qSZ/UpFtn7Tn8E7tKEe+Q1t3ouwVeuTD/5Thf+9gBN0Us5pPdv9Gwz4xuNKbTWSoviA8ogbLt2QrpNtqE9PqKyYAYCpsOTT4nQseUkjhZnFGT8eBLijoMUltyYoiydMZRiMg=="; npx:hasSignatureTarget this:; npx:signedBy . }