https://w3id.org/np/RAiK7CHf1u26RQ4igfhsHhVFjy3gVD9_HqHe_cXDhq4oE
.trig | .trig.txt | .jelly | .jelly.txt | .jsonld | .jsonld.txt | .nq | .nq.txt | .xml | .xml.txt
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@prefix sub: <https://w3id.org/np/RAiK7CHf1u26RQ4igfhsHhVFjy3gVD9_HqHe_cXDhq4oE/> .
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sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
np:hasProvenance sub:provenance;
np:hasPublicationInfo sub:pubinfo .
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sub:assertion {
<https://w3id.org/delphi/resource/assessment/maynardsmith-hitchhiking--claim-test>
a <https://w3id.org/delphi/ontology/Assessment>;
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.";
<http://www.w3.org/2000/01/rdf-schema#comment> "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.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of maynardsmith-hitchhiking: supports, confidence 0.85";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/math-bio-claims/maynardsmith-hitchhiking/result.json>;
prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1>;
<https://w3id.org/delphi/ontology/admissibleDatasets> "Planned datasets: 1000genomes-phase3-chr22-genotypes-20130502, hapmap-phaseII-genetic-map-grch37";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "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.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "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).";
<https://w3id.org/delphi/ontology/expectedObservation> "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.";
<https://w3id.org/delphi/ontology/failCriterion> "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.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.85"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/maynardsmith-hitchhiking--claim-test--dataset-1>,
<https://w3id.org/delphi/resource/evidence/maynardsmith-hitchhiking--claim-test--dataset-2>;
<https://w3id.org/delphi/ontology/hasVerdict> "supports";
<https://w3id.org/delphi/ontology/hypothesis> "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.";
<https://w3id.org/delphi/ontology/inferenceMethod> "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.";
<https://w3id.org/delphi/ontology/passCriterion> "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.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
<https://w3id.org/delphi/resource/claim/maynardsmith-hitchhiking> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/maynardsmith-hitchhiking--claim-test> .
<https://w3id.org/delphi/resource/evidence/maynardsmith-hitchhiking--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
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)";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: 1000 Genomes Project Phase 3 integrated variant call set, chromosome 22 (release 20130502, 2504 samples, GRCh37)";
prov:atLocation <https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz>;
prov:wasDerivedFrom <https://www.internationalgenome.org/category/phase-3/>;
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<https://w3id.org/delphi/resource/evidence/maynardsmith-hitchhiking--claim-test--dataset-2>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "cumulative genetic position (cM) to compute recombination rate per 200 kb window";
dc:license "public domain (NCBI FTP)";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: HapMap Phase II LD-based recombination map lifted to GRCh37 (NCBI HapMap FTP, 2011-01 release)";
prov:atLocation <https://ftp.ncbi.nlm.nih.gov/hapmap/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz>;
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sub:provenance {
<https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1> a
prov:SoftwareAgent;
<http://www.w3.org/2000/01/rdf-schema#label> "delphisci claim tester (claude-fable-5-1; scienceclaw-c4 (claims thread, ScienceClaw hack))";
prov:actedOnBehalfOf <https://orcid.org/0009-0007-4948-9192>;
<https://w3id.org/delphi/ontology/usesModel> <https://w3id.org/delphi/resource/model/claude-fable-5-1> .
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dc:identifier "claude-fable-5-1" .
sub:assertion prov:wasAttributedTo <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1>;
prov:wasDerivedFrom <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/math-bio-claims/maynardsmith-hitchhiking/result.json>;
prov:wasGeneratedBy sub:test .
sub:plan prov:hadPlan <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md> .
sub:test a prov:Activity;
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prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1> .
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sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.886Z"^^xsd:dateTime;
dc:creator <https://orcid.org/0009-0007-4948-9192>;
dc:license <https://creativecommons.org/licenses/by/4.0/>;
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npx:introduces <https://w3id.org/delphi/resource/assessment/maynardsmith-hitchhiking--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of maynardsmith-hitchhiking: supports, confidence 0.85";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/math-bio-claims> .
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