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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." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "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": [ { "@value": "Claim test of maynardsmith-hitchhiking: supports, confidence 0.85" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/math-bio-claims/maynardsmith-hitchhiking/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "Planned datasets: 1000genomes-phase3-chr22-genotypes-20130502, hapmap-phaseII-genetic-map-grch37" } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "biological" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "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": [ { "@value": "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." }, { "@value": "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." }, { "@value": "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." }, { "@value": "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": [ { "@value": "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": [ { "@value": "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": [ { "@value": "0.85", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/maynardsmith-hitchhiking--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/maynardsmith-hitchhiking--claim-test--dataset-2" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "supports" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "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": [ { "@value": "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. 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