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Spearman and Pearson correlations between pi and rate across windows are computed and the pre-registered rule applied." } g_iri { prefix_id: 2 name_id: 4 } } } rows { prefix { value: "https://w3id.org/delphi/ontology/" } } rows { name { value: "Assessment" } } rows { quad { p_iri { prefix_id: 4 name_id: 10 } o_iri { prefix_id: 10 name_id: 14 } } } rows { prefix { value: "http://www.w3.org/2000/01/rdf-schema#" } } rows { name { value: "comment" } } rows { quad { p_iri { prefix_id: 11 } o_literal { lex: "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." } } } rows { name { value: "label" } } rows { quad { p_iri { } o_literal { lex: "Claim test of maynardsmith-hitchhiking: supports, confidence 0.85" } } } rows { name { value: "seeAlso" } } rows { prefix { value: "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/math-bio-claims/maynardsmith-hitchhiking/" } } rows { name { value: "result.json" } } rows { quad { p_iri { } o_iri { prefix_id: 12 } } } rows { name { value: "wasAttributedTo" } } rows { prefix { value: "https://w3id.org/delphi/resource/agent/" } } rows { name { value: "delphisci-claim-tester-claude-fable-5-1" } } rows { quad { p_iri { prefix_id: 5 } o_iri { prefix_id: 13 } } } rows { name { value: "admissibleDatasets" } } rows { quad { p_iri { prefix_id: 10 } o_literal { lex: "Planned datasets: 1000genomes-phase3-chr22-genotypes-20130502, hapmap-phaseII-genetic-map-grch37" } } } rows { name { value: "assessmentType" } } rows { quad { p_iri { } o_literal { lex: "claim-test/0.1.0" } } } rows { name { value: "dataKind" } } rows { quad { p_iri { } o_literal { lex: "biological" } } } rows { name { value: "disconfirmingObservation" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "evidenceAgainst" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { quad { o_literal { lex: "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." } } } rows { quad { o_literal { lex: "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." } } } rows { quad { o_literal { lex: "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)." } } } rows { name { value: "expectedObservation" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "failCriterion" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "hasConfidence" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#double" } } rows { quad { p_iri { } o_literal { lex: "0.85" datatype: 1 } } } rows { name { value: "hasEvidence" } } rows { prefix { value: "https://w3id.org/delphi/resource/evidence/" } } rows { name { value: "maynardsmith-hitchhiking--claim-test--dataset-1" } } rows { quad { p_iri { } o_iri { prefix_id: 14 } } } rows { name { value: "maynardsmith-hitchhiking--claim-test--dataset-2" } } rows { quad { o_iri { } } } rows { name { value: "hasVerdict" } } rows { quad { p_iri { prefix_id: 10 } o_literal { lex: "supports" } } } rows { name { value: "hypothesis" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "inferenceMethod" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "passCriterion" } } rows { quad { p_iri { } o_literal { lex: "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." } } } rows { name { value: "preregistered" } } rows { datatype { value: "http://www.w3.org/2001/XMLSchema#boolean" } } rows { quad { p_iri { } o_literal { lex: "false" datatype: 2 } } } rows { prefix { value: "https://w3id.org/delphi/resource/claim/" } } rows { name { value: "maynardsmith-hitchhiking" } } rows { name { value: "hasAssessment" } } rows { quad { s_iri { prefix_id: 15 } p_iri { prefix_id: 10 } o_iri { prefix_id: 9 name_id: 12 } } } rows { quad { s_iri { prefix_id: 14 name_id: 30 } p_iri { prefix_id: 7 name_id: 13 } o_literal { lex: "allele frequencies (INFO AF) of biallelic PASS SNPs for per-window nucleotide diversity" } } } rows { name { value: "license" } } rows { quad { p_iri { name_id: 39 } o_literal { lex: "open (Fort Lauderdale principles; IGSR terms of use)" } } } rows { name { value: "EvidenceItem" } } rows { quad { p_iri { prefix_id: 4 name_id: 10 } o_iri { prefix_id: 10 name_id: 40 } } } rows { quad { p_iri { prefix_id: 11 name_id: 16 } o_literal { lex: "Dataset: 1000 Genomes Project Phase 3 integrated variant call set, chromosome 22 (release 20130502, 2504 samples, GRCh37)" } } } rows { name { value: "atLocation" } } rows { prefix { value: "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" } } rows { name { value: "ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz" } } rows { quad { p_iri { prefix_id: 5 name_id: 41 } o_iri { prefix_id: 16 } } } rows { name { value: "wasDerivedFrom" } } rows { prefix { id: 6 value: "https://www.internationalgenome.org/category/phase-3/" } } rows { quad { p_iri { prefix_id: 5 } o_iri { prefix_id: 6 name_id: 2 } } } rows { name { value: "hasChecksum" } } rows { quad { p_iri { prefix_id: 10 name_id: 44 } o_literal { lex: "sha256:a90c16c4ff2b3196476d506ae13cb3047fae8670163c7c932c4b0239aef3daf5" } } } rows { quad { s_iri { prefix_id: 14 name_id: 31 } p_iri { prefix_id: 7 name_id: 13 } o_literal { lex: "cumulative genetic position (cM) to compute recombination rate per 200 kb window" } } } rows { quad { p_iri { name_id: 39 } o_literal { lex: "public domain (NCBI FTP)" } } } rows { quad { p_iri { prefix_id: 4 name_id: 10 } o_iri { prefix_id: 10 name_id: 40 } } } rows { quad { p_iri { prefix_id: 11 name_id: 16 } o_literal { lex: "Dataset: HapMap Phase II LD-based recombination map lifted to GRCh37 (NCBI HapMap FTP, 2011-01 release)" } } } rows { prefix { id: 8 value: "https://ftp.ncbi.nlm.nih.gov/hapmap/recombination/2011-01_phaseII_B37/" } } rows { name { value: "genetic_map_HapMapII_GRCh37.tar.gz" } } rows { quad { p_iri { prefix_id: 5 name_id: 41 } o_iri { prefix_id: 8 name_id: 45 } } } rows { quad { p_iri { prefix_id: 5 name_id: 43 } o_iri { prefix_id: 8 name_id: 2 } } } rows { quad { p_iri { prefix_id: 10 name_id: 44 } o_literal { lex: "sha256:8287508135f43a4266bf34fae34988d69e5ebf356e450d7e1d8ce45a83e61468" } } } rows { name { value: "SoftwareAgent" } } rows { quad { s_iri { prefix_id: 13 name_id: 20 } p_iri { prefix_id: 4 name_id: 10 } o_iri { prefix_id: 5 name_id: 46 } g_iri { prefix_id: 2 name_id: 7 } } } rows { quad { p_iri { prefix_id: 11 name_id: 16 } o_literal { lex: "delphisci claim tester (claude-fable-5-1; 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