https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs/Head https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs/assertion https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs/provenance https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs/pubinfo https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs/assertion https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test http://purl.org/dc/terms/description fetch.py downloads combined_data.tsv at the pinned commit. analysis.py keeps Animalia rows with a diversity value > 0 and a log10_popsize value (one row per species), drops the 13 class-Aves species (held out, never fitted), and on the remaining species computes Spearman rho between log10 diversity and log10 census size and an ordinary-least-squares regression of log10 diversity on log10 census size with a t-based 95% confidence interval on the slope. The decision rule is the pre-registered one. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.10731485075894663 OLS slope of log10(pi) on log10(census N); the law with Ne proportional to N predicts about 1 (n = 160 non-bird metazoan species (diversity sources: {'Leffler et al.': 90, 'Romiguier et al.': 58, 'Corbett-Detig et al.': 12}), 95% CI [0.078, 0.137]; SE 0.0150). Interpretation: The claim is about effective population size Ne. Independent Ne estimates do not exist for most species, so census size N is used as the proxy, which is how Lewontin (1974) and Buffalo (2021) framed the paradox of variation. Mutation rates per site per generation vary by roughly an order of magnitude across metazoa and are not available per species here, so they are not included; a slope far below 1 therefore means that Ne is decoupled from N (by linked selection, demography or variation in mu), not that the within-model theorem is wrong. This is a test of the claim as the assessment proposed it ('regress genome-wide neutral diversity on estimates of Ne*mu across species'), with N standing in for Ne*mu. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of kimura-heterozygosity: refutes, confidence 0.9 https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/math-bio-claims/kimura-heterozygosity/result.json https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1 https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: buffalo2021-paradox-variation-combined-data, holdout: class Aves rows excluded from fitting (see holdout/README.md) https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Pre-registered. REFUTES if the 95% confidence interval of the slope lies entirely below 0.25 (diversity rises less than a quarter as fast as census size on a log scale, so the law with N as the proxy for Ne is quantitatively wrong by orders of magnitude across the range of N: the Lewontin's-paradox pattern) OR rho <= 0. MIXED otherwise. INCONCLUSIVE (underpowered) if fewer than 50 species qualify; INCONCLUSIVE (data-unavailable) if the file cannot be downloaded. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Census size stands in for effective size and per-site mutation rate is not included, so the refutation is of the law as operationalized (diversity should track census size), which is exactly Lewontin's paradox: diversity does rise with N (rho about 0.5, p < 1e-10) but roughly ten times too slowly on a log scale, across 12 orders of magnitude of N. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Census sizes are model-based estimates (species range times a body-size-predicted density) with large uncertainty; measurement error in N attenuates the slope, but not by the factor of ten needed to rescue the law (Buffalo 2021 reaches the same conclusion with error-in-variables models). https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Class Aves (13 species) was excluded before fitting at the holdout thread's request and can be scored later with 'analysis.py --exam'. The first run of the script, before the gate was added, printed the birds' mean residual once; it was not used to change anything. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Diversity estimates mix synonymous, non-coding and genome-wide measures from three collations, and are averaged where several entries exist for a species. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Post-hoc discriminating-power check (perturbation.py, added 2026-10-31 after the result; simulation, not observation): with the observed census sizes and residual scatter, the pre-registered rule returns 'supports' in 100% of 2000 simulated datasets when the true slope is 1.0 or 0.75 and in 97.6% at 0.5, 'mixed' in 97.6% at 0.25, and 'refutes' in 100% at slope 0; the observed slope of 0.107 returns 'refutes'. The refutation is therefore not a failure of test sensitivity. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/evidenceAgainst This is a cross-species pattern; it does not test the within-model derivation H = theta/(1+theta), which is a theorem. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/expectedObservation Pre-registered. Data: Buffalo (2021) combined_data.tsv from github.com/vsbuffalo/paradox_variation (commit b8f91d5, 2021-09-27), metazoan species (kingdom == Animalia) with a non-missing diversity value (pairwise nucleotide diversity, column 'diversity') and a non-missing census-size estimate (column 'log10_popsize', the posterior mean of log10 census size from the author's range x density model; if the file carries another census-size point estimate instead, the column actually used is recorded in 'method'). One row per species. SUPPORTS if Spearman rho(log10 pi, log10 N) > 0.5 with p < 0.001 AND the ordinary-least-squares slope of log10 pi on log10 N has a point estimate >= 0.3 with a 95% confidence interval that includes some value >= 0.5 (diversity rises at least about a third as fast as census size on a log scale, i.e. within a factor of about 3 of the law's slope of 1). AMENDMENT (2026-10-31, before any data were downloaded, at the request of the holdout thread): species of class Aves are excluded from the primary analysis and from all criteria above; bird rows are held out and only reported separately, unfitted, as a holdout check. The taxonomic class is taken from the file's own taxonomy columns. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered. REFUTES if the 95% confidence interval of the slope lies entirely below 0.25 (diversity rises less than a quarter as fast as census size on a log scale, so the law with N as the proxy for Ne is quantitatively wrong by orders of magnitude across the range of N: the Lewontin's-paradox pattern) OR rho <= 0. MIXED otherwise. INCONCLUSIVE (underpowered) if fewer than 50 species qualify; INCONCLUSIVE (data-unavailable) if the file cannot be downloaded. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.9 https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/kimura-heterozygosity--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/hasVerdict refutes https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/hypothesis If neutral equilibrium heterozygosity H = theta/(1+theta) with theta = 4*Ne*mu holds and effective size scales with census size across species, then genome-wide nucleotide diversity (pi, the per-site heterozygosity) across metazoan species rises with census population size N: for pi << 1, H is approximately 4*Ne*mu, so log10(pi) should increase with log10(N) with a slope near 1 when mu and Ne/N are comparable across species, and the rank correlation between pi and N should be strongly positive. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/inferenceMethod fetch.py downloads combined_data.tsv at the pinned commit. analysis.py keeps Animalia rows with a diversity value > 0 and a log10_popsize value (one row per species), drops the 13 class-Aves species (held out, never fitted), and on the remaining species computes Spearman rho between log10 diversity and log10 census size and an ordinary-least-squares regression of log10 diversity on log10 census size with a t-based 95% confidence interval on the slope. The decision rule is the pre-registered one. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered. Data: Buffalo (2021) combined_data.tsv from github.com/vsbuffalo/paradox_variation (commit b8f91d5, 2021-09-27), metazoan species (kingdom == Animalia) with a non-missing diversity value (pairwise nucleotide diversity, column 'diversity') and a non-missing census-size estimate (column 'log10_popsize', the posterior mean of log10 census size from the author's range x density model; if the file carries another census-size point estimate instead, the column actually used is recorded in 'method'). One row per species. SUPPORTS if Spearman rho(log10 pi, log10 N) > 0.5 with p < 0.001 AND the ordinary-least-squares slope of log10 pi on log10 N has a point estimate >= 0.3 with a 95% confidence interval that includes some value >= 0.5 (diversity rises at least about a third as fast as census size on a log scale, i.e. within a factor of about 3 of the law's slope of 1). AMENDMENT (2026-10-31, before any data were downloaded, at the request of the holdout thread): species of class Aves are excluded from the primary analysis and from all criteria above; bird rows are held out and only reported separately, unfitted, as a holdout check. The taxonomic class is taken from the file's own taxonomy columns. https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/kimura-heterozygosity https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/kimura-heterozygosity--claim-test https://w3id.org/delphi/resource/evidence/kimura-heterozygosity--claim-test--dataset-1 http://purl.org/dc/terms/description per-species diversity (column 'diversity') and log10 census size (column 'log10_popsize', posterior mean) https://w3id.org/delphi/resource/evidence/kimura-heterozygosity--claim-test--dataset-1 http://purl.org/dc/terms/license not stated in the repository; the article is CC BY 4.0 https://w3id.org/delphi/resource/evidence/kimura-heterozygosity--claim-test--dataset-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/kimura-heterozygosity--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Buffalo (2021) 'Why do species get a thin slice of pi?' combined species table: pairwise nucleotide diversity (collated from Leffler et al. 2012, Romiguier et al. 2014, Corbett-Detig et al. 2015) and census population size estimates (range x density model) for 300 metazoan species https://w3id.org/delphi/resource/evidence/kimura-heterozygosity--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://raw.githubusercontent.com/vsbuffalo/paradox_variation/b8f91d5c34675733db8cae8dcab625dcbb55c30a/data/combined_data.tsv https://w3id.org/delphi/resource/evidence/kimura-heterozygosity--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://github.com/vsbuffalo/paradox_variation https://w3id.org/delphi/resource/evidence/kimura-heterozygosity--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:df559451dad94b53ba8675e09811708107a57eeb6ffe8f72b944bcbbf3a1f2eb https://w3id.org/np/RA0HqdwTZeHek4KcUZwTg7fNbYKzWvKqyGNWSgkH57YVs/provenance https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.w3.org/ns/prov#SoftwareAgent https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1 http://www.w3.org/2000/01/rdf-schema#label delphisci claim tester (claude-fable-5-1; 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