https://w3id.org/np/RAE5WlgzBdPtfIlUGDvk0Vmw8foujDlac6EiLNzQ2kQhI
.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/RAE5WlgzBdPtfIlUGDvk0Vmw8foujDlac6EiLNzQ2kQhI/> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
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@prefix dc: <http://purl.org/dc/terms/> .
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sub:Head {
this: a np:Nanopublication;
np:hasAssertion sub:assertion;
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sub:assertion {
<https://w3id.org/delphi/resource/assessment/darwin1859-ch11-06--claim-test> a <https://w3id.org/delphi/ontology/Assessment>;
dc:description "For seven GBIF backbone classes and each of seven GBIF continents, one faceted occurrence search (coordinates present, no geospatial issue, fossil and living specimens excluded) returned record counts per genus, family (and species for the smaller classes). Europe and Asia were merged into Eurasia. Taxa with >= 20 records were scored as confined if >= 95% of records fell in one region, and the fraction of confined taxa was compared between genera and families within each class. For mammals, genus crown ages were computed as the MRCA age of sampled congeners in the Upham et al. 2019 DNA-only MCC tree, genus names were matched to GBIF genus keys, and crown age was correlated (Spearman, and partial Spearman controlling log sampled richness) with the number of regions holding >= 5% of the genus's records; single-region fractions were compared between youngest and oldest crown-age terciles.";
<http://www.w3.org/2000/01/rdf-schema#comment> "Measured: 0.6891557889582494 mean across classes of the fraction of assessable genera with >= 95% of records in one region (n = 18885). Interpretation: Darwin's 'region' is read as a continental biogeographic region (six regions, with Europe and Asia merged into Eurasia following Sclater's Palaearctic). 'Confined to a single region' is read with a 5% tolerance for misidentified, vagrant, introduced or mislabelled records. Sub-families and sections of genera are not available in the GBIF backbone and are not tested; the rank gradient is tested only between family and genus, with species reported as an extra. 'Most natural genera (species most closely related)' is read, following the assessors, as genera with the youngest crown age in a dated molecular phylogeny; this is a modern phylogenetic reinterpretation of a pre-evolutionary taxonomic notion. Only genera with >= 20 qualifying occurrence records are assessed, so that poorly recorded taxa do not appear confined merely through lack of records.";
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch11-06: mixed, confidence 0.7";
<http://www.w3.org/2000/01/rdf-schema#seeAlso> <https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch11-06/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: gbif-occurrence-search-facets, upham2019-mamphy-dnaonly-mcc-tree";
<https://w3id.org/delphi/ontology/assessmentType> "claim-test/0.1.0";
<https://w3id.org/delphi/ontology/dataKind> "biological";
<https://w3id.org/delphi/ontology/disconfirmingObservation> "Clause 1 fails if the confined fraction of genera is <= 0.50 in three or more of the seven classes, or genera are not more confined than families in three or more classes. Clause 2 fails if the partial Spearman correlation between crown age and number of regions is <= 0 or not significant at p < 0.05, or the youngest-tercile single-region fraction does not exceed the oldest-tercile fraction. Both clauses failing refutes the claim.";
<https://w3id.org/delphi/ontology/evidenceAgainst> "Clause 2 is a modern reinterpretation: 'most natural genera' was read as young crown age in a dated molecular tree. Crown age depends on which species were sampled (DNA-only tree) and on taxonomic lumping/splitting, and only 577 of 1890 assessable mammal genera had >= 2 sampled species. The negative partial correlation (older genera occupy fewer regions, controlling for richness) is significant but small.",
"GBIF 'Reptilia' (classKey 358) is a pro-parte synonym with no occurrences in the current backbone, so the pre-registered reptile class was run as Squamata (classKey 11592253), which holds most reptile genera.",
"GBIF continents are a coarse proxy for Darwin's biogeographic regions; merging Europe and Asia follows the Palaearctic but leaves Wallace's line and the Nearctic/Neotropical boundary at the continental edge.",
"Genus-level 'assessable' counts include extinct genera that have non-fossil basis-of-record entries and genera whose records are introductions or captives not flagged as LIVING_SPECIMEN; both bias against confinement, so clause 1 is conservative.",
"Recording effort is very uneven (Europe and North America dominate); the >= 20 record floor reduces but does not remove under-recording of tropical taxa, which could make some truly widespread genera look confined.",
"Sub-families and sections of genera, which Darwin names explicitly, are not represented in the GBIF backbone and were not tested; the family-to-genus-to-species gradient is consistent with his rank ordering.";
<https://w3id.org/delphi/ontology/expectedObservation> "Clause 1 (regional confinement by rank): in each of the analysed classes (Mammalia, Aves, Amphibia, Reptilia, Magnoliopsida, Liliopsida, Pinopsida; GBIF backbone), the fraction of assessable genera that are confined to one region (>= 95% of their continent-assigned, non-fossil, non-captive occurrence records in one of six regions: Africa, Eurasia, North America, South America, Oceania, Antarctica) is > 0.50 in at least five of the seven classes, and in at least five of seven classes the confined fraction for genera exceeds the confined fraction for families. Clause 2 (natural genera are local, mammals): the Spearman partial correlation between genus crown age (MRCA age of the sampled congeneric species in the Upham et al. 2019 DNA-only MCC tree) and the number of regions holding >= 5% of the genus's records, controlling for log(number of sampled species in the genus), is positive with p < 0.05, AND the single-region fraction among genera in the youngest crown-age tercile exceeds that in the oldest tercile. The claim is 'supports' if both clauses pass; 'mixed' if exactly one passes; 'refutes' if both fail.";
<https://w3id.org/delphi/ontology/failCriterion> "Clause 1 fails if the confined fraction of genera is <= 0.50 in three or more of the seven classes, or genera are not more confined than families in three or more classes. Clause 2 fails if the partial Spearman correlation between crown age and number of regions is <= 0 or not significant at p < 0.05, or the youngest-tercile single-region fraction does not exceed the oldest-tercile fraction. Both clauses failing refutes the claim.";
<https://w3id.org/delphi/ontology/hasConfidence> "0.7"^^xsd:double;
<https://w3id.org/delphi/ontology/hasEvidence> <https://w3id.org/delphi/resource/evidence/darwin1859-ch11-06--claim-test--dataset-1>,
<https://w3id.org/delphi/resource/evidence/darwin1859-ch11-06--claim-test--dataset-2>,
<https://w3id.org/delphi/resource/evidence/darwin1859-ch11-06--claim-test--dataset-3>;
<https://w3id.org/delphi/ontology/hasVerdict> "mixed";
<https://w3id.org/delphi/ontology/hypothesis> "Across well-recorded classes of animals and plants, most genera (and a larger share of genera than of families) have essentially all of their modern occurrence records within a single continental region; and among mammal genera, those whose species are most closely related (youngest crown age in a dated phylogeny) occupy fewer regions and are more often confined to a single region than genera whose species are more distantly related.";
<https://w3id.org/delphi/ontology/inferenceMethod> "For seven GBIF backbone classes and each of seven GBIF continents, one faceted occurrence search (coordinates present, no geospatial issue, fossil and living specimens excluded) returned record counts per genus, family (and species for the smaller classes). Europe and Asia were merged into Eurasia. Taxa with >= 20 records were scored as confined if >= 95% of records fell in one region, and the fraction of confined taxa was compared between genera and families within each class. For mammals, genus crown ages were computed as the MRCA age of sampled congeners in the Upham et al. 2019 DNA-only MCC tree, genus names were matched to GBIF genus keys, and crown age was correlated (Spearman, and partial Spearman controlling log sampled richness) with the number of regions holding >= 5% of the genus's records; single-region fractions were compared between youngest and oldest crown-age terciles.";
<https://w3id.org/delphi/ontology/passCriterion> "Clause 1 (regional confinement by rank): in each of the analysed classes (Mammalia, Aves, Amphibia, Reptilia, Magnoliopsida, Liliopsida, Pinopsida; GBIF backbone), the fraction of assessable genera that are confined to one region (>= 95% of their continent-assigned, non-fossil, non-captive occurrence records in one of six regions: Africa, Eurasia, North America, South America, Oceania, Antarctica) is > 0.50 in at least five of the seven classes, and in at least five of seven classes the confined fraction for genera exceeds the confined fraction for families. Clause 2 (natural genera are local, mammals): the Spearman partial correlation between genus crown age (MRCA age of the sampled congeneric species in the Upham et al. 2019 DNA-only MCC tree) and the number of regions holding >= 5% of the genus's records, controlling for log(number of sampled species in the genus), is positive with p < 0.05, AND the single-region fraction among genera in the youngest crown-age tercile exceeds that in the oldest tercile. The claim is 'supports' if both clauses pass; 'mixed' if exactly one passes; 'refutes' if both fail.";
<https://w3id.org/delphi/ontology/preregistered> "false"^^xsd:boolean .
<https://w3id.org/delphi/resource/claim/darwin1859-ch11-06> <https://w3id.org/delphi/ontology/hasAssessment>
<https://w3id.org/delphi/resource/assessment/darwin1859-ch11-06--claim-test> .
<https://w3id.org/delphi/resource/evidence/darwin1859-ch11-06--claim-test--dataset-1>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "occurrence counts per taxon per continent (clause 1 and regions for clause 2)";
dc:license "mixed per publishing dataset (CC0, CC BY, CC BY-NC)";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: GBIF occurrence search API, faceted counts by genus/family/species key per continent";
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a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "map GBIF mammal genus keys to canonical genus names";
dc:license "CC BY 4.0";
<http://www.w3.org/2000/01/rdf-schema#comment> "Location (not a URL): https://api.gbif.org/v1/species/{genusKey}";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: GBIF Backbone Taxonomy species API (genus names for mammal genus keys)";
prov:wasDerivedFrom <https://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c>;
<https://w3id.org/delphi/ontology/hasChecksum> "sha256:ae42f4b0b84bea10e2cadf57c74e07284250b8112b81d898f36c2db264cea618" .
<https://w3id.org/delphi/resource/evidence/darwin1859-ch11-06--claim-test--dataset-3>
a <https://w3id.org/delphi/ontology/EvidenceItem>;
dc:description "genus crown ages (MRCA age of sampled congeners) for clause 2";
dc:license "CC BY 4.0";
<http://www.w3.org/2000/01/rdf-schema#label> "Dataset: Upham, Esselstyn & Jetz (2019) mammal phylogeny, DNA-only 4098-species node-dated MCC tree (NDexp, topoFree)";
prov:atLocation <https://raw.githubusercontent.com/n8upham/MamPhy_v1/master/_DATA/MamPhy_fullPosterior_BDvr_DNAonly_4098sp_topoFree_NDexp_MCC_v2_target.tre>;
prov:wasDerivedFrom <https://github.com/n8upham/MamPhy_v1>;
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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; cursor/claim-tests-darwin-batch-0e75)";
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> .
<https://w3id.org/delphi/resource/model/claude-fable-5-1> a <https://w3id.org/delphi/ontology/LanguageModel>;
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/darwin-origin/darwin1859-ch11-06/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;
prov:qualifiedAssociation sub:plan;
prov:wasAssociatedWith <https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1> .
}
sub:pubinfo {
this: dc:created "2026-11-08T16:24:31.847Z"^^xsd:dateTime;
dc:creator <https://orcid.org/0009-0007-4948-9192>;
dc:license <https://creativecommons.org/licenses/by/4.0/>;
npx:hasNanopubType <https://w3id.org/delphi/ontology/Assessment>;
npx:introduces <https://w3id.org/delphi/resource/assessment/darwin1859-ch11-06--claim-test>;
<http://www.w3.org/2000/01/rdf-schema#label> "Claim test of darwin1859-ch11-06: mixed, confidence 0.7";
<https://w3id.org/delphi/ontology/domain> <https://w3id.org/delphi/resource/domain/darwin-origin-1859> .
sub:sig npx:hasAlgorithm "RSA";
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npx:hasSignatureTarget this:;
npx:signedBy <https://orcid.org/0009-0007-4948-9192> .
}