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The two youngest stages in the marine table were dropped from both. Foote per-capita origination and extinction were computed where X_bt >= 5 and each environment has at least 20 occurrences. On stages present in both, the difference in rates was regressed on the difference in log10 occurrence counts. The verdict uses the intercept. No subsample was taken." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 0.043789 sampling-controlled intercept of freshwater minus marine origination rate (per genus per Myr) (n = 72, origination intercept 0.043789 (one-sided p for <0 0.9911); extinction intercept 0.047047 (one-sided p for <0 0.9998)). Interpretation: Darwin's 'freshwater basins' are the PBDB environments lacustrine and fluvial together. Marine is the comparison he names. Terrestrial is in the claim's scope sentence but is not the contrast this test scores. 'New forms have arisen more slowly' is the Foote per-capita origination rate; 'old forms have been exterminated more slowly' is the Foote per-capita extinction rate. The small area of basins, the severity of competition, and the survival of ancient anomalous forms are not measured. Living-lineage age is not used. A lower fossil rate can be produced by poor preservation, which is why the intercept is taken after the sampling difference rather than from the raw rates." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of darwin1859-ch04-16: refutes, confidence 0.5" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch04-16/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "A public fossil occurrence compilation that can be filtered to freshwater (lacustrine or fluvial) versus marine and that returns boundary-crosser counts by stage. Extant-only phylogenies are not substituted. Terrestrial occurrences are not part of this contrast." } ], "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": "Both intercepts are positive, each with one-sided p < 0.05, so freshwater genera originate and go extinct faster than marine genera after the sampling difference." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Foote rates still depend on preservation. The intercept removes the linear association with the log occurrence-count difference and nothing else." }, { "@value": "Freshwater is lacustrine plus fluvial. Brackish, terrestrial and other environments are not in the contrast." }, { "@value": "Genera are not Darwin's varieties, and the fossil record of fresh water is the thinner of the two." }, { "@value": "The small area of basins, the severity of competition, and the presence of ancient anomalous forms were not measured." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "On paired stages, the sampling-controlled intercept of (freshwater rate minus marine rate) is negative for both origination and extinction." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered. REFUTES if both intercepts are positive and the one-sided p-value for intercept > 0 is < 0.05 (freshwater faster for both origination and extinction). Any other completed comparison is mixed. Inconclusive if either diversity call fails, if the freshwater envtype is rejected (the two freshwater environments are not added as separate tables), or if fewer than 20 stages meet the pair rule (underpowered)." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.5", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch04-16--claim-test--dataset-1" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "refutes" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "Per-capita origination and per-capita extinction of animal genera are both lower in freshwater than in the sea, stage by stage, after the difference in sampling is accounted for." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Paired stages, Foote per-capita rates, OLS intercept of the rate difference on the log10 occurrence-count difference. One-sided p < 0.05. Stages need X_bt >= 5 and at least 20 occurrences in each environment. The two youngest stages are dropped." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered. Two PBDB occs/diversity tables, Animalia, genera, stage resolution: envtype=marine and envtype=lacustrine,fluvial. Foote rates p = ln((X_bt+X_Ft)/X_bt)/dt and q = ln((X_bt+X_bL)/X_bt)/dt. Drop the two youngest marine stages from both tables. A stage is paired only if both environments have X_bt >= 5, duration > 0 and at least 20 occurrences. Sampling control: for each rate, regress the paired difference (freshwater minus marine) on the paired difference in log10 occurrence count, and test the intercept. SUPPORTS if both intercepts are negative and the one-sided p-value for intercept < 0 is < 0.05, with at least 20 paired stages. No subsample and no terrestrial comparison." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch04-16--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "marine and freshwater (lacustrine, fluvial) genus boundary-crosser counts by stage" } ], "http://purl.org/dc/terms/license": [ { "@value": "" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: Paleobiology Database occs/diversity by environment" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": "https://paleobiodb.org/data1.2/occs/diversity.json?base_name=Animalia&interval=Phanerozoic&count=genera&time_reso=stage&vocab=pbdb&envtype=lacustrine%2Cfluvial" }, { "@id": "https://paleobiodb.org/data1.2/occs/diversity.json?base_name=Animalia&interval=Phanerozoic&count=genera&time_reso=stage&vocab=pbdb&envtype=marine" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://paleobiodb.org/" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:68ba1fa914505f7f29bdb826cb825c8f9c7da0525fc7c8c271aaeaeb7b5fa014" }, { "@value": "sha256:8bcc154a5c40eae6407a1ca46c2a3238169bb2dc70eadb876dd63fdd489b309d" } ] }, { "@id": "https://w3id.org/delphi/resource/claim/darwin1859-ch04-16", "https://w3id.org/delphi/ontology/hasAssessment": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch04-16--claim-test" } ] } ] } ]