[ { "@id": "https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/provenance", "@graph": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1", "@type": [ "http://www.w3.org/ns/prov#SoftwareAgent" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "delphisci claim tester (claude-fable-5.1; cursor/claim-tests-thompson-batch-2216)" } ], "http://www.w3.org/ns/prov#actedOnBehalfOf": [ { "@id": "https://orcid.org/0009-0007-4948-9192" } ], "https://w3id.org/delphi/ontology/usesModel": [ { "@id": "https://w3id.org/delphi/resource/model/claude-fable-5-1" } ] }, { "@id": "https://w3id.org/delphi/resource/model/claude-fable-5-1", "http://purl.org/dc/terms/identifier": [ { "@value": "claude-fable-5.1" } ], "@type": [ "https://w3id.org/delphi/ontology/LanguageModel" ] }, { "@id": "https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/assertion", "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch16-13/result.json" } ], "http://www.w3.org/ns/prov#wasGeneratedBy": [ { "@id": "https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/test" } ] }, { "@id": "https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/test", "@type": [ "http://www.w3.org/ns/prov#Activity" ], "http://www.w3.org/ns/prov#qualifiedAssociation": [ { "@id": "https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/plan" } ], "http://www.w3.org/ns/prov#wasAssociatedWith": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1" } ] }, { "@id": "https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/plan", "http://www.w3.org/ns/prov#hadPlan": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/README.md" } ] } ] }, { "@id": "https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test", "http://purl.org/dc/terms/description": [ { "@value": "fetch.py downloads both Dryad version zips and records their SHA-256. analysis.py parses the IDAV landmark files, computes for each thoracic and lumbar vertebra the distance from the most distal spinous-process landmark to the centroid of the cranial centrum-face landmarks divided by the largest diameter of that face (h), averages h over T1-T4 (W), T10-T13 (P) and the last three lumbars, and forms WI = W/P and HI per specimen and then per species. Pinnipeds (n = 2 species) are compared with the 40 terrestrial carnivorans (otters and mink excluded from the reference set; sensitivity run includes them) by exact one-sided Mann-Whitney U tests and by position relative to the terrestrial quantiles. For the cetaceans, h = Lnp/Hc is computed for all 8722 measured vertebrae, WI = mean h of the first three thoracics / mean h of the last three thoracics per specimen, averaged per species, and compared with the terrestrial carnivoran WI distribution." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 1.023 withers index WI (mean of the two pinniped species); terrestrial carnivoran WI min 1.238, median 1.910 (n = 45 carnivoran species (951 vertebrae) incl. 2 pinnipeds; 74 cetacean species (204 specimens, 8722 vertebrae), exact one-sided Mann-Whitney U, pinnipeds < terrestrial: W p = 0.0023, WI p = 0.0012 (n = 2 vs 40; smallest attainable p = 0.0012)). Interpretation: Thompson's 'high arched vertebral spines over the withers' are read as a regional peak of tall neural spines in the anterior thoracic vertebrae, and the 'corresponding structures over the hind-limbs' as tall posterior lumbar (haunch) spines; 'disappeared' is read as absence of that peak relative to the posterior-thoracic trough and relative shortness compared with terrestrial relatives. Spine height is normalised by centrum height within each vertebra so that it is size-free. Pinnipeds are compared with terrestrial members of the same order (Carnivora), as the claim requires ('terrestrial relatives'). Cetaceans have no terrestrial comparator in the same dataset, so for them only the within-column profile (withers index) is compared with the terrestrial carnivoran reference distribution. Sirenians and the bird-pelvis part of the claim are not tested: no public tabular morphometric dataset covering them was identified before pre-registration; this is recorded as a caveat and the verdict is restricted to pinnipeds and cetaceans. In the landmark data the 'spine apex to centrum reference' distance is from the most distal spinous-process landmark to the centroid of the four cranial centrum-face landmarks (so it includes the neural arch), and centrum height is the largest diameter of that face; in the cetacean data it is the authors' neural-spine height (Lnp) over centrum height (Hc). Because the two definitions differ, absolute h values are not compared across datasets, only the within-column ratio WI." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of thompson1917-ch16-13: supports, confidence 0.7" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch16-13/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: dryad-3j9kd51ft-figueirido-2021-carnivoran-vertebrae, dryad-7dj6850-gillet-2019-cetacean-vertebrae" } ], "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. Because the claim says the spines have 'entirely disappeared' in 'all aquatic mammals', a single aquatic group retaining a terrestrial-grade withers refutes it. REFUTES if (A) any pinniped species has W >= the terrestrial carnivoran median W, or (B) at least 20% of cetacean species have WI >= the terrestrial carnivoran median WI (an anterior-thoracic peak of terrestrial proportions). If neither the supports nor the refutes conditions are met, the verdict is 'mixed'. If a required measurement (spine landmarks, Lnp or Hc) is missing from the files, that component is 'inconclusive / data-unavailable'." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Gillet et al. label 74 species where the paper reports 73 (one specimen label is spelled 'Feresa_attenuta'); species means were taken as labelled." }, { "@value": "No phylogenetic comparative model was fitted (two pinniped species cannot support one); the Mann-Whitney test treats species as independent." }, { "@value": "Only two pinniped species (one phocid, one otariid) are in the carnivoran dataset; sirenians are absent from both datasets, and the bird-pelvis half of the claim was not tested at all. The verdict therefore covers pinnipeds and cetaceans only, not Thompson's 'all aquatic mammals'." }, { "@value": "Pinniped anterior-thoracic spines are reduced (W 2.3-2.7 vs terrestrial 2.6-5.3) and the withers peak is absent (WI about 1.0), but the spines have not literally 'entirely disappeared'; Otaria byronia's W lies above the lowest terrestrial species (Martes foina)." }, { "@value": "Relative spine height from landmarks includes the neural arch and depends on where the authors placed the spinous-process landmarks; the cetacean values come from a different measurement protocol, so only the within-column ratio WI is compared across datasets." }, { "@value": "Semi-aquatic carnivorans (otters, mink) retain a terrestrial-grade withers index (1.6-1.7), consistent with Thompson's restriction to animals whose weight is carried by water, but they were excluded from the terrestrial reference set by a decision taken before analysis; including them does not change the result." }, { "@value": "The 'haunch' part is not discriminating in Carnivora: terrestrial carnivorans themselves show no posterior-lumbar spine peak (median HI 0.80 < 1), and pinniped HI falls inside the terrestrial range (p = 0.77). Thompson's haunch spines refer mainly to ungulates, for which no comparable public data were used." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Pre-registered. Per vertebra, relative spine height h = (neural spine apex to centrum reference distance) / cranial centrum height. Per species: W = mean h over T1-T4 ('withers'); P = mean h over the posterior thoracics T10-T13 (terrestrial trough region); WI = W/P ('withers index'); HI = mean h over the last three lumbars / P ('haunch index'). Test A (Carnivora landmark data, Figueirido et al. 2021): SUPPORTS-component if every pinniped species has W below the 25th percentile of terrestrial carnivoran W and one-sided Mann-Whitney U tests give p < 0.05 for pinnipeds < terrestrial on both W and WI. Test B (cetacean linear data, Gillet et al. 2019, h = Lnp/Hc; W over the first three thoracics, P over the last three thoracics, WI = W/P): SUPPORTS-component if the median cetacean WI <= 1 and at least 80% of cetacean species have WI below the minimum WI of the terrestrial carnivorans from Test A. Overall verdict 'supports' only if both components support." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Pre-registered. Because the claim says the spines have 'entirely disappeared' in 'all aquatic mammals', a single aquatic group retaining a terrestrial-grade withers refutes it. REFUTES if (A) any pinniped species has W >= the terrestrial carnivoran median W, or (B) at least 20% of cetacean species have WI >= the terrestrial carnivoran median WI (an anterior-thoracic peak of terrestrial proportions). If neither the supports nor the refutes conditions are met, the verdict is 'mixed'. If a required measurement (spine landmarks, Lnp or Hc) is missing from the files, that component is 'inconclusive / data-unavailable'." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.7", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "supports" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "If buoyancy has removed the tall arched neural spines over the withers and haunches, then secondarily aquatic mammals (pinnipeds, cetaceans) should show no anterior-thoracic ('withers') peak of relative neural-spine height along the thoracolumbar column, and their anterior-thoracic spines should be relatively shorter than those of terrestrial quadrupeds; the haunch (posterior lumbar) spines should likewise not be elevated." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "fetch.py downloads both Dryad version zips and records their SHA-256. analysis.py parses the IDAV landmark files, computes for each thoracic and lumbar vertebra the distance from the most distal spinous-process landmark to the centroid of the cranial centrum-face landmarks divided by the largest diameter of that face (h), averages h over T1-T4 (W), T10-T13 (P) and the last three lumbars, and forms WI = W/P and HI per specimen and then per species. Pinnipeds (n = 2 species) are compared with the 40 terrestrial carnivorans (otters and mink excluded from the reference set; sensitivity run includes them) by exact one-sided Mann-Whitney U tests and by position relative to the terrestrial quantiles. For the cetaceans, h = Lnp/Hc is computed for all 8722 measured vertebrae, WI = mean h of the first three thoracics / mean h of the last three thoracics per specimen, averaged per species, and compared with the terrestrial carnivoran WI distribution." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Pre-registered. Per vertebra, relative spine height h = (neural spine apex to centrum reference distance) / cranial centrum height. Per species: W = mean h over T1-T4 ('withers'); P = mean h over the posterior thoracics T10-T13 (terrestrial trough region); WI = W/P ('withers index'); HI = mean h over the last three lumbars / P ('haunch index'). Test A (Carnivora landmark data, Figueirido et al. 2021): SUPPORTS-component if every pinniped species has W below the 25th percentile of terrestrial carnivoran W and one-sided Mann-Whitney U tests give p < 0.05 for pinnipeds < terrestrial on both W and WI. Test B (cetacean linear data, Gillet et al. 2019, h = Lnp/Hc; W over the first three thoracics, P over the last three thoracics, WI = W/P): SUPPORTS-component if the median cetacean WI <= 1 and at least 80% of cetacean species have WI below the minimum WI of the terrestrial carnivorans from Test A. 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