https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/Head https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/assertion https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/provenance https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/pubinfo https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/assertion https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test http://purl.org/dc/terms/description 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/resource/assessment/thompson1917-ch16-13--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/thompson1917-ch16-13--claim-test http://www.w3.org/2000/01/rdf-schema#comment 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. https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of thompson1917-ch16-13: supports, confidence 0.7 https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch16-13/result.json https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--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/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: dryad-3j9kd51ft-figueirido-2021-carnivoran-vertebrae, dryad-7dj6850-gillet-2019-cetacean-vertebrae https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation 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/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Gillet et al. label 74 species where the paper reports 73 (one specimen label is spelled 'Feresa_attenuta'); species means were taken as labelled. https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/evidenceAgainst No phylogenetic comparative model was fitted (two pinniped species cannot support one); the Mann-Whitney test treats species as independent. https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/evidenceAgainst 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'. https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/evidenceAgainst 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). https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/evidenceAgainst 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. https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/evidenceAgainst 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. https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/evidenceAgainst 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/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/expectedObservation 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/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/failCriterion 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/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.7 https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/hypothesis 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/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/inferenceMethod 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/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/passCriterion 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/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/thompson1917-ch16-13 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/thompson1917-ch16-13--claim-test https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-1 http://purl.org/dc/terms/description 3D landmarks on every thoracic and lumbar vertebra of 45 carnivoran species (after merging Felis_concolor/Puma_concolor labels), including the pinnipeds Phoca vitulina and Otaria byronia; source of relative neural-spine heights for Test A and of the terrestrial reference distribution https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-1 http://purl.org/dc/terms/license CC0 1.0 https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--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/thompson1917-ch16-13--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Data from: Serial disparity in the carnivoran backbone unveil a complex adaptive role in metameric evolution (Figueirido et al. 2021, Communications Biology) https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://datadryad.org/api/v2/versions/72212/download https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://datadryad.org/dataset/doi:10.5061/dryad.3j9kd51ft https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:be2e0a6a2ce43d8d6b7e95ddd10a710a9a936dff4454b4fb2212ae651baa55fa https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2 http://purl.org/dc/terms/description Calliper neural-spine height (Lnp) and centrum height (Hc) for every thoracic, lumbar and anterior caudal vertebra of 204 cetacean specimens (74 species labels); source of the cetacean withers index for Test B https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2 http://purl.org/dc/terms/license CC0 1.0 https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: Data from: Divergent evolutionary morphology of the axial skeleton as a potential key innovation in modern cetaceans (Gillet, Frédérich & Parmentier 2019, Proceedings B) https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://datadryad.org/api/v2/versions/41370/download https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2 http://www.w3.org/ns/prov#wasDerivedFrom https://datadryad.org/dataset/doi:10.5061/dryad.7dj6850 https://w3id.org/delphi/resource/evidence/thompson1917-ch16-13--claim-test--dataset-2 https://w3id.org/delphi/ontology/hasChecksum sha256:05e8ab68a205c411b4d27cb8a56e040fbbe1bae7bd442727b3a316795741ffbd https://w3id.org/np/RA2Ct00z52z_T-3fZ_ccrn-YVBnGqWwx4bVk9SupEWI8o/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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