https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8/Head https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8/assertion https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8/provenance https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8/pubinfo https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test http://purl.org/dc/terms/description Catalogue of Life dataset 3LR supplied extant orders of Mammalia, Aves, Amphibia and Lepidosauria and the tree count of species under each order. For the first species name returned for that order, the TimeTree timeline supplied the order node and its parent. Stem length is the parent age minus the order age. Quartiles of stem length per living species were fixed before the fossil comparison. PBDB taxa/list counted extinct species (extant=no, rank=species). A one-sided Mann-Whitney test compared the extinct-per-living ratio in the top quartile with the bottom quartile. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--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/darwin1859-ch13-10--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 8.2 median PBDB extinct species per living CoL species, long-stem quartile (n = 39, one-sided p that the long-stem quartile has the higher ratio 0.0004; short-stem median ratio 0.1408). Interpretation: Darwin's aberrant or osculant groups are read as orders whose stem is long relative to how many species are alive now. That is evolutionary distinctiveness per species, using the stem rather than a hand-picked list of oddities. 'Very few species' is inside that ratio, so a lower species count is not scored again as independent evidence. 'Very distinct from each other' would be a within-crown distance; it is not a separate test, because the crown age is already the quantity subtracted to get the stem. 'Remnants of failing groups that suffered heavy extinction' is the fossil ratio of extinct species to living species. The universe is four tetrapod classes, narrower than every aberrant group in nature. Open Tree topology is not used: the synthetic tree was not relied on for time. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch13-10: supports, confidence 0.45 https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch13-10/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/admissibleDatasets A living-species checklist, a dated tree that gives a stem age and a crown age for the same orders, and a fossil count of extinct species for those orders. The three have to be joined on the order name. A list of groups already called aberrant in a textbook is not admissible. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation The short-stem quartile has the higher extinct-to-living ratio, one-sided p < 0.05. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Aberrant is the top quartile of stem length per living species. The species count is in that ratio, so 'few species' is not a separate result. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Orders whose name TimeTree or PBDB did not match were dropped. Lepidosauria contributed an order only if one joined. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst PBDB species and Catalogue of Life species are different lists. The ratio uses PBDB extinct species over CoL living species. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The grouping ratio and the fossil ratio both divide by living species count. Median extinct-species counts are reported beside the ratios. They were not used to change the pre-registered verdict. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The stem is read from one Catalogue of Life species, the first name the search returned whose timeline names the order. Stem length is the nearest named ancestor's age minus the order-node age. Unnamed nodes immediately above the order are skipped because they are not the sister split. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The universe is extant orders of four tetrapod classes, not every aberrant group. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Within-order distinctness of the living species was not tested. The crown age is only the quantity subtracted to get the stem. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/expectedObservation Orders in the top quartile of stem length per living species have a higher extinct-to-living species ratio than orders in the bottom quartile. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered. REFUTES if the median fossil ratio is higher in the short-stem group, one-sided p < 0.05. Any other completed comparison is mixed. Inconclusive if a dated tree with node ages cannot be fetched, if CoL species counts cannot be fetched, if fewer than 8 orders fall in either quartile, or if PBDB does not return an extinct-species count for those orders (not-operationalizable or underpowered). https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.45 https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3 https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/hypothesis Tetrapod orders with a long stem relative to their number of living species are remnants of failing groups: they have a higher ratio of extinct fossil species to living species than orders with a short stem per living species. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/inferenceMethod Quartiles of stem/n_living fixed from CoL and TimeTree before the PBDB ratio is compared. One-sided Mann-Whitney on the extinct/living ratio, p < 0.05, at least 8 orders in each tail. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered. Aberrant is operationalized before any fossil ratio is computed, as a long stem per living species, not as a hand-picked list. Universe: extant orders of Mammalia, Aves, Amphibia and Lepidosauria in Catalogue of Life. Living species count is the CoL accepted-species total for the order. Stem length, in millions of years, is the age of the split from the sister minus the crown age of the order, taken from one dated TimeTree per class. Evolutionary distinctiveness per species = stem length / living species count. Aberrant = orders at or above the 75th percentile of that ratio; the comparison group is orders at or below the 25th percentile. The fossil ratio is PBDB extinct species divided by the CoL living-species count. SUPPORTS if the median fossil ratio is higher in the aberrant group, one-sided Mann-Whitney p < 0.05, and both groups have at least 8 orders. No further subsample. https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch13-10 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-1 http://purl.org/dc/terms/description extant orders and living species counts https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-1 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--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/darwin1859-ch13-10--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#comment Location (not a URL): https://api.checklistbank.org/dataset/3LR/tree/{id}/children and nameusage/search https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Catalogue of Life via ChecklistBank dataset 3LR https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://www.catalogueoflife.org/ https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:a6eca4d3dbc92373ea2a5ab070f1ee6508621f9ff8cefb143646f365f7539557 https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-2 http://purl.org/dc/terms/description stem and crown ages on one species timeline per order https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-2 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--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/darwin1859-ch13-10--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#comment Location (not a URL): https://api.timetree.org/timeline/{species}/json https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: TimeTree timeline API https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-2 http://www.w3.org/ns/prov#wasDerivedFrom https://www.timetree.org/ https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-2 https://w3id.org/delphi/ontology/hasChecksum sha256:a6eca4d3dbc92373ea2a5ab070f1ee6508621f9ff8cefb143646f365f7539557 https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3 http://purl.org/dc/terms/description extinct species counts joined on the order name https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3 http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/EvidenceItem https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3 http://www.w3.org/2000/01/rdf-schema#label Dataset: Paleobiology Database taxa/list extinct species counts https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3 http://www.w3.org/ns/prov#atLocation https://paleobiodb.org/data1.2/taxa/list.json?rank=species&extant=no&limit=1 https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3 http://www.w3.org/ns/prov#wasDerivedFrom https://paleobiodb.org/ https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3 https://w3id.org/delphi/ontology/hasChecksum sha256:a6eca4d3dbc92373ea2a5ab070f1ee6508621f9ff8cefb143646f365f7539557 https://w3id.org/np/RAOtiWAjmMdiKNi1KTL_62B9SuDXAgryhkJEAI55tlNN8/provenance https://w3id.org/delphi/resource/agent/delphisci-claim-tester-grok-4-7 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-grok-4-7 http://www.w3.org/2000/01/rdf-schema#label delphisci claim tester (grok-4.7; 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