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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." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "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." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of darwin1859-ch13-10: supports, confidence 0.45" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch13-10/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 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/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "biological" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "The short-stem quartile has the higher extinct-to-living ratio, one-sided p < 0.05." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "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." }, { "@value": "Orders whose name TimeTree or PBDB did not match were dropped. Lepidosauria contributed an order only if one joined." }, { "@value": "PBDB species and Catalogue of Life species are different lists. The ratio uses PBDB extinct species over CoL living species." }, { "@value": "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." }, { "@value": "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." }, { "@value": "The universe is extant orders of four tetrapod classes, not every aberrant group." }, { "@value": "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/ontology/expectedObservation": [ { "@value": "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/ontology/failCriterion": [ { "@value": "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/ontology/hasConfidence": [ { "@value": "0.45", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-2" }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "supports" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "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/ontology/inferenceMethod": [ { "@value": "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/ontology/passCriterion": [ { "@value": "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/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "extant orders and living species counts" } ], "http://purl.org/dc/terms/license": [ { "@value": "" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Location (not a URL): https://api.checklistbank.org/dataset/3LR/tree/{id}/children and nameusage/search" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: Catalogue of Life via ChecklistBank dataset 3LR" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://www.catalogueoflife.org/" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:a6eca4d3dbc92373ea2a5ab070f1ee6508621f9ff8cefb143646f365f7539557" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-2", "http://purl.org/dc/terms/description": [ { "@value": "stem and crown ages on one species timeline per order" } ], "http://purl.org/dc/terms/license": [ { "@value": "" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Location (not a URL): https://api.timetree.org/timeline/{species}/json" } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: TimeTree timeline API" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://www.timetree.org/" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:a6eca4d3dbc92373ea2a5ab070f1ee6508621f9ff8cefb143646f365f7539557" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch13-10--claim-test--dataset-3", "http://purl.org/dc/terms/description": [ { "@value": "extinct species counts joined on the order name" } ], "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 taxa/list extinct species counts" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": "https://paleobiodb.org/data1.2/taxa/list.json?rank=species&extant=no&limit=1" } ], "http://www.w3.org/ns/prov#wasDerivedFrom": [ { "@id": "https://paleobiodb.org/" } ], "https://w3id.org/delphi/ontology/hasChecksum": [ { "@value": "sha256:a6eca4d3dbc92373ea2a5ab070f1ee6508621f9ff8cefb143646f365f7539557" } ] }, { "@id": "https://w3id.org/delphi/resource/claim/darwin1859-ch13-10", "https://w3id.org/delphi/ontology/hasAssessment": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch13-10--claim-test" } ] } ] } ]