https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU/Head https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU/assertion https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU/provenance https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU/pubinfo https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAgn4HknuVQNUorsA0U5vFeCm13reSWtuxCOPIStTXWCU/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test http://purl.org/dc/terms/description Open Tree TNRS resolved the six names. Source trees returned by find_trees for those ott ids were downloaded as newick (40 study-tree pairs). A tree is admissible when at least four of the five categories (caballus, asinus, hemionus, quagga, zebra/grevyi) are present (10 trees). The selected tree is pg_1889 tree3841, chosen by category count, then tip count, then study id. Monophyletic=True; outsiders=[]. The share of admissible trees that are monophyletic is 0.9. The stripe clauses were not scored: File names do not show horse, ass or hemionus codes. The stripe clauses stay untested. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--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-ch05-16--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 1 1 if the selected source tree has the targets as an Equus clade, else 0 (n = 6). Interpretation: Full quote (Origin, 1st ed., ch. V): "For myself, I venture confidently to look back thousands on thousands of generations, and I see an animal striped like a zebra, but perhaps otherwise very differently constructed, the common parent of our domestic horse, whether or not it be descended from one or more wild stocks, of the ass, the hemionus, quagga, and zebra." Common ancestry and the striped ancestor are separate. This test scores common ancestry: the named animals form a clade. It does not score whether that ancestor was striped, and it does not score the further claim that ancestry explains occasional stripes in domestic horses, asses and hybrids. Quagga is Equus quagga. Zebra, listed separately from quagga, is Equus zebra or Equus grevyi. A tree can support shared ancestry without saying anything about coat pattern. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch05-16: supports, confidence 0.7 https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--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-ch05-16/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--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-ch05-16--claim-test https://w3id.org/delphi/ontology/admissibleDatasets A public phylogenetic tree from a named study, with tip labels for at least four of the five taxa. A taxonomy-only polytomy with no supporting study is not admissible. Coat data are admissible for the stripe clause only when they code the non-zebra equids too. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Every well-populated source tree places a non-Equus inside the ancestor of those animals, or no source tree includes at least four of them. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Open Tree study licenses were not in the downloaded tree files, so license is null rather than guessed. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Quagga counts only when the tip label contains quagga. A plains-zebra tip that does not say quagga is not that target. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The tree was chosen by how many of the five names it contains, then by study id, not by whether the clade was Equus-only. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The verdict is common ancestry only. The ancestor being striped like a zebra, and that pattern explaining occasional stripes in horses, asses and hybrids, were not tested. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/expectedObservation In a published source tree, horse, ass, hemionus, quagga and a zebra form a clade that contains no non-Equus. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/failCriterion Refute if that common ancestor also has a descendant that is not Equus. If no admissible source tree contains at least four targets, inconclusive with reason data-unavailable. The striped-ancestor clause and the claim that it explains occasional stripes are not part of this pass/fail. They are scored only if Dryad 10.5061/dryad.s13rt codes stripe state for the horse, the ass and the hemionus as well as a zebra. Otherwise they stay untested. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.7 https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/hypothesis A published phylogenetic tree places the domestic horse, ass, hemionus, quagga and a zebra together as a clade of Equus, so they share a common ancestor. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/inferenceMethod Monophyly of the matched tips on one pre-selected source tree. Selection is by tip count, then study id, never by the monophyly outcome. The fraction of admissible trees that agree is reported and does not replace the selected tree. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/passCriterion On the selected Open Tree source tree, the most recent common ancestor of the matched targets has no descendant outside Equus. Targets are Equus caballus, Equus asinus, Equus hemionus, Equus quagga, and Equus zebra or Equus grevyi. At least four of those five must be in the tree. The selected tree is the admissible source tree with the most of these tips; ties break by study id ascending, not by the monophyly result. The synthetic taxonomy polytomy is not admissible. https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch05-16 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch05-16--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-1 http://purl.org/dc/terms/description published source trees for the monophyly test https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-1 http://purl.org/dc/terms/license https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--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-ch05-16--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Open Tree of Life source studies containing 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https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://api.opentreeoflife.org/v3/study/pg_1889/tree/tree3847.tre https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://api.opentreeoflife.org/v3/study/pg_1889/tree/tree3848.tre https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://api.opentreeoflife.org/v3/study/pg_1889/tree/tree3849.tre https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://api.opentreeoflife.org/v3/study/pg_2067/tree/tree4257.tre https://w3id.org/delphi/resource/evidence/darwin1859-ch05-16--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://api.opentreeoflife.org/v3/study/pg_2067/tree/tree4258.tre 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