https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw/Head https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw/assertion https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw/provenance https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw/pubinfo https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAxQeO2uxkDfrNXZKbfOx4U_PYjyVePQeeFQbj2yDGgiw/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test http://purl.org/dc/terms/description The 103 pre-registered representative taxa were resolved with the Open Tree TNRS (exact matches, context All life; Pteropoda did not match) and an induced subtree of the synthetic tree was requested. Eleven further taxa are non-monophyletic in the synthesis and mapped to internal nodes already containing other sampled tips, so 91 of 103 (0.88) were placed as tips. For each 1859 class the tips were coded as members or not and the cheapest reconstruction under weighted parsimony (gain 2, loss 1, ties broken toward fewer gains) was found by dynamic programming over the (polytomous) tree; origins = gains, plus one if the root is reconstructed as a member. The Dollo count of maximal all-member clades was recorded alongside. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--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-ch14-01--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 17 of 22 classes as circumscribed in 1859 that have a single origin under weighted parsimony (gain 2, loss 1) on the Open Tree synthetic tree (n = 22, fraction 0.773; mapped fraction of representative taxa 0.883). Interpretation: Darwin's 'class' is read as the classes his contemporaries used (Cuvier's Règne animal as modified by Owen and Milne-Edwards; de Candolle's three plant classes), not modern monophyletic classes, because the claim says descent embraces 'all the members of the same class' as then delimited: Pisces include cyclostomes, Reptilia include turtles, crocodiles, lizards and snakes but not birds, Acephala include bivalves and tunicates, Insecta include myriapods, Echinodermata include sipunculans and priapulids, Entozoa unite parasitic worms, Acalephae unite jellyfish and comb jellies, Polypi unite corals, hydroids, bryozoans and sponges, Infusoria unite ciliates, flagellates, rotifers and diatoms, Dicotyledones include gymnosperms, and Acotyledones unite ferns, mosses, algae and fungi. 'Embraced by descent with modification' is read as single origin on the genealogy: a paraphyletic class (one origin, nested classes 'lost' from it, e.g. Reptilia relative to Aves) counts as embraced, a polyphyletic class (several origins) does not. Representatives are fixed in advance; the 'independently estimated' genealogy is the Open Tree synthetic tree whose backbone comes mostly from molecular studies. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch14-01: mixed, confidence 0.6 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--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-ch14-01/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--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/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: opentree-synthetic-tree-api https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Pre-registered: REFUTES if 50% or fewer of the classes (<= 11 of 22) are of single descent. Between 12 and 17 is MIXED. If the Open Tree API is unreachable or fewer than 85% of the representative taxa can be placed as tips, the result is inconclusive (data-unavailable). The Dollo count (number of maximal all-member clades) is recorded as a secondary descriptive statistic. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst 17 of 22 classes (0.77) are of single descent, just below the pre-registered 0.80 support threshold and far above the 0.50 refutation threshold, so the verdict is MIXED. The five multiple-origin classes are exactly the ones later dismantled as artificial: Acephala (bivalves + tunicates), Echinodermata as including sipunculans and priapulids, Entozoa, Acalephae (jellyfish + comb jellies) and Polypi (corals, hydroids, bryozoans, sponges). Every vertebrate, mollusc proper, arthropod and plant class is of single descent. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Representatives are 3-9 fixed taxa per class, and 12 of them (including Crocodylia, Rotifera, Bacillariophyta, Acari) could not be placed as tips because they are non-monophyletic in the synthetic tree; the origin count can only be under-estimated by missing representatives. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The 1859 circumscriptions follow Cuvier's Règne animal as modified by Owen and de Candolle's plant classes; other contemporary systems (e.g. Owen's separate Protozoa, Huxley's Molluscoida) would change a few memberships. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The gain:loss cost ratio of 2:1 lets a class with members scattered across the tree be reconstructed as ancestral at the root with later losses (Infusoria: 3 pure clades but 1 origin; Acotyledones: 7 pure clades but 1 origin). Under a stricter rule (Dollo pure clades = 1) only 11 of 22 classes would pass, which would be REFUTES; the pre-registered rule was chosen because paraphyletic classes such as Reptilia and Pisces are 'embraced by descent' in Darwin's sense, but the result is sensitive to this choice. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The synthetic tree has no branch support; the backbone for protists and basal animals is a supertree of heterogeneous studies. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/expectedObservation Pre-registered: for 22 classes as circumscribed in the Cuvier/Owen system current in 1859, each represented by 3-7 fixed modern taxa, an induced subtree of the Open Tree of Life synthetic tree is obtained. For each class, membership is coded on the tips and reconstructed by weighted parsimony (gain cost 2, loss cost 1; among equally cheap reconstructions the one with fewest gains); the number of origins = gains + 1 if the root is reconstructed as a member. A class is 'of single descent' if origins = 1. SUPPORTS if at least 80% of the classes (>= 18 of 22) are of single descent. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered: REFUTES if 50% or fewer of the classes (<= 11 of 22) are of single descent. Between 12 and 17 is MIXED. If the Open Tree API is unreachable or fewer than 85% of the representative taxa can be placed as tips, the result is inconclusive (data-unavailable). The Dollo count (number of maximal all-member clades) is recorded as a secondary descriptive statistic. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.6 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch14-01--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/hasVerdict mixed https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/hypothesis On an independently estimated (largely molecular) tree of life, each class of animals and plants as recognised in 1859 forms a group of single origin: the most parsimonious reconstruction of class membership on the tree requires only one origin of the class (with any number of losses to nested groups), not several independent origins. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/inferenceMethod The 103 pre-registered representative taxa were resolved with the Open Tree TNRS (exact matches, context All life; Pteropoda did not match) and an induced subtree of the synthetic tree was requested. Eleven further taxa are non-monophyletic in the synthesis and mapped to internal nodes already containing other sampled tips, so 91 of 103 (0.88) were placed as tips. For each 1859 class the tips were coded as members or not and the cheapest reconstruction under weighted parsimony (gain 2, loss 1, ties broken toward fewer gains) was found by dynamic programming over the (polytomous) tree; origins = gains, plus one if the root is reconstructed as a member. The Dollo count of maximal all-member clades was recorded alongside. https://w3id.org/delphi/resource/assessment/darwin1859-ch14-01--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered: for 22 classes as circumscribed in the Cuvier/Owen system current in 1859, each represented by 3-7 fixed modern taxa, an induced subtree of the Open Tree of Life synthetic tree is obtained. For each class, membership is coded on the tips and reconstructed by weighted parsimony (gain cost 2, loss cost 1; among equally cheap reconstructions the one with fewest gains); the number of origins = gains + 1 if the root is reconstructed as a member. A class is 'of single descent' if origins = 1. 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