https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0/Head https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0/assertion https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0/provenance https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0/pubinfo https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test http://purl.org/dc/terms/description The pre-registered family names were resolved with the Open Tree TNRS (exact matches only, context Vertebrates / Arthropods) and an induced subtree of the synthetic tree was requested for the matched ott ids. Taxa pruned from the synthesis (Lamnidae) or non-monophyletic in it and mapped to an internal node already containing other sampled tips were dropped; the rest were coded 1 (electric / luminous) or 0 (background). Unary node chains were collapsed, then the number of maximal all-1 clades (Dollo minimum number of independent origins) and the Fitch parsimony minimum number of state changes were computed on the induced tree. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--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-ch06-10--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 6 minimum independent origins (Dollo) of electric organs among fish families on the Open Tree synthetic tree (n = 45, Fitch parsimony minimum changes = 6; 10 electric tips of 45). Interpretation: Darwin's claim has two parts: that similar organs sometimes arose independently in distantly related organisms (testable from a phylogeny) and that natural selection acting on analogous variations produced them (a mechanism not tested here). Only the first, pattern part is tested. 'Electric organs of fishes' = the families with electrogenic organs in the modern literature: Torpedinidae, Narcinidae, Narkidae, Hypnidae (Torpediniformes), Rajidae (skates), Mormyridae and Gymnarchidae (Mormyroidea), Gymnotidae, Apteronotidae, Sternopygidae, Hypopomidae, Rhamphichthyidae (Gymnotiformes), Malapteruridae (electric catfish) and Uranoscopidae (stargazers); Darwin knew Torpedo, Gymnotus and the electric catfish. 'Luminous organs of insects' = Lampyridae, Phengodidae, Rhagophthalmidae, Elateridae (Pyrophorini), Keroplatidae (Arachnocampa, Orfelia). 'Independently estimated phylogeny' = the Open Tree of Life synthetic tree, whose fish and insect backbones derive mostly from molecular studies. Independence is counted on a tree whose tips are families; origins within a family are not counted separately, which makes the count conservative. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch06-10: supports, confidence 0.95 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--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-ch06-10/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--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-ch06-10--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: opentree-synthetic-tree-api https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Pre-registered: REFUTES if the electric-organ-bearing families form a single clade in the synthetic tree (Dollo origins = 1, Fitch changes = 1). MIXED if Dollo origins = 2, or if the two statistics disagree about whether >= 3 changes are needed. If the Open Tree API is unreachable or fewer than 80% of the listed families map to the tree, the result is inconclusive (data-unavailable). https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Only the pattern half of the claim (independent origins) is tested; whether natural selection on 'analogous variations' produced them is not addressed by a phylogeny. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Seven of 52 fish names (Narcinidae, Gymnotidae, Sternopygidae, Hypopomidae, Rhinobatidae, Serranidae, Lamnidae) could not be placed as tips because they are non-monophyletic in the synthetic tree or pruned from it; every dropped electric family belongs to a clade (Torpediniformes, Gymnotiformes) that is already represented, so the count is unchanged. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The luminous-insect case gives 2 independent origins (Lampyridae + Rhagophthalmidae; Keroplatidae) because Elateridae and Phengodidae could not be placed as tips; the literature count is higher. It was pre-registered as reported-only. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The six electric clades recovered (Torpediniformes, Rajidae, Mormyroidea, Gymnotiformes, Malapteruridae, Uranoscopidae) are separated by many non-electric families, so the result is insensitive to the exact background sample; it also matches the count in the modern literature, which was not used as input. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The synthetic tree is a supertree whose fish backbone comes mostly from molecular studies; it carries no branch support, so no uncertainty on the origin count is given. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/expectedObservation Pre-registered: on the Open Tree of Life synthetic tree induced on a fixed list of electric-organ-bearing fish families and a fixed list of non-electric fish families, count (i) the Dollo minimum number of independent origins = number of maximal clades whose tips are all electric, and (ii) the Fitch parsimony minimum number of state changes. SUPPORTS if, for the electric-fish case, (i) >= 3 and (ii) >= 3 (no reconstruction with a single origin and fewer than three changes exists). The insect light-organ case is scored the same way and reported; it does not decide the verdict because the claim is existential ('has sometimes'). https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered: REFUTES if the electric-organ-bearing families form a single clade in the synthetic tree (Dollo origins = 1, Fitch changes = 1). MIXED if Dollo origins = 2, or if the two statistics disagree about whether >= 3 changes are needed. If the Open Tree API is unreachable or fewer than 80% of the listed families map to the tree, the result is inconclusive (data-unavailable). https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.95 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/hypothesis Electric organs (Darwin's stated example) occur in fish lineages that are separated on an independently estimated phylogeny by lineages lacking electric organs, so that the organ must have arisen more than once rather than being inherited from one common ancestor; the same holds for light-producing organs in insects (his second example). https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/inferenceMethod The pre-registered family names were resolved with the Open Tree TNRS (exact matches only, context Vertebrates / Arthropods) and an induced subtree of the synthetic tree was requested for the matched ott ids. Taxa pruned from the synthesis (Lamnidae) or non-monophyletic in it and mapped to an internal node already containing other sampled tips were dropped; the rest were coded 1 (electric / luminous) or 0 (background). Unary node chains were collapsed, then the number of maximal all-1 clades (Dollo minimum number of independent origins) and the Fitch parsimony minimum number of state changes were computed on the induced tree. https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered: on the Open Tree of Life synthetic tree induced on a fixed list of electric-organ-bearing fish families and a fixed list of non-electric fish families, count (i) the Dollo minimum number of independent origins = number of maximal clades whose tips are all electric, and (ii) the Fitch parsimony minimum number of state changes. SUPPORTS if, for the electric-fish case, (i) >= 3 and (ii) >= 3 (no reconstruction with a single origin and fewer than three changes exists). The insect light-organ case is scored the same way and reported; it does not decide the verdict because the claim is existential ('has sometimes'). https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch06-10 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch06-10--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 http://purl.org/dc/terms/description independently estimated family-level phylogeny of fishes and of insects on which the electric / luminous character states were mapped https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 http://purl.org/dc/terms/license CC0 (Open Tree synthesis products) https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--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-ch06-10--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: Open Tree of Life synthetic tree opentree16.1 (taxonomy 3.7draft3) via the v3 API: tnrs/match_names and tree_of_life/induced_subtree https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://api.opentreeoflife.org/v3/tnrs/match_names https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://api.opentreeoflife.org/v3/tree_of_life/about https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://api.opentreeoflife.org/v3/tree_of_life/induced_subtree https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://tree.opentreeoflife.org/ https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:830eb15fd0a2f053a3d66e27de7b42e5b8dfc485638b5f983521760c018d43d5 https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:aa8103ee4fe56d946d224583eeccbcc1294fdb6bafbfb2f6ba2c44897c5b317c https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:b13a704ec122f6ff268afdabe3c1d212423fdd7c4579c7a1f3743ab865821672 https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:c48251d66423673f3b2806d1f5f5b95def5eb9f831fdf27d54e74ba79b50ddfb https://w3id.org/delphi/resource/evidence/darwin1859-ch06-10--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:d3956a21b5bd886366a664cff91290b2eadeb276f633e7544191f7809af2e339 https://w3id.org/np/RAxFnFi9NPymqBGPSVf6cGOT7vYmn7H7QC1vWrqt0rLg0/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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