https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA/Head https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA/assertion https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA/provenance https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA/pubinfo https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test http://purl.org/dc/terms/description analysis.py downloads the FishBase 24.07 species, country and countref CSVs, keeps species flagged fresh-water only (Fresh, not Brack, not Saltwater) whose AnaCat is not anadromous/catadromous/amphidromous/oceanodromous (16,213 species, 16,174 with native country records), joins their native/endemic country records to FishBase's Continent field, collapses Europe+Asia into Eurasia, and counts species with native records on both sides of each ocean-separated landmass pair. A species is 'robust' if it has >= 2 native countries on each side. Two post-hoc checks, labelled as such in measured.extra.post_hoc, were added after inspecting the output: removing Indonesia/Timor-Leste from the Asian side of the Eurasia|Oceania pair (Indonesian Papua is on New Guinea), and re-running the Eurasia|North America pair with brackish-tolerant non-diadromous species admitted. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--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-ch12-02--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 6 strictly fresh-water, non-diadromous fish species native (>= 2 countries each side) on both sides of an ocean-separated continent pair (n = 16174, exact count from FishBase 24.07 status fields; FishBase status errors can move single species in or out). Interpretation: Darwin's 'fresh-water fish' is mapped to FishBase species that are flagged fresh-water only and are not diadromous, because he treats migratory marine-linked fishes separately and the claim concerns fish confined to fresh water. 'Distant continents' is mapped to continents separated by sea today; Eurasia is one landmass and North and South America are joined, so those pairs are not 'distant' for this test (a sensitivity count over all pairs of FishBase's six continents is also reported). Native status comes from FishBase's country status field (native, endemic), which excludes introductions, the main modern confound Darwin could not have foreseen. The second clause (within a continent, river systems share some species and not others) is near-tautological and is not tested here. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch12-02: refutes, confidence 0.8 https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--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-ch12-02/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--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-ch12-02--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: fishbase-2024-07-species, fishbase-2024-07-country, fishbase-2024-07-countref https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Five or more such species have native status in >= 2 countries on each side of an ocean-separated pair (robust counterexamples, not single-country errors): refutes. Between 1 and 4 robust species, or only single-country cases: mixed. The share of strictly fresh-water species that are shared across an ocean is reported to distinguish 'never' from 'rarely'. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Darwin's generalization is nonetheless very nearly true: 6 of 16,174 species (0.04 %) meet the robust rule and 83 (0.5 %) share any country pair across an ocean, almost all of them artefacts; genuine sharing is confined to the Bering Strait region, where a Pleistocene land connection joined river systems, which is the mechanism Darwin himself proposed for dispersal of fresh-water fish. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst FishBase is licensed CC BY-NC; the data are not redistributed here, only fetched and summarised. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst FishBase treats Alaska, Canada and USA as separate 'countries', which makes North American counts easier to satisfy than Russian ones (a single country for all of Siberia); this biases the robust rule against Eurasia|North America cases, not in favour of them. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The pre-registered mechanical count is 6 robust species (>= 5, 'refutes'), but inspection shows that count is partly artefactual: Upeneus guttatus is a marine goatfish mis-flagged as fresh-water only, Cichlasoma bimaculatum's 'native' Eurasian records are status errors, and three Indo-Pacific gobies/pipefishes (Glossogobius clitellus, Redigobius oyensi, Lophocampus retzii) reach Oceania from the Philippines/Indonesia; such island gobioids have marine larval phases that FishBase does not always code as amphidromous. 72 of the 77 Eurasia|Oceania 'shared' species are Indonesian-Papua vs Papua New Guinea/Australia records on the single landmass of New Guinea/Sahul, an artefact of FishBase filing Indonesia under Asia. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The verdict nevertheless stands on the genuine Holarctic cases: under the strict filter Thymallus arcticus (robust), Prosopium coulterii and Dallia pectoralis are native in both Siberia and North America; admitting brackish-tolerant non-diadromous species (post hoc) adds Esox lucius, Lota lota, Catostomus catostomus, Cottus cognatus and Prosopium cylindraceum (10 species listed, of which Atractosteus spatula and Gasterosteus microcephalus look like status errors). Northern pike and burbot in both England and Canada falsify 'never' on Darwin's own terms. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The within-continent clause of the claim (river systems share some species and not others) was not tested. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/expectedObservation Among FishBase species flagged as fresh-water only (Fresh = 1, Brack = 0, Saltwater = 0) and not anadromous, catadromous, amphidromous or oceanodromous, zero species have 'native' or 'endemic' country status (FishBase country table) in at least one country on each side of any ocean-separated continent pair. Ocean-separated pairs are all pairs among {Eurasia (Europe + Asia), Africa, North America (incl. Central America and the Caribbean), South America, Oceania (Australia + New Guinea + Pacific)} except Eurasia-Africa and North America-South America, which are joined by land. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/failCriterion Five or more such species have native status in >= 2 countries on each side of an ocean-separated pair (robust counterexamples, not single-country errors): refutes. Between 1 and 4 robust species, or only single-country cases: mixed. The share of strictly fresh-water species that are shared across an ocean is reported to distinguish 'never' from 'rarely'. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.8 https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-3 https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/hasVerdict refutes https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/hypothesis If Darwin is right, no strictly fresh-water, non-diadromous fish species has a native range that includes two continents separated by ocean (e.g. Eurasia and North America, Africa and South America, Asia and Australia). https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/inferenceMethod analysis.py downloads the FishBase 24.07 species, country and countref CSVs, keeps species flagged fresh-water only (Fresh, not Brack, not Saltwater) whose AnaCat is not anadromous/catadromous/amphidromous/oceanodromous (16,213 species, 16,174 with native country records), joins their native/endemic country records to FishBase's Continent field, collapses Europe+Asia into Eurasia, and counts species with native records on both sides of each ocean-separated landmass pair. 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Central America and the Caribbean), South America, Oceania (Australia + New Guinea + Pacific)} except Eurasia-Africa and North America-South America, which are joined by land. https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch12-02 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch12-02--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-1 http://purl.org/dc/terms/description Fresh/Brack/Saltwater habitat flags and AnaCat migratory category per species https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-1 http://purl.org/dc/terms/license CC BY-NC 3.0 (FishBase) https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--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-ch12-02--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: FishBase species table (v24.07), CSV export distributed by rfishbase https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://huggingface.co/datasets/cboettig/fishbase/resolve/main/data/fb/v24.07/csv/species.csv https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://huggingface.co/datasets/cboettig/fishbase https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:0d8219c9d70ffb8bfe92278c3324933380f16461834b3c453f6215a9ea605e83 https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-2 http://purl.org/dc/terms/description native and endemic country records per species https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-2 http://purl.org/dc/terms/license CC BY-NC 3.0 (FishBase) https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--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-ch12-02--claim-test--dataset-2 http://www.w3.org/2000/01/rdf-schema#label Dataset: FishBase country table (v24.07): species x country occurrence with native/introduced status https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-2 http://www.w3.org/ns/prov#atLocation https://huggingface.co/datasets/cboettig/fishbase/resolve/main/data/fb/v24.07/csv/country.csv https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-2 http://www.w3.org/ns/prov#wasDerivedFrom https://huggingface.co/datasets/cboettig/fishbase https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-2 https://w3id.org/delphi/ontology/hasChecksum sha256:db5f53f19b03e3de5ba9c66b8f7bd0412d33290880339e66b2dc3dc4c4d3c1bc https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-3 http://purl.org/dc/terms/description country to continent mapping https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-3 http://purl.org/dc/terms/license CC BY-NC 3.0 (FishBase) https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--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-ch12-02--claim-test--dataset-3 http://www.w3.org/2000/01/rdf-schema#label Dataset: FishBase countref table (v24.07): country reference list with Continent field https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-3 http://www.w3.org/ns/prov#atLocation https://huggingface.co/datasets/cboettig/fishbase/resolve/main/data/fb/v24.07/csv/countref.csv https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-3 http://www.w3.org/ns/prov#wasDerivedFrom https://huggingface.co/datasets/cboettig/fishbase https://w3id.org/delphi/resource/evidence/darwin1859-ch12-02--claim-test--dataset-3 https://w3id.org/delphi/ontology/hasChecksum sha256:bc62f38f58462674319bc249025cd4e17b43fb13816aa15af5d3a07c2bfaa711 https://w3id.org/np/RA-i3Yc_McUZi_8s-uWisnjOKhgJi_6KslCZgMeLOcyxA/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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