[ { "@id": "https://w3id.org/np/RAt0_uop4lHw17FUd5G_fWUoGDBsxmyeBWY1U-r7aKHBg/Head", "@graph": [ { "@id": "https://w3id.org/np/RAt0_uop4lHw17FUd5G_fWUoGDBsxmyeBWY1U-r7aKHBg", "http://www.nanopub.org/nschema#hasAssertion": [ { "@id": "https://w3id.org/np/RAt0_uop4lHw17FUd5G_fWUoGDBsxmyeBWY1U-r7aKHBg/assertion" } ], "http://www.nanopub.org/nschema#hasProvenance": [ { "@id": "https://w3id.org/np/RAt0_uop4lHw17FUd5G_fWUoGDBsxmyeBWY1U-r7aKHBg/provenance" } ], "http://www.nanopub.org/nschema#hasPublicationInfo": [ { "@id": "https://w3id.org/np/RAt0_uop4lHw17FUd5G_fWUoGDBsxmyeBWY1U-r7aKHBg/pubinfo" } ], "@type": [ "http://www.nanopub.org/nschema#Nanopublication" ] } ] }, { "@id": "https://w3id.org/np/RAt0_uop4lHw17FUd5G_fWUoGDBsxmyeBWY1U-r7aKHBg/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/assessment/darwin1859-ch12-08--claim-test", "http://purl.org/dc/terms/description": [ { "@value": "analysis.py queries the GBIF occurrence API for class Amphibia (classKey 131) within each of 41 pre-registered oceanic island units (ISO territory code or WGS84 bounding box), excluding fossil and living/captive specimens, and facets by speciesKey. For each species recorded in a unit it fetches the species' global record count (for bounding-box units both counts are restricted to georeferenced records without geospatial issues, so that un-georeferenced museum specimens do not deflate the fraction) and flags the species endemic to the unit if it has >= 10 records worldwide and >= 95 % of them inside the unit. The measured value is the number of units with at least one endemic amphibian; the verdict follows the pre-registered rule (0 supports, 1 mixed, >= 2 refutes)." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 3 oceanic island units with >= 1 endemic (hence native) amphibian species (n = 41, endemism rule: >= 10 records worldwide and >= 95 % inside the unit; counts are GBIF snapshot values at retrieval time). Interpretation: Darwin's 'islands with which the great oceans are studded' is read as geologically oceanic islands, which he distinguishes from continental islands elsewhere in the chapter (he explicitly excludes New Zealand and the Falklands as continental). Batrachians = class Amphibia (GBIF classKey 131). 'Never been found' is read as no native population; introductions, which Darwin himself discusses (Madeira, Azores, Mauritius), are excluded by requiring endemism. Pre-registered oceanic units (ISO code or bounding box): Fiji FJ, Samoa WS, American Samoa AS, Tonga TO, Palau PW, Micronesia FM, Marshall Is. MH, Northern Marianas MP, Guam GU, French Polynesia PF, Cook Is. CK, Vanuatu VU, Niue NU, Tuvalu TV, Kiribati KI, Nauru NR, Wallis & Futuna WF, Tokelau TK, Pitcairn PN, Norfolk I. NF, Bermuda BM, St Helena/Ascension/Tristan SH, Iceland IS, Sao Tome & Principe ST, Cape Verde CV, Comoros KM, Mayotte YT, Mauritius MU, Reunion RE, Christmas I. CX, Cocos (Keeling) CC, Hawaii (box), Galapagos (box), Canary Is. (box), Azores (box), Madeira (box), Juan Fernandez (box), Fernando de Noronha (box), Ogasawara/Bonin (box), Easter I. (box), Lord Howe I. (box). Excluded as continental fragments or shelf islands: New Zealand, Seychelles (granitic), Socotra, New Caledonia, Solomon Is., Bioko, Falklands, Faroes, Japan, Sri Lanka, Madagascar, Taiwan, British Isles, Caribbean Greater Antilles. Classification follows the standard volcanic/arc versus continental distinction used in island biogeography (e.g. Weigelt et al. 2013 PNAS) and is a judgement made before any data were examined." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of darwin1859-ch12-08: refutes, confidence 0.93" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/darwin-origin/darwin1859-ch12-08/result.json" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-fable-5-1" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "Planned datasets: gbif-occurrence-api-amphibia, gbif-backbone-taxonomy" } ], "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": "Two or more independent oceanic island units each have at least one endemic amphibian species by the rule above: the universal statement is refuted. Exactly one such unit: 'mixed' (a single counterexample Darwin himself might have disputed, like his New Zealand frog). The proportion of units with native amphibians is reported in either case to characterise the 'general absence' Darwin also asserted." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Darwin's wider point also holds in the data: 38 of 41 oceanic units (92.7 %) have no endemic amphibian, and in the well-sampled ones (Hawaii, Bermuda, Canaries, Azores, Madeira, Mauritius, Reunion) every recorded amphibian is a widespread species consistent with introduction. The universal statement is false; the strong tendency is real." }, { "@value": "Endemism is a sufficient but not necessary proof of native status; non-endemic native species are not detected, which can only make the test more conservative." }, { "@value": "GBIF counts are a live snapshot; occurrence totals will drift between runs, but the identity of endemic species is stable. Species-level misidentifications in GBIF are mitigated by the >= 10 record rule." }, { "@value": "The pre-registration text says 40 units but the enumerated list (unchanged) contains 41; the count in the text was a miscount." }, { "@value": "Three independent oceanic units have endemic, hence native, amphibians: Fiji (Cornufer vitiensis, 207 of 210 records; C. vitianus at 86 % narrowly misses the rule), Palau (Cornufer pelewensis, 1482 of 1505) and Sao Tome and Principe (six endemic species including the caecilian Schistometopum thomense). Mayotte's Boophis nauticus (93 %) and Blommersia transmarina (89 %) fall just under the 95 % rule and are not counted, so the count of 3 is conservative." }, { "@value": "Whether Fiji and Palau are 'oceanic' in Darwin's sense is a geological judgement: both are intra-oceanic island arcs never connected to a continent, but Fiji includes some old arc crust. Sao Tome and Principe are unambiguous volcanic hot-spot islands." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "Across a pre-registered list of 40 oceanic island units (see planned unit list in interpretation), zero units have an amphibian species that is endemic to the unit by GBIF occurrence data, where 'endemic' means the species has >= 10 non-fossil, non-captive occurrence records worldwide and >= 95 % of them fall inside the unit. An endemic species cannot be a human introduction, so endemism is used as a conservative proof of native status." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Two or more independent oceanic island units each have at least one endemic amphibian species by the rule above: the universal statement is refuted. Exactly one such unit: 'mixed' (a single counterexample Darwin himself might have disputed, like his New Zealand frog). The proportion of units with native amphibians is reported in either case to characterise the 'general absence' Darwin also asserted." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.93", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch12-08--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch12-08--claim-test--dataset-2" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "refutes" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "If Darwin is right, no geologically oceanic island or archipelago (volcanic hot-spot island, atoll or intra-oceanic island arc that has never been joined to a continent) has a native amphibian species; every amphibian recorded there is a human introduction." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "analysis.py queries the GBIF occurrence API for class Amphibia (classKey 131) within each of 41 pre-registered oceanic island units (ISO territory code or WGS84 bounding box), excluding fossil and living/captive specimens, and facets by speciesKey. For each species recorded in a unit it fetches the species' global record count (for bounding-box units both counts are restricted to georeferenced records without geospatial issues, so that un-georeferenced museum specimens do not deflate the fraction) and flags the species endemic to the unit if it has >= 10 records worldwide and >= 95 % of them inside the unit. The measured value is the number of units with at least one endemic amphibian; the verdict follows the pre-registered rule (0 supports, 1 mixed, >= 2 refutes)." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Across a pre-registered list of 40 oceanic island units (see planned unit list in interpretation), zero units have an amphibian species that is endemic to the unit by GBIF occurrence data, where 'endemic' means the species has >= 10 non-fossil, non-captive occurrence records worldwide and >= 95 % of them fall inside the unit. An endemic species cannot be a human introduction, so endemism is used as a conservative proof of native status." } ], "https://w3id.org/delphi/ontology/preregistered": [ { "@value": "false", "@type": "http://www.w3.org/2001/XMLSchema#boolean" } ] }, { "@id": "https://w3id.org/delphi/resource/evidence/darwin1859-ch12-08--claim-test--dataset-1", "http://purl.org/dc/terms/description": [ { "@value": "per-unit amphibian species lists and per-species global record counts used to compute endemism" } ], "http://purl.org/dc/terms/license": [ { "@value": "per-dataset CC0 / CC BY / CC BY-NC (GBIF aggregate terms)" } ], "@type": [ "https://w3id.org/delphi/ontology/EvidenceItem" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Dataset: GBIF occurrence search API (class Amphibia, non-fossil, non-captive records), faceted by species per island unit" } ], "http://www.w3.org/ns/prov#atLocation": [ { "@id": 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