https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE/Head https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE/assertion https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE/provenance https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE/pubinfo https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA1Uj7-DI-q0RDCimr83FTPeIWx6418O2k5Ak2MYebHsE/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test http://purl.org/dc/terms/description analysis.py fetches every GenBank mitochondrial record of Columba livia and of all other Columba species, extracts COI and CYTB from the C. livia reference NC_013978.1, and places each record on those genes by best ungapped k-mer-anchored offset (>= 400 bp overlap, >= 80 % identity; complete mitogenomes contribute their annotated genes). Records are domestic if the organism is 'domestica', a /breed qualifier or 'breed:' note is present, or a breed name occurs in the record; breed names are parsed from those fields. For each domestic record and gene, p-distances over >= 300 shared positions give the nearest non-domestic C. livia record and the nearest record of each other Columba species ('Columba sp.' excluded as unidentified). The measured value is the number of domestic records nearer to another species than to C. livia. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--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-ch01-10--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0 domestic-labelled Columba livia records whose nearest non-domestic mitochondrial sequence (COI or CYTB) belongs to another Columba species (n = 107, max p-distance from a domestic record to the nearest C. livia record 0.013740458015267175; MIN_SHARED 300 bp). Interpretation: Darwin's claim concerns descent of all domestic breeds from one wild species; mitochondrial DNA tests the maternal component of that descent, which is what pre-genomic public data allow. 'Columba livia with its geographical sub-species' is taken as all records with organism Columba livia (any subspecies, including domestica for the domestic set). Columba rupestris, the hill pigeon, is a separate species in modern taxonomy and is treated as an alternative wild stock, although Darwin may have regarded it as a form of C. livia; a domestic sequence nearest to C. rupestris is therefore reported separately in the extra fields as well as counted. Alignment is by best ungapped offset because indels are rare in these coding genes; sequences overlapping the reference gene by < 400 bp are discarded. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch01-10: supports, confidence 0.75 https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--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-ch01-10/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--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-ch01-10--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: genbank-columba-mitochondrial-records https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation At least 2 domestic sequences from at least 2 different breeds (or records) are nearer to another Columba species (C. rupestris, C. oenas, C. palumbus, C. guinea, C. leuconota, C. hodgsonii, etc.) than to any C. livia sequence, or exceed 2 % from all C. livia sequences while being within 2 % of another species: refutes (a second wild stock contributes maternal ancestry). Exactly one such sequence: mixed. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst 107 domestic records covering 22 named breeds (English and Indian Fantail, Kassel and other Tumblers, Jacobin, Hungarian Cropper (a pouter), Runt, King, Mondain, German Nun, German Magpie, German Beard, Vienna Highflier, Archangel, Ice pigeon, Lahore, Wroclaw Meat, Shiqi, three Egyptian breeds, 'Lucky') are all nearest to C. livia (mean 0.10 %, maximum 1.37 % p-distance) rather than to any of 20 other Columba species; none approaches C. oenas, C. palumbus, C. guinea or C. leuconota, the species Darwin's contemporaries proposed as alternative stocks. Carriers and Barbs, two breeds Darwin emphasised, are not among the named records. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Breed labelling was refined twice after inspecting record metadata (parsing 'breed:' notes and isolate names such as '693_Jacobin pigeon'); this changed only how many named breeds were counted (3 -> 22), not the distances or the pre-registered criterion. 'Columba sp.' records were removed from the other-species set after the first run because they are unidentified, not an alternative wild species; no violation existed with them included either. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Discriminating power against Columba rupestris is limited: the hill pigeon is only 1.2-2.6 % from domestic sequences in COI/CYTB, and C. livia and C. rupestris are sister species that hybridise. Every domestic record is nonetheless nearer to C. livia than to C. rupestris (0 of 115 record-gene comparisons the other way). Darwin's own wording ('with its geographical sub-species') would arguably absorb rupestris anyway. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Mitochondrial DNA tests maternal ancestry only; nuclear genomic work (Shapiro et al. 2013 Science; Stringham et al. 2012 Current Biology) also places all breeds within C. livia and is literature, not data used here. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Non-domestic 'Columba livia' comparators include feral and unlabelled birds, some of which may be domestic in origin; this does not bias the test toward 'supports' because the alternative hypothesis predicts domestic sequences nesting with another species, which would be detected regardless. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Several GenBank 'Columba janthina' COI barcodes are identical to C. livia sequences and are almost certainly mislabelled; they never became the unique nearest neighbour because an equally close C. livia record always existed, so they did not affect the count. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/expectedObservation Using GenBank mitochondrial records of Columba livia and of all other Columba species, aligned by best ungapped offset to the COI and CYTB genes of the C. livia reference mitogenome NC_013978: every domestic-labelled sequence (organism 'Columba livia domestica', a /breed qualifier, or a breed name in the record) has its nearest non-domestic sequence in C. livia (or in a wild C. livia subspecies), and the maximum p-distance from any domestic sequence to the nearest C. livia sequence is < 2 %. Requires >= 10 domestic-labelled sequences from >= 5 named breeds or 'domestica' records; otherwise inconclusive (underpowered). https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/failCriterion At least 2 domestic sequences from at least 2 different breeds (or records) are nearer to another Columba species (C. rupestris, C. oenas, C. palumbus, C. guinea, C. leuconota, C. hodgsonii, etc.) than to any C. livia sequence, or exceed 2 % from all C. livia sequences while being within 2 % of another species: refutes (a second wild stock contributes maternal ancestry). Exactly one such sequence: mixed. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.75 https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch01-10--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/hasVerdict supports https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/hypothesis If all domestic pigeon breeds descend from Columba livia (with its geographical sub-species) and not from several wild stocks, then every domestic-breed mitochondrial sequence should fall within the Columba livia cluster: nearer to C. livia sequences than to any other Columba species, and within intraspecific distance of C. livia. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/inferenceMethod analysis.py fetches every GenBank mitochondrial record of Columba livia and of all other Columba species, extracts COI and CYTB from the C. livia reference NC_013978.1, and places each record on those genes by best ungapped k-mer-anchored offset (>= 400 bp overlap, >= 80 % identity; complete mitogenomes contribute their annotated genes). Records are domestic if the organism is 'domestica', a /breed qualifier or 'breed:' note is present, or a breed name occurs in the record; breed names are parsed from those fields. For each domestic record and gene, p-distances over >= 300 shared positions give the nearest non-domestic C. livia record and the nearest record of each other Columba species ('Columba sp.' excluded as unidentified). The measured value is the number of domestic records nearer to another species than to C. livia. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/passCriterion Using GenBank mitochondrial records of Columba livia and of all other Columba species, aligned by best ungapped offset to the COI and CYTB genes of the C. livia reference mitogenome NC_013978: every domestic-labelled sequence (organism 'Columba livia domestica', a /breed qualifier, or a breed name in the record) has its nearest non-domestic sequence in C. livia (or in a wild C. livia subspecies), and the maximum p-distance from any domestic sequence to the nearest C. livia sequence is < 2 %. Requires >= 10 domestic-labelled sequences from >= 5 named breeds or 'domestica' records; otherwise inconclusive (underpowered). https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch01-10 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch01-10--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch01-10--claim-test--dataset-1 http://purl.org/dc/terms/description COI and CYTB sequences of domestic pigeon breeds, non-domestic C. livia and 20 other Columba species https://w3id.org/delphi/resource/evidence/darwin1859-ch01-10--claim-test--dataset-1 http://purl.org/dc/terms/license NCBI public domain terms https://w3id.org/delphi/resource/evidence/darwin1859-ch01-10--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-ch01-10--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: NCBI GenBank (nuccore) mitochondrial records of Columba livia (534) and of all other Columba species (645), including the C. livia reference mitogenome NC_013978.1, retrieved through E-utilities https://w3id.org/delphi/resource/evidence/darwin1859-ch01-10--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation 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