https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q/Head https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q/assertion https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q/provenance https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q/pubinfo https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RALJq7AP8wVSZcYAdslFLb9MNMh3P1aaSjtAqnHgVsw9Q/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test http://purl.org/dc/terms/description analysis.py runs eight esearch queries (complete mitochondrial genomes of dog, wild wolf, coyote, golden jackal, African wolf, Ethiopian wolf, dhole, African wild dog), takes every third dog UID (453 of 1,357) and all UIDs for the other groups, efetches GenBank flat files, extracts the CYTB and COX1 CDS from the feature table (IUPAC codes kept as N so coordinates are preserved), keeps records with the modal gene lengths (1,140 + 1,545 bp), and computes pairwise ungapped p-distances over the 2,685 bp concatenation. For each dog it records the distance to the nearest wild wolf and to the nearest sequence of each other species; the measured value is the number of dogs whose nearest non-dog sequence is not Canis lupus. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--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-ch01-09--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0 sampled dog mitogenomes whose nearest non-dog sequence belongs to a species other than Canis lupus (n = 446, fraction 0.0000; p-distances over 2685 bp of CYTB+COX1). Interpretation: Darwin's 'several wild species' is read as more than one wild canid species contributing ancestry to domestic dogs. The species Darwin would have counted (wolf, jackals, coyote, dhole, African wild dog, Ethiopian wolf) are the wild canids with GenBank mitogenomes. Mitochondrial DNA tests maternal ancestry only; if even the maternal lineages are exclusively wolf-derived, the multi-species claim is refuted for the component that pre-genomic data can address, and nuclear genomic literature is cited in caveats but is not used as data. Dingoes and 'Canis lupus dingo' records are reported separately and excluded from the dog sample; records of 'Canis lupus' other than familiaris and dingo are treated as wild wolves (GenBank labels, which can include captive or admixed animals, are taken at face value). Modern taxonomy already files the dog inside Canis lupus, which the test does not assume. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch01-09: refutes, confidence 0.85 https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--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-ch01-09/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--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-ch01-09--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: genbank-canid-mitogenomes https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Zero dog sequences are nearer to a non-wolf species than to wild wolves: refutes (every maternal lineage sampled is wolf-derived). One or two such sequences (consistent with mislabelled hybrids) or the per-cent threshold unmet: mixed. If fewer than 100 dog sequences or fewer than 20 wild wolf sequences can be retrieved and parsed: inconclusive (underpowered). https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/evidenceAgainst A first run dropped IUPAC ambiguity characters from the sequences, which shifted coordinates in a handful of records and produced spurious distances; the parser was corrected before the result above was produced, and the pre-registered criterion was not changed. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Every one of 446 sampled dog mitogenomes is nearer to a wild grey wolf (mean 0.15 %, maximum 0.41 % p-distance) than to any other canid species (minimum 3.0 %, to Canis lupaster); no dog maternal lineage traces to a jackal, coyote, dhole, Ethiopian wolf or African wild dog. Darwin's 'several wild species' therefore fails for maternal ancestry. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/evidenceAgainst GenBank 'Canis lupus' records include some African wolves labelled as the former subspecies C. lupus lupaster, which is why the minimum wolf-to-other-species distance is 0.11 %; this inflates the 'wild wolf' set with a few non-wolf sequences and could only have made a non-wolf dog origin easier, not harder, to detect. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Mitochondrial DNA is a single maternally inherited locus. Nuclear-genome studies (e.g. Freedman et al. 2014 PLoS Genetics; Frantz et al. 2016 Science; Bergstrom et al. 2020 Science) reach the same conclusion, that dogs derive from one wild species, the grey wolf, possibly from more than one wolf population; those are literature, not data used here. Low-level admixture from other canids into particular dog populations would not be excluded by this test. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/evidenceAgainst None of the dog records carries a /breed qualifier, so breed coverage of the sample cannot be documented from metadata; the 1,357 records come from many independent studies (village dogs, ancient DNA, breed panels) and the systematic one-in-three sample was fixed before any sequence was examined. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Taxonomic labels in GenBank are taken at face value; mislabelled wolf-dog hybrids would not affect the direction of the result. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/expectedObservation Using complete mitochondrial genomes from GenBank (a systematic one-in-three sample of all 'Canis lupus familiaris' records, every wild 'Canis lupus' record, and every record of the other wild canid species), with CYTB and COX1 coding sequences extracted and compared by ungapped p-distance: at least 3 dog sequences AND at least 2 % of sampled dog sequences have their nearest non-dog sequence in a species other than Canis lupus. That outcome supports a multi-species origin. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/failCriterion Zero dog sequences are nearer to a non-wolf species than to wild wolves: refutes (every maternal lineage sampled is wolf-derived). One or two such sequences (consistent with mislabelled hybrids) or the per-cent threshold unmet: mixed. If fewer than 100 dog sequences or fewer than 20 wild wolf sequences can be retrieved and parsed: inconclusive (underpowered). https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.85 https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch01-09--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/hasVerdict refutes https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/hypothesis If Darwin is right that domestic dogs descend from several distinct wild species (he had in mind wolves and jackals), then some domestic dog maternal lineages should trace to a wild canid species other than the grey wolf: a non-trivial fraction of dog mitochondrial genomes should be closer to Canis aureus, C. lupaster, C. latrans, C. simensis, Cuon alpinus or Lycaon pictus than to any wild Canis lupus. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/inferenceMethod analysis.py runs eight esearch queries (complete mitochondrial genomes of dog, wild wolf, coyote, golden jackal, African wolf, Ethiopian wolf, dhole, African wild dog), takes every third dog UID (453 of 1,357) and all UIDs for the other groups, efetches GenBank flat files, extracts the CYTB and COX1 CDS from the feature table (IUPAC codes kept as N so coordinates are preserved), keeps records with the modal gene lengths (1,140 + 1,545 bp), and computes pairwise ungapped p-distances over the 2,685 bp concatenation. For each dog it records the distance to the nearest wild wolf and to the nearest sequence of each other species; the measured value is the number of dogs whose nearest non-dog sequence is not Canis lupus. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/passCriterion Using complete mitochondrial genomes from GenBank (a systematic one-in-three sample of all 'Canis lupus familiaris' records, every wild 'Canis lupus' record, and every record of the other wild canid species), with CYTB and COX1 coding sequences extracted and compared by ungapped p-distance: at least 3 dog sequences AND at least 2 % of sampled dog sequences have their nearest non-dog sequence in a species other than Canis lupus. That outcome supports a multi-species origin. https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch01-09 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch01-09--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch01-09--claim-test--dataset-1 http://purl.org/dc/terms/description CYTB and COX1 coding sequences for 446 dogs, 129 wild wolves and 54 other canids https://w3id.org/delphi/resource/evidence/darwin1859-ch01-09--claim-test--dataset-1 http://purl.org/dc/terms/license NCBI public domain terms https://w3id.org/delphi/resource/evidence/darwin1859-ch01-09--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-ch01-09--claim-test--dataset-1 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