https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs/Head https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs/assertion https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs/provenance https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs/pubinfo https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RAQ2mCri0tHIoPD_NDtBJ2Dlfrm73-Wdjl76xvSd73PKs/assertion https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test http://purl.org/dc/terms/description analysis.py downloads the AVONET xlsx, reads the Migration column of the AVONET1_BirdLife sheet and computes P (share coded 2 among all scored species) and Q (share coded 2 among species coded 2 or 3), plus a per-order table (derived/avonet_migration_by_order.csv). For each of the 12 pre-registered species it resolves the GBIF taxon key and counts records in sixteen 5-degree latitude bands from 0 to 80 N for June-July and for December plus January-February (GBIF month ranges cannot wrap the year, so winter is two calls). The summer core is the set of bands overlapping the 10th-90th percentile of summer records; W is the share of winter records in those bands. Partial and obligate sets are compared with a one-sided Mann-Whitney U test. The verdict follows the pre-registered thresholds (P 0.20 / 0.05; W medians; p < 0.05). https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--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-ch07-04--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 0.1089 share of bird species coded as partially migratory (AVONET Migration = 2) among all species with a migration score (n = 10986, AVONET expert coding; GBIF winter residency index from 5-degree band counts (eBird-dominated, effort-biased)). Interpretation: Darwin's examples of instinct variation are migration (extent, direction, total loss) and nest form; this test addresses the migration example only. 'Varies within species in a state of nature' is operationalised as partial migration: a species whose populations or individuals differ in whether or how far they migrate. AVONET's Migration score (1 sedentary, 2 partially migratory, 3 migratory) is an expert synthesis from handbooks; it is used for the global prevalence P. The GBIF index W checks that this classification corresponds to an observable pattern: a species whose individuals all migrate should have few winter records at breeding latitudes, whereas a partial migrant retains many. Recent records (2000 onward) are used because eBird dominates GBIF bird data and gives dense year-round coverage; the Northern Hemisphere restriction avoids mixing austral seasons. Latitude bands are global in longitude, so for species occurring on more than one continent (Sturnus vulgaris, introduced in North America) the index pools populations. Thresholds: 20 % of all bird species being partial migrants is taken as 'common'; 5 % as 'rare'. Direction of migration and the evolutionary loss of migration are not measured separately, since occurrence data cannot attribute a wintering bird to its breeding population. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of darwin1859-ch07-04: mixed, confidence 0.7 https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--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-ch07-04/result.json https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--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-ch07-04--claim-test https://w3id.org/delphi/ontology/admissibleDatasets Planned datasets: avonet-supplementary-dataset-1, gbif-occurrence-api-birds https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation Refutes if P < 0.05 (within-species variation in migratory extent is a rare anomaly) or if the obligate set has median W >= the partial set (the trait classification does not correspond to any measurable difference in winter residency). Otherwise mixed. The nest-construction clause is not tested (no public, geographically coded nest-architecture dataset at the within-species level was identified) and is recorded as untested in caveats. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst AVONET's codes for the six species I pre-registered as partial migrants are 3, 1, 3, 2, 2, 3 (Erithacus rubecula, Turdus merula and Sylvia atricapilla are coded fully migratory, Turdus merula sedentary), illustrating that a single species-level code compresses continuous within-species variation and will be assigned by predominant behaviour; this makes P a conservative estimate of how many species show some within-species variation in migration. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst P = 1196 / 10986 = 10.9 % of all bird species are coded as partial migrants, below the pre-registered 20 % 'common' threshold but far above the 5 % 'rare' threshold, so the primary criterion lands in the mixed zone. The threshold was set against all birds, most of which (80 %) are sedentary tropical species for which the migratory instinct does not arise; among the 2,182 species that migrate at all, 54.8 % (Q) are partial migrants, i.e. within-species variation in migratory extent is the majority condition among migrants. Had the pre-registration used Q the verdict would have been supports; it is reported as mixed because the rule is fixed in advance. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The 'direction' and 'total loss' components of Darwin's migration example are not measured separately: occurrence counts cannot assign a wintering bird to its breeding population, and AVONET has no population-level codes. The nest-construction clause is untested; no public, within-species, geographically coded nest-architecture dataset was identified (NestWatch and BTO Nest Record Scheme data require application). https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The secondary GBIF test passes clearly: median winter residency index W = 0.8561 for the six species pre-registered as partial migrants versus 0.2998 for the six obligate long-distance migrants (one-sided Mann-Whitney p = 0.0022). Winter records per summer record in the breeding core are 0.37-2.5 for the partial set versus 0.0007-0.11 for the obligate set, so the pattern Darwin described (some individuals of a species stay where others leave) is directly visible in occurrence data. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst W for obligate migrants is inflated by a small number of winter records that are probably misidentifications, stragglers or data errors (e.g. Cuculus canorus W = 0.72 from 4,863 winter records against 579,201 summer records, a 0.8 % ratio); W is a ratio among winter records only and does not weight by how few they are. The winter/summer ratio reported above corrects for this. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/evidenceAgainst eBird dominates GBIF bird records, so counts reflect observer effort as much as bird abundance; the latitude-band design pools longitudes and continents (relevant for Sturnus vulgaris, native in Eurasia and introduced in North America, both populations partially migratory). https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/expectedObservation Primary (AVONET, Tobias et al. 2022, BirdLife taxonomy sheet): P = share of bird species with a coded Migration score that are coded 2 (partially migratory) among all species, and Q = share coded 2 among non-sedentary species (score 2 or 3). Secondary (GBIF occurrence counts, Northern Hemisphere, years 2000 onward, non-fossil non-captive records, 5-degree latitude bands 0-80 N): for 12 pre-registered species, W = fraction of December-February records that fall in the latitude bands holding the central 80 % of June-July records (winter residency index). Partial-migrant set: Erithacus rubecula, Turdus merula, Sylvia atricapilla, Fringilla coelebs, Sturnus vulgaris, Turdus migratorius. Obligate-migrant set: Hirundo rustica, Apus apus, Phylloscopus trochilus, Setophaga striata, Tyrannus tyrannus, Cuculus canorus. Supports if P >= 0.20 and W is higher in the partial-migrant set than in the obligate set by a one-sided Mann-Whitney test at p < 0.05 with median W of the partial set >= 0.25. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/failCriterion Refutes if P < 0.05 (within-species variation in migratory extent is a rare anomaly) or if the obligate set has median W >= the partial set (the trait classification does not correspond to any measurable difference in winter residency). Otherwise mixed. The nest-construction clause is not tested (no public, geographically coded nest-architecture dataset at the within-species level was identified) and is recorded as untested in caveats. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.7 https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/hasVerdict mixed https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/hypothesis If Darwin is right that the migratory instinct varies within species in extent and may be lost, then partial migration (some individuals or populations of a species migrate while others of the same species stay resident) is a common condition among birds rather than a rare anomaly, and species classified as partial migrants show measurably more winter presence inside their breeding latitudes than obligate migrants do. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/inferenceMethod analysis.py downloads the AVONET xlsx, reads the Migration column of the AVONET1_BirdLife sheet and computes P (share coded 2 among all scored species) and Q (share coded 2 among species coded 2 or 3), plus a per-order table (derived/avonet_migration_by_order.csv). For each of the 12 pre-registered species it resolves the GBIF taxon key and counts records in sixteen 5-degree latitude bands from 0 to 80 N for June-July and for December plus January-February (GBIF month ranges cannot wrap the year, so winter is two calls). The summer core is the set of bands overlapping the 10th-90th percentile of summer records; W is the share of winter records in those bands. Partial and obligate sets are compared with a one-sided Mann-Whitney U test. The verdict follows the pre-registered thresholds (P 0.20 / 0.05; W medians; p < 0.05). https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/passCriterion Primary (AVONET, Tobias et al. 2022, BirdLife taxonomy sheet): P = share of bird species with a coded Migration score that are coded 2 (partially migratory) among all species, and Q = share coded 2 among non-sedentary species (score 2 or 3). Secondary (GBIF occurrence counts, Northern Hemisphere, years 2000 onward, non-fossil non-captive records, 5-degree latitude bands 0-80 N): for 12 pre-registered species, W = fraction of December-February records that fall in the latitude bands holding the central 80 % of June-July records (winter residency index). Partial-migrant set: Erithacus rubecula, Turdus merula, Sylvia atricapilla, Fringilla coelebs, Sturnus vulgaris, Turdus migratorius. Obligate-migrant set: Hirundo rustica, Apus apus, Phylloscopus trochilus, Setophaga striata, Tyrannus tyrannus, Cuculus canorus. Supports if P >= 0.20 and W is higher in the partial-migrant set than in the obligate set by a one-sided Mann-Whitney test at p < 0.05 with median W of the partial set >= 0.25. https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/ontology/preregistered false https://w3id.org/delphi/resource/claim/darwin1859-ch07-04 https://w3id.org/delphi/ontology/hasAssessment https://w3id.org/delphi/resource/assessment/darwin1859-ch07-04--claim-test https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--claim-test--dataset-1 http://purl.org/dc/terms/description Migration score (1 sedentary, 2 partially migratory, 3 migratory) for 10,986 species in the BirdLife taxonomy https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--claim-test--dataset-1 http://purl.org/dc/terms/license CC BY 4.0 https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--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-ch07-04--claim-test--dataset-1 http://www.w3.org/2000/01/rdf-schema#label Dataset: AVONET: morphological, ecological and geographical data for all birds (Tobias et al. 2022), Supplementary dataset 1, sheet AVONET1_BirdLife, column Migration https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--claim-test--dataset-1 http://www.w3.org/ns/prov#atLocation https://ndownloader.figshare.com/files/34480856 https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--claim-test--dataset-1 http://www.w3.org/ns/prov#wasDerivedFrom https://figshare.com/articles/dataset/AVONET_morphological_ecological_and_geographical_data_for_all_birds_Tobias_et_al_2021_Ecology_Letters_/16586228 https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--claim-test--dataset-1 https://w3id.org/delphi/ontology/hasChecksum sha256:eb645e83dddb40f1654a3e8d721998dbca76eff540231b7b809267c1e96f8d3e https://w3id.org/delphi/resource/evidence/darwin1859-ch07-04--claim-test--dataset-2 http://purl.org/dc/terms/description winter residency index W per species; 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