Animal Ancient DNA Evidence

Animal ancient-DNA publication normally begins with a source-backed sample, not a project title or species mention. Papers, archive projects, supplements, sample tables, sites, chronology statements, and coordinates remain distinct evidence units until their relationships are explicitly curated. Every current animal point is backed by admitted sample identities. Project-only context remains inspectable in the source and refusal records, not as a published point.

Evidence Chain

flowchart LR
    Paper["paper DOI"] --> Project["archive project"]
    Supplement["captured supplement"] --> Project
    Project --> Sample["stable sample identity"]
    Sample --> Locality["sample locality evidence"]
    Sample --> Chronology["sample chronology evidence"]
    Locality --> Coordinate["coordinate basis and precision"]
    Sample --> Species["species-normalized view"]
    Chronology --> Decision{"product admission"}
    Coordinate --> Decision
    Species --> Decision
    Decision -->|admit or qualify| Published["atlas and country evidence row"]
    Decision -->|exclude| Accountability["gap, conflict, or refusal surface"]

Evidence Units And Authorities

Evidence unit	Governing surface	Required distinction
project	source_library/project_registry.json	archive identity is not a sample identity
paper	source_library/paper_registry.json	publication identity is not project identity
captured artifact	project source bundle and supporting-material manifest	discovered URL is not recovered content
sample	project sample_master.json	source labels and stable repository identity remain linked
locality	project sample_locality_evidence.json and species site_evidence.json	verbatim place, resolved site, and publication precision differ
chronology	project sample_chronology_evidence.json and chronology review surfaces	source text, normalized interval, basis, and caveat remain linked
coordinate	species coordinate_provenance.json	supplied, resolved, approximate, substituted, and unresolved differ
publication	atlas evidence row and product manifest	visible membership is downstream of admission

Recovery States

stateDiagram-v2
    [*] --> Discovered
    Discovered --> Captured: paper and supporting material acquired
    Captured --> Extracted: stable sample rows recovered
    Extracted --> Reviewed: locality, chronology, taxonomy, and coordinates evaluated
    Reviewed --> Admitted: product requirements satisfied
    Reviewed --> Qualified: material precision limit remains visible
    Reviewed --> Excluded: required evidence is absent or conflicting
    Discovered --> Deferred: required source material unavailable
    Captured --> Deferred: sample-bearing content not recoverable

Tracked but deferred evidence is not equivalent to a negative scientific result. It records what is known about the source and what remains unavailable.

Current Evidence Depth

The governed foundation currently contains 1,450 final sample rows across 10 species and 21 contributing projects. Of those rows, 557 are fully grounded, 335 are partly grounded, 11 are blocked by missing metadata, 391 by missing location detail, and 156 by weak chronology. This is the final sample evidence-preparation population, not a publication-feature count.

The generated project intake review separately covers 40 tracked projects and contains 1,455 recovered raw sample-master rows, of which 1,450 enter the final sample population. Only four projects have an exact expected-sample denominator. The repository therefore does not present either total as a complete census of every deposited sample.

The point-evidence review contains 170 published locality features representing 331 distinct admitted samples. The features comprise 117 domesticated_core localities and 53 wild_or_progenitor_context localities. These are admitted evidence features, not proof that every project, species, locality, or chronology has reached the same maturity.

All 170 published features are backed by at least one admitted sample. Wadi Halfa dromedary context for project SRP073444 remains useful source context, but it is not published. Map-readiness accounting retains it among the 134 not-materialized rows with reason no_admitted_sample_backed_locality_candidate.

Point population	Rows	Identity and coordinate posture
domesticated-core localities	117	admitted sample backing and product scope retained
wild or progenitor context localities	53	admitted sample backing with context role retained
total published locality features	170	represents 331 distinct admitted samples

Three Ledgers Answer Three Questions

Ledger	Unit	Question answered
foundation truth	curated preparation row	how completely is the available identity, locality, chronology, and metadata evidence grounded?
project sample master	recovered sample identity	which source labels resolve to a stable sample within a project?
point publication	locality feature and represented sample	which sample-backed domesticated-core or wild/progenitor-context localities satisfy this map contract?

No universal completeness percentage spans all three. A preparation blocker is not necessarily an identity ambiguity; a final identity is not necessarily point-ready; and retained project context is not a published sample-backed locality.

Evidence Depth Is Dimension-Specific

Dimension	What the repository can establish	Remaining boundary
source discovery	which projects, papers, and supplements are tracked	discovery does not prove sample-bearing material was recovered
sample recovery	which source rows became stable sample records	most projects do not have an exact expected-row denominator
locality	which verbatim localities resolve to sample- or group-owned sites	regional or conflicting assignments remain non-point evidence
coordinate	whether a pair is source-supplied or repository-resolved, with confidence	coordinate class does not imply uniform real-world precision
chronology	which source statement, interval, and basis belong to a sample	broad or contextual time does not authorize synthetic numeric bounds
publication	which rows satisfy a named product contract	admission does not establish collection completeness

There is therefore no single collection-wide maturity score. A project can be well documented at the paper and supplement level while its locality recovery is incomplete; a spatially admitted sample can still have chronology that is too broad for numeric comparison. The governing files preserve those different states instead of averaging them into one quality label.

flowchart LR
    Inventory["40 tracked projects"] --> Recovery["1,455 recovered raw rows"]
    Recovery --> Foundation["1,450 final sample rows"]
    Foundation --> Review["identity, locality, chronology, coordinate review"]
    Review --> Samples["331 distinct admitted samples"]
    Samples --> Points["170 published locality features"]
    Review --> Excluded["134 coordinate-ready rows not materialized"]
    Inventory --> Gaps["blocked, under-recovered, and unresolved projects"]
    Gaps --> Accountability["recovery review and refusal surfaces"]

The generated reports make both branches visible. The published branch shows what satisfies the point contract; the accountability branch prevents the admitted subset from masquerading as collection completeness.

A Published Point Is A Typed Projection

The point row does not become a new authority for the facts it displays. It is a product-specific projection over separately governed evidence:

Point field	Governing owner	Projection rule
feature identity	publication manifest and evidence-row identity	stable within the named product and linked to one or more admitted governed samples
sample label and accession	project sample master	display the admitted identity without replacing source-native aliases
species	species-normalized sample record and taxonomy decision	use the governed taxon posture, including qualification or conflict
locality label	sample locality and site evidence	display at the admitted resolution; broad text remains broad
geometry	coordinate-provenance decision	supplied, resolved, approximate, substituted, or withheld posture travels with the pair
time label or interval	sample chronology evidence	preserve source wording, normalized basis, ownership, and comparability caveat
admission posture	named product rule	distinguish sample-backed scope classes from excluded and deferred populations

flowchart LR
    Sample["sample identity"] --> Projection["product projection"]
    Locality["locality and site evidence"] --> Projection
    Coordinate["coordinate provenance"] --> Projection
    Chronology["chronology evidence"] --> Projection
    Taxonomy["species decision"] --> Projection
    Projection --> Member["typed publication member"]
    Projection --> Refusal["qualification or exclusion"]

This model permits a narrow supported point without declaring the whole project complete. It also permits curation to strengthen later without rewriting history: a new evidence decision creates a reviewable projection change and affected product diff rather than silently mutating the earlier source claim.

Audit A Published Animal Point

1. resolve its feature and evidence-row identifiers in the product traceability surface;
2. confirm the species record under data/adna/species/<latin_name>/normalized/sample_records.json;
3. inspect the species site_evidence.json, then follow its project linkage to sample_sites.json and sample_locality_evidence.json;
4. inspect project sample_chronology_evidence.json and the cross-project chronology review for temporal posture;
5. inspect coordinate_provenance.json for basis and precision;
6. follow the sample lineage to the project sample master, source bundle, paper, and captured supporting artifact;
7. confirm that the product manifest records the point's admission posture.

Publication Boundary

A species-level presence, archive project, or paper citation cannot substitute for a recoverable sample row. A broad locality cannot become an exact point. A cultural period cannot acquire a synthetic numeric interval. A visible point cannot outrank its governing evidence.

The point contract is also narrower than “animal evidence available.” A project can contribute paper, supplement, taxonomy, or broad locality evidence without contributing an atlas point. Conversely, a point admitted under its present traceability and precision does not certify complete recovery of its project. The release posture records the narrower claim that the admitted subset satisfies its point contract while project-level recovery denominators, blocked sources, and unresolved evidence remain visible outside that subset.

Wadi Halfa is a concrete example of why publication decisions must travel with the evidence row. Its source context and approximate named-place coordinate remain traceable, but the current product does not materialize it without an admitted sample-backed locality candidate. Analyses must preserve that explicit exclusion rather than infer a point from retained context.

Continue with animal source intake, sample records, locality evidence, chronology, and point publication rules.