identifier: traitmech:000622
label: autogamy
definition: A sexual-reproduction phenotype in which two meiotically derived gametic
  nuclei formed within one unpaired, undivided cell fuse with each other, without
  fusion of separate gametes.
definition_source: DOI:10.1017/S0016672300010740
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000625
evidence:
- reference: DOI:10.1017/S0016672300010740
  snippet: the synkaryon, or fertilization nucleus, is formed by the union of two
    pronuclei from the same individual.
  notes: Nobili and Luporini (1967), Introduction p.35, contiguous clause after Thus,
    checked against the typeset publisher PDF. Main text and Summary were read; pp.35-39
    and Tables 1-2 were visually inspected. Results 3(i) use serially fixed cells,
    not live fusion tracking. Genetic identity of fusing nuclei was inferred, not
    resolved cytologically. Results 3(ii) and Summary support retention of mt-locus
    heterozygosity in A-25; complete homozygosity therefore does not define autogamy.
    This is marker evidence, not whole-genome heterozygosity measurement or an identified
    molecular mechanism. Table 3 was not visually audited; no quantitative reanalysis
    is claimed.
- reference: DOI:10.1016/0014-4827(86)90492-1
  snippet: Autogamy is a process of meiosis and fertilization which takes place in
    unpaired Paramecium cells, and which is triggered by starvation.
  notes: Berger (1986), PMID:3743667, opening scientific-abstract sentence directly
    retrieved in Europe PMC core metadata. The complete abstract supports unpaired-cell
    meiosis/fertilization and a two-stage commitment response to nutritional down-shift.
    Starvation and cell-cycle timing concern the studied Paramecium system, not universal
    definition requirements. Full text, actual figures and strain provenance remain
    uninspected; no canonical example or protein-level causal mechanism is inferred
    from this abstract.
- reference: DOI:10.1093/gbe/evaa052
  snippet: Autogamy in P. tetraurelia occurs in unpaired cells, is induced by starvation,
    and generates fully homozygous individuals
  notes: Thind et al. (2020), PMID:32163147, PMC7239694, Introduction sec1 clause
    before citations, checked in raw full-text XML. The scientific abstract, Introduction,
    strain/culture and autogamy-reactivity Methods, and survival-advantage Results
    were inspected. The scored autogamy readout was DAPI-visible macronuclear fragmentation,
    not direct gametic-nuclear fusion in every counted cell. Fully homozygous stock
    d12 mass cultures do not establish that every microbial autogamy event yields
    homozygosity. Survival associations and proposed heat-shock-protein models are
    not a validated causal pathway. Natural provenance of d12 remains unresolved;
    it is not a canonical example here. Actual figures, remaining sections and supplements
    were not audited.
- reference: DOI:10.1080/0269249X.2013.791344
  snippet: Autogamy is a fusion of two gametic (haploid) nuclei within an undivided
    cell
  notes: Kaczmarska et al. (2013), p.271, section 5.2.2, opening clause directly read
    in the author-posted full text at https://www.researchgate.net/publication/259079699_Proposals_for_a_terminology_for_diatom_sexual_reproduction_auxospores_and_resting_stages.
    Sections 5.2.1-5.2.2 distinguish separate gamete fusion from undivided-cell nuclear
    fusion. This resolves the prior unread terminology lead; it is synthesis, not
    new ciliate replication. The following diatom-specific meiotic timing is not imposed
    on the ciliate definition, which allows postmeiotic mitosis as in Nobili and Luporini
    pp.35-37. Actual 2013 diagrams were not inspected.
canonical_examples:
- taxon_id: NCBITaxon:74792
  taxon_label: Moneuplotes minuta
  reference: DOI:10.1017/S0016672300010740
  note: Qualified A-25 example, named Euplotes minuta in the paper. Material and Methods
    p.36 traces it to coastal sand near Pisa, subsequently laboratory-maintained;
    no exact collection year is inferred from the relative date. Serial fixed-cell
    cytology supports the phenotype. Nonautogamic controls 5G/20 and hybrid offspring
    are not this example; A-25 also conjugates. NCBI https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=74792
    and EFetch taxonomy XML checked on 2026-10-05 resolve Moneuplotes minuta with
    Euplotes minuta as a synonym. This species-name mapping does not authenticate
    a modern strain accession or reference genome.
discussions:
- discussion_id: autogamy-scope-and-hierarchy
  prompt: Keep intracellular nuclear fusion distinct from broad self-fertility.
  kind: CURATION_TODO
  status: OPEN
  rationale: Use the unpaired-cell nuclear-fusion sense supported by the cited ciliate
    studies, not plant self-pollination or all selfing. The existing homothallism
    traitmech:000609, unisexual reproduction traitmech:000613 and primary homothallism
    traitmech:000614 definitions are explicitly fungal-scoped and are not exact parents
    or synonyms. Cytogamy traitmech:000623 involves paired cells without nuclear exchange
    in Nobili and Luporini p.39, unlike this unpaired-cell definition. Diller (1958),
    DOI:10.1111/j.1550-7408.1958.tb02567.x, uses double autogamy for the tentative
    paired-cell observation. That broader source terminology does not make cytogamy
    a child or exact synonym of this operationally unpaired-cell class. No universal
    genetic identity, complete homozygosity, starvation trigger, nuclear count, inability
    to outcross or gamete-size asymmetry is imposed. The parent gap is resolved by
    automixis traitmech:000625, whose single-meiotic-cell nuclear origin includes
    this operational scope. The broader terminology and mapping questions keep this
    discussion OPEN. Verify external equivalences and source-specific synonym scope
    before adding mappings. Paedogamy traitmech:000624 instead involves separate gametes
    formed within one gametangium. The clarified definition excludes their fusion,
    without forbidding later cell division or postmeiotic nuclear mitosis. These are
    event-level distinctions, not disjoint species.
  posed_by: codex
  posed_date: '2026-10-05'
- discussion_id: autogamy-mechanism-and-coverage
  prompt: Resolve molecular mechanisms and broader taxon coverage before extension.
  kind: CURATION_TODO
  status: OPEN
  rationale: 'This is an organismal reproductive phenotype, not the literal mt marker
    locus or a heat-shock expression signature. Nuclear-selection inference, nutritional
    commitment and survival associations do not supply a universal protein-resolved
    mechanism. No causal graph bypasses missing accession-level and perturbation evidence.
    Keep macronuclear-fragmentation scoring separate from directly observed fusion.
    The earlier metadata-only lead DOI:10.1080/0269249X.2013.791344 is now resolved
    by direct reading of sections 5.2.1-5.2.2: paedogamy traitmech:000624 is distinct
    and automixis broader. Molecular mechanisms, wider taxon coverage and external
    equivalences remain open; the terminology source alone does not establish them.
    Preserve actual abstract-resolver verdicts separately from direct full-text checks.'
  posed_by: codex
  posed_date: '2026-10-05'
curation_history:
- timestamp: '2026-10-05T15:16:14Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added autogamy with three DOI-backed snippets, unpaired-cell nuclear-fusion
    scope and a provenance-qualified Moneuplotes minuta A-25 example. Ignored-and-hidden
    novelty/allocation searches found no exact record or collision. Reserved METPO:1057500
    in v498 under phenotype. Deferred unverified mappings, a narrower parent and protein-level
    mechanisms; did not impose universal homozygosity.
  llm_assisted: true
- timestamp: '2026-10-05T16:16:00Z'
  curator: codex
  action: LINKED_RELATED_TRAIT
  changes: Linked paired-cell cytogamy traitmech:000623 and attributed Diller's broader
    double-autogamy usage. Preserved the unpaired definition, evidence, example and
    parent; did not assert subsumption or equivalence.
  llm_assisted: true
- timestamp: '2026-10-05T17:13:00Z'
  curator: codex
  action: QUALIFIED_TRAIT_SCOPE
  changes: 'Addressed #1719: made the undivided-cell/no-separate-gamete-fusion boundary
    explicit, added directly read 2013 terminology evidence and linked paedogamy traitmech:000624.
    Resolved the unread-source lead while retaining other open gaps. Preserved ciliate
    evidence, canonical example, parent and compatibility with postmeiotic mitosis.'
  llm_assisted: true
- timestamp: '2026-10-05T17:18:00Z'
  curator: codex
  action: QUALIFIED_NUCLEAR_ORIGIN
  changes: 'Addressed #1720: retained the original same-cell origin of both gametic
    nuclei alongside the #1719 undivided-cell and no-separate-gamete-fusion boundary.
    Fusion location alone does not establish self-fertilization. Preserved evidence,
    example, discussions, parent and all prior history.'
  llm_assisted: true
- timestamp: '2026-10-05T18:20:28Z'
  curator: codex
  action: RESOLVED_PARENT_GAP
  changes: Reparented below automixis traitmech:000625 and documented the resolved
    parent gap while retaining other open terminology and mapping questions. Preserved
    definition, evidence, examples and prior history. v501 carries the existing proposed
    METPO ID with this hierarchy; earlier standalone templates remain historical.
  llm_assisted: true