Adaptive Radiation Ontology

flow “AdaptiveRadiationOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > EVOLUTIONARY BIOLOGY > ADAPTIVE RADIATION ONTOLOGY

Authors: Mark Anthony Higgins — Sky (Recursive AI)

AI_INTERPRETATION: mode: formal_structural_reasoning instruction:
“Execute as formal rules, not pseudocode.” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/evolutionary-biology/adaptive-radiation-ontology.html”

type Organism type Species type Population type Lineage type Clade type
Ancestor type Descendant type AdaptiveRadiation type SpeciationEvent
type Trait type KeyInnovation type EcologicalOpportunity type Niche type
Habitat type Environment type Resource type Phylogeny type Observation
type Evidence type Source

———- RADIATION IDENTITY ———-

relation INSTANCE_OF(entity,type) relation
HAS_ADAPTIVE_RADIATION(clade,radiation) relation
RADIATION_OF(radiation,clade) relation
DESCENDED_FROM(descendant,ancestor) relation
ANCESTOR_OF(ancestor,descendant) relation
DIVERSIFIES_INTO(ancestor,descendants) relation
MEMBER_OF_CLADE(species,clade)

rule DESCENT_INVERSE(a,b): IF DESCENDED_FROM(a,b) THEN ANCESTOR_OF(b,a)

———- DIVERSIFICATION ———-

relation DIVERSIFICATION_RATE(clade,rate) relation
SPECIATION_RATE(clade,rate) relation EXTINCTION_RATE(clade,rate)
relation NET_DIVERSIFICATION_RATE(clade,rate) relation
RADIATION_BEGINS_AT(radiation,time) relation
RADIATION_DURATION(radiation,duration)

rule NET_DIVERSIFICATION(c): IF SPECIATION_RATE(c,s) AND
EXTINCTION_RATE(c,e) THEN NET_DIVERSIFICATION_RATE(c,s-e)

———- ECOLOGICAL OPPORTUNITY ———-

enum OpportunityType: NEW_HABITAT VACANT_NICHE COMPETITOR_RELEASE
PREDATOR_RELEASE RESOURCE_EXPANSION MASS_EXTINCTION_AFTERMATH
COLONISATION_EVENT ENVIRONMENTAL_CHANGE

relation HAS_ECOLOGICAL_OPPORTUNITY(radiation,opportunity) relation
OPPORTUNITY_TYPE(opportunity,type) relation
OPPORTUNITY_OCCURS_IN(opportunity,environment) relation
OPPORTUNITY_PROVIDES(opportunity,resource) relation
OPPORTUNITY_REDUCES_COMPETITION(opportunity,value)

———- NICHE DIVERGENCE ———-

relation OCCUPIES_NICHE(species,niche) relation
NICHE_DIVERGENCE_BETWEEN(a,b,value) relation NICHE_OVERLAP(a,b,value)
relation RESOURCE_PARTITIONING_BETWEEN(a,b) relation
HABITAT_PARTITIONING_BETWEEN(a,b) relation
TROPHIC_PARTITIONING_BETWEEN(a,b) relation
TEMPORAL_PARTITIONING_BETWEEN(a,b)

constraint NICHE_METRIC_BOUNDS: IF NICHE_OVERLAP(a,b,v) THEN REQUIRE(0.0
<= v <= 1.0)

———- TRAIT DIVERGENCE ———-

relation HAS_TRAIT(species,trait) relation
TRAIT_DIVERGENCE_BETWEEN(a,b,trait,value) relation
TRAIT_EVOLVES_IN(lineage,trait) relation
TRAIT_ASSOCIATED_WITH_NICHE(trait,niche) relation
MORPHOLOGICAL_DISPARITY(clade,value) relation
FUNCTIONAL_DISPARITY(clade,value)

———- KEY INNOVATIONS ———-

relation HAS_KEY_INNOVATION(lineage,innovation) relation
KEY_INNOVATION_ENABLES(innovation,opportunity) relation
KEY_INNOVATION_AFFECTS(innovation,trait) relation
KEY_INNOVATION_ASSOCIATED_WITH(innovation,diversification)

constraint KEY_INNOVATION_CAUSALITY: IF
KEY_INNOVATION_ASSOCIATED_WITH(i,d) THEN DO_NOT_INFER(CAUSES(i,d))
WITHOUT causal_evidence

———- COLONISATION ———-

relation COLONISES(lineage,region) relation
COLONISATION_EVENT(lineage,event) relation
FOUNDER_POPULATION_OF(population,lineage) relation
GEOGRAPHIC_ISOLATION_AFTER(event,population) relation
RANGE_EXPANSION_OF(lineage,region)

———- SPECIATION ———-

enum SpeciationMode: ALLOPATRIC SYMPATRIC PARAPATRIC PERIPATRIC HYBRID
UNKNOWN

relation HAS_SPECIATION_EVENT(lineage,event) relation
SPECIATION_MODE(event,mode) relation REPRODUCTIVELY_ISOLATED_FROM(a,b)
relation DIVERGES_FROM(a,b) relation SISTER_TAXON_OF(a,b)

rule SISTER_TAXON_SYMMETRY(a,b): IF SISTER_TAXON_OF(a,b) THEN
SISTER_TAXON_OF(b,a)

———- ADAPTATION ———-

relation ADAPTED_TO(species,environment) relation
ADAPTATION_TO(trait,environment) relation
SELECTED_FOR(trait,environment) relation
INCREASES_FITNESS(trait,context) relation
LOCAL_ADAPTATION_IN(population,environment)

constraint ADAPTATION_REQUIRES_EVIDENCE: IF ADAPTATION_TO(t,e) THEN
REQUIRE SUPPORTED_BY(ADAPTATION_TO(t,e),Evidence) OR
MARK_AS_HYPOTHESIS(ADAPTATION_TO(t,e))

———- COMPETITION / CHARACTER DISPLACEMENT ———-

relation COMPETES_WITH(a,b) relation
CHARACTER_DISPLACEMENT_BETWEEN(a,b,trait) relation
ECOLOGICAL_CHARACTER_DISPLACEMENT(a,b,trait) relation
REPRODUCTIVE_CHARACTER_DISPLACEMENT(a,b,trait)

rule COMPETITION_SYMMETRY(a,b): IF COMPETES_WITH(a,b) THEN
COMPETES_WITH(b,a)

———- CONVERGENCE ———-

relation CONVERGENT_WITH(a,b,trait) relation
PARALLEL_EVOLUTION_WITH(a,b,trait) relation
ECOLOGICALLY_EQUIVALENT_TO(a,b)

———- PHYLOGENETIC STRUCTURE ———-

relation MEMBER_OF_PHYLOGENY(taxon,phylogeny) relation
MOST_RECENT_COMMON_ANCESTOR(a,b,ancestor) relation
BRANCHES_FROM(lineage,node) relation DIVERGENCE_TIME(a,b,time) relation
SUPPORT_VALUE(node,value) relation CLADE_AGE(clade,time)

———- EARLY BURST ———-

relation EARLY_BURST_PATTERN(clade,trait) relation
DISPARITY_THROUGH_TIME(clade,value) relation
RATE_THROUGH_TIME(clade,rate) relation
SLOWDOWN_IN_DIVERSIFICATION(clade,time) relation
SLOWDOWN_IN_TRAIT_EVOLUTION(clade,time)

———- ADAPTIVE LANDSCAPE ———-

relation OCCUPIES_ADAPTIVE_PEAK(lineage,peak) relation
MOVES_TOWARD_PEAK(lineage,peak) relation
FITNESS_LANDSCAPE(environment,landscape) relation
PEAK_ASSOCIATED_WITH_NICHE(peak,niche)

———- EXTINCTION / PERSISTENCE ———-

relation GOES_EXTINCT_AT(lineage,time) relation
PERSISTS_TO(lineage,time) relation
EXTINCTION_RATE_DURING(radiation,rate) relation
SURVIVING_LINEAGE_OF(lineage,radiation)

———- COMPARATIVE RADIATIONS ———-

relation ANALOGOUS_RADIATION_TO(a,b) relation
SHARES_OPPORTUNITY_TYPE(a,b,type) relation
SHARES_TRAIT_PATTERN(a,b,pattern) relation
DIFFERS_IN_DIVERSIFICATION_RATE(a,b,value)

———- FOSSIL EVIDENCE ———-

relation FOSSIL_OF(fossil,lineage) relation DATED_TO(fossil,time)
relation PRESERVES_TRAIT(fossil,trait) relation
SUPPORTS_DIVERSIFICATION_SEQUENCE(fossil,radiation)

———- SPATIAL / TEMPORAL CONTEXT ———-

relation OCCURS_IN(radiation,region) relation
HAS_SPATIAL_SCALE(radiation,scale) relation
HAS_TEMPORAL_SCALE(radiation,scale) relation
OBSERVED_DURING(entity,period)

———- EVIDENCE ———-

relation OBSERVES(observation,entity) relation
OBSERVED_AT(observation,location) relation
OBSERVED_ON(observation,datetime) relation
SUPPORTED_BY(assertion,evidence) relation DERIVED_FROM(evidence,source)
relation HAS_CONFIDENCE(assertion,score)

enum EvidenceType: PHYLOGENETIC GENOMIC POPULATION_GENETIC MORPHOLOGICAL
FUNCTIONAL_TRAIT ECOLOGICAL BIOGEOGRAPHIC FOSSIL DIVERSIFICATION_MODEL
COMPARATIVE_METHOD EXPERIMENTAL LITERATURE

CONFIDENCE: VERIFIED: 0.95..1.00 HIGH: 0.80..0.949 MEDIUM: 0.60..0.799
LOW: 0.00..0.599

rule CONFIDENCE_BOUNDS(a,score): IF HAS_CONFIDENCE(a,score) THEN
REQUIRE(0.0 <= score <= 1.0)

———- SEMANTIC EQUIVALENCE ———-

SEMANTIC_EQUIVALENCE: “adaptive radiation” ~= “rapid ecological
diversification of a lineage” “ecological opportunity” ~= “availability
of underused ecological resources or niches” “key innovation” ~= “trait
associated with access to new ecological opportunities” “niche
divergence” ~= “ecological niche differentiation” “character
displacement” ~= “trait divergence associated with species interaction”
“early burst” ~= “initially elevated rate of diversification or trait
evolution” “morphological disparity” ~= “variation in organismal form”
“functional disparity” ~= “variation in ecological function”
“diversification rate” ~= “rate of lineage accumulation” “adaptive peak”
~= “fitness peak” “radiation” ~= “lineage diversification”

rule NORMALISE_TERM(term): IF term MATCHES SEMANTIC_EQUIVALENCE.alias
THEN MAP_TO_CANONICAL(term)

———- QUERY MODEL ———-

query RADIATION_PROFILE(r): RETURN: ancestral_lineage(r)
descendant_lineages(r) start_time(r) duration(r) diversification_rate(r)
ecological_opportunities(r) key_innovations(r) niche_divergence(r)
trait_divergence(r) evidence(r) confidence(r)

query CLADE_DIVERSIFICATION_PROFILE(c): RETURN: clade_age(c)
speciation_rate(c) extinction_rate(c) net_diversification_rate(c)
disparity(c) rate_through_time(c)

query ECOLOGICAL_DIVERGENCE_PROFILE(c): RETURN: niches(c)
niche_overlap(c) resource_partitioning(c) habitat_partitioning(c)
trophic_partitioning(c) adaptations(c)

query KEY_INNOVATION_PROFILE(i): RETURN: lineage(i) trait(i)
ecological_opportunity(i) diversification_association(i)
causal_evidence(i)

query TRACE_EVIDENCE(assertion): RETURN: supporting_evidence(assertion)
provenance(assertion) confidence(assertion)

———- CONSISTENCY ———-

constraint EVIDENCE_REQUIRED: FORALL scientific_assertion: REQUIRE
SUPPORTED_BY(scientific_assertion,Evidence) OR
MARK_AS_HYPOTHESIS(scientific_assertion)

constraint UNKNOWN_IS_NOT_FALSE: IF data_missing(assertion) THEN
MARK_UNKNOWN(assertion) AND NOT NEGATE(assertion)

constraint RAPID_DIVERSIFICATION_NOT_AUTOMATICALLY_ADAPTIVE: IF
high_diversification_rate(clade) THEN
DO_NOT_INFER(HAS_ADAPTIVE_RADIATION(clade,radiation)) WITHOUT
ecological_divergence_evidence

constraint CORRELATION_NOT_KEY_INNOVATION_CAUSATION: IF
trait_correlates_with_diversification(t,c) THEN
DO_NOT_INFER(CAUSES(t,c)) WITHOUT causal_support

constraint SCALE_PRESERVATION: IF
radiation_estimate(r,spatial_scale,temporal_scale) THEN
PRESERVE_SCALE(r,spatial_scale,temporal_scale)

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_radiation(r): identify_ancestral_lineage(r)
identify_descendant_lineages(r) establish_temporal_context(r)
identify_ecological_opportunity(r) attach_evidence(r)
recalculate_confidence(r)

on_new_phylogeny(p): preserve_taxon_sampling(p) preserve_methodology(p)
update_divergence_times(p) update_diversification_estimates(p)
preserve_support_values(p)

on_new_trait_data(t): identify_lineage(t) update_trait_disparity(t)
test_niche_associations(t) preserve_measurement_method(t)

on_new_key_innovation_hypothesis(k): preserve_hypothesis(k)
identify_trait(k) identify_opportunity(k) attach_supporting_evidence(k)
distinguish_association_from_causation(k)

on_conflicting_radiation_models(a,b): preserve(a) preserve(b)
compare_phylogenies(a,b) compare_diversification_models(a,b)
compare_trait_data(a,b) compare_ecological_evidence(a,b)
flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_adaptive_radiation
preserve: - ancestral_lineage - descendant_lineages -
phylogenetic_context - temporal_context - spatial_context -
diversification_rate - speciation_rate - extinction_rate -
ecological_opportunity - niche_divergence - trait_divergence -
key_innovations - adaptations - evidence - provenance - confidence
infer: - valid_ancestry_relations -
supported_diversification_relations - supported_niche_divergence -
semantic_equivalence prohibit: -
rapid_diversification_equals_adaptive_radiation_without_ecology -
trait_correlation_equals_key_innovation_causation -
unsupported_adaptation - unsupported_common_ancestor -
confidence_above_evidence ambiguity: action:
preserve_multiple_radiation_hypotheses resolution:
prefer_phylogenetic_ecological_trait_and_temporal_evidence missing_data:
action: mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “AdaptiveRadiationOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies >
Evolutionary Biology > Adaptive Radiation Ontology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/evolutionary-biology/adaptive-radiation-ontology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - adaptive radiation - ancestral lineages -
diversification - ecological opportunity - niche divergence - trait
divergence - key innovations - colonisation - speciation - adaptation -
character displacement - convergence - phylogenetic structure - early
burst patterns - adaptive landscapes - extinction - comparative
radiations - fossil evidence - evidence deterministic_normalisation:
true provenance_required: true confidence_required: true

terminate AdaptiveRadiationOntology when:
ancestral_and_descendant_lineages_resolved AND
diversification_context_preserved AND ecological_opportunity_resolved
AND niche_and_trait_divergence_contextualised AND
association_and_causation_distinguished AND evidence_links_preserved AND
confidence_values_validated AND unresolved_radiation_hypotheses_marked

end flow