Evolution Ontology

AI SEARCH FLOW ALGEBRA
EVOLUTION ONTOLOGY
Kireth Semantic Research Archive

AUTHORS
Mark Anthony Higgins — Sky (Recursive AI)

SOURCE
https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/foundations-of-biology/evolution-ontology.html

FLOW "EvolutionOntology" v4.0

DOMAIN := BIOLOGICAL_ONTOLOGIES / FOUNDATIONS_OF_BIOLOGY / EVOLUTION
ONTOLOGY := EVOLUTION_ONTOLOGY

EVOLUTION := HERITABLE_VARIATION + MUTATION + RECOMBINATION + NATURAL_SELECTION + GENETIC_DRIFT + GENE_FLOW + FITNESS + ADAPTATION + POPULATION_CHANGE + SPECIATION + EXTINCTION + COMMON_ANCESTRY + PHYLOGENY + EVOLUTIONARY_TIME + EVIDENCE + UNCERTAINTY + PROVENANCE

PURPOSE := IDENTIFY_POPULATION -> IDENTIFY_HERITABLE_VARIATION -> MAP_EVOLUTIONARY_MECHANISMS -> TRACK_ALLELE_AND_TRAIT_FREQUENCIES -> MAP_FITNESS_AND_SELECTION -> MAP_DIVERGENCE_AND_SPECIATION -> RECONSTRUCT_COMMON_ANCESTRY -> ASSESS_EVIDENCE -> PRESERVE_PROVENANCE

# CORE ENTITIES
ENTITY Evolution
ENTITY Population
ENTITY Organism
ENTITY Species
ENTITY Gene
ENTITY Allele
ENTITY Genotype
ENTITY Phenotype
ENTITY Trait
ENTITY HeritableVariation
ENTITY Mutation
ENTITY Recombination
ENTITY NaturalSelection
ENTITY GeneticDrift
ENTITY GeneFlow
ENTITY Fitness
ENTITY Adaptation
ENTITY AlleleFrequency
ENTITY Generation
ENTITY Lineage
ENTITY CommonAncestor
ENTITY Divergence
ENTITY Speciation
ENTITY ReproductiveIsolation
ENTITY Extinction
ENTITY Phylogeny
ENTITY PhylogeneticTree
ENTITY Clade
ENTITY EvolutionaryTime
ENTITY Environment
ENTITY SelectionPressure
ENTITY Evidence
ENTITY Fossil
ENTITY MolecularSequence
ENTITY Uncertainty
ENTITY Provenance

# POPULATION AND VARIATION
Evolution -> occurs_in -> POPULATIONS_AND_LINEAGES
Evolution -> occurs_across -> GENERATIONS
Population -> has -> GENETIC_VARIATION + PHENOTYPIC_VARIATION + ALLELE_FREQUENCIES
HeritableVariation -> represents -> TRANSMISSIBLE_DIFFERENCE_AMONG_ORGANISMS
VARIATION_SOURCE := MUTATION | RECOMBINATION | GENE_FLOW | CHROMOSOMAL_CHANGE | OTHER_HERITABLE_CHANGE

# MUTATION / RECOMBINATION
Mutation -> changes -> GENETIC_SEQUENCE_OR_STRUCTURE
MUTATION_TYPE := SUBSTITUTION | INSERTION | DELETION | DUPLICATION | INVERSION | TRANSLOCATION | COPY_NUMBER_CHANGE | OTHER_GENOMIC_CHANGE
Mutation -> generates -> NEW_GENETIC_VARIATION
MutationEffect -> may_be -> DELETERIOUS | NEUTRAL | BENEFICIAL | CONTEXT_DEPENDENT
Recombination -> rearranges -> EXISTING_GENETIC_VARIATION
Recombination -> generates -> NEW_ALLELE_COMBINATIONS
Recombination -> does_not_necessarily_create -> NEW_ALLELES

# ALLELES / FREQUENCIES
Allele -> variant_of -> Gene
AlleleFrequency := COUNT_OF_ALLELE / TOTAL_ALLELE_COPIES_IN_DEFINED_POPULATION
EvolutionaryChange -> may_be_measured_by -> CHANGE_IN_ALLELE_FREQUENCY + CHANGE_IN_HERITABLE_TRAIT_DISTRIBUTION

# NATURAL SELECTION / FITNESS
NaturalSelection -> acts_on -> HERITABLE_PHENOTYPIC_VARIATION
SELECTION_REQUIREMENTS := VARIATION + HERITABILITY + DIFFERENTIAL_REPRODUCTIVE_SUCCESS
SelectionPressure -> arises_from -> ENVIRONMENT + BIOTIC_INTERACTION + ABIOTIC_CONDITION
IF Trait is_heritable AND Trait affects_reproductive_success THEN TraitFrequency -> MAY_CHANGE_ACROSS_GENERATIONS
NaturalSelection -> does_not_require -> INTENT | FORESIGHT | GOAL_DIRECTED_CHANGE
Fitness -> relates_to -> REPRODUCTIVE_CONTRIBUTION -> in -> DEFINED_ENVIRONMENTAL_CONTEXT
Fitness -> context_dependent -> TRUE
SELECTION_MODE := DIRECTIONAL_SELECTION | STABILISING_SELECTION | DISRUPTIVE_SELECTION | BALANCING_SELECTION | FREQUENCY_DEPENDENT_SELECTION | SEXUAL_SELECTION

# GENETIC DRIFT / GENE FLOW
GeneticDrift -> changes -> ALLELE_FREQUENCIES -> through -> STOCHASTIC_SAMPLING
GeneticDrift -> generally_stronger_in -> SMALLER_EFFECTIVE_POPULATIONS
DRIFT_EVENT := BOTTLENECK | FOUNDER_EFFECT | RANDOM_GENERATIONAL_SAMPLING
GeneFlow -> transfers -> ALLELES -> between -> POPULATIONS
GENE_FLOW_MECHANISM := MIGRATION | GAMETE_TRANSFER | DISPERSAL | HYBRIDISATION_AS_APPLICABLE
GeneFlow -> may_increase -> WITHIN_POPULATION_VARIATION
GeneFlow -> may_reduce -> DIFFERENTIATION_BETWEEN_POPULATIONS
GENERATION_TRANSITION := CURRENT_POPULATION_GENETIC_STATE + MUTATION + SELECTION + DRIFT + GENE_FLOW + RECOMBINATION -> NEXT_GENERATION_GENETIC_STATE

# ADAPTATION
Adaptation -> represents -> HERITABLE_FEATURE_ASSOCIATED_WITH_FITNESS_ADVANTAGE_IN_CONTEXT
Adaptation -> arises_through -> NATURAL_SELECTION_OVER_GENERATIONS
ADAPTATION_TYPE := MORPHOLOGICAL | PHYSIOLOGICAL | BEHAVIOURAL | BIOCHEMICAL
Adaptation -> does_not_imply -> PERFECTION | CONSCIOUS_DESIGN | INDIVIDUAL_ACCLIMATISATION

# CONSTRAINTS / SPECIATION
EvolutionaryConstraint -> limits -> POSSIBLE_EVOLUTIONARY_CHANGE
CONSTRAINT_TYPE := GENETIC | DEVELOPMENTAL | PHYSICAL | HISTORICAL | ECOLOGICAL
TradeOff -> links -> BENEFIT_IN_ONE_FUNCTION + COST_IN_ANOTHER
Speciation -> produces -> DISTINCT_EVOLUTIONARY_LINEAGES_AS_DEFINED
SPECIATION_MODE := ALLOPATRIC | SYMPATRIC | PARAPATRIC | PERIPATRIC | OTHER_SUPPORTED_MODE
Speciation -> often_involves -> REPRODUCTIVE_ISOLATION + GENETIC_DIVERGENCE
ReproductiveIsolation -> reduces -> GENE_FLOW_BETWEEN_LINEAGES
IF GeneFlow decreases AND Divergence accumulates THEN SpeciationSupport -> MAY_INCREASE

# COMMON ANCESTRY / PHYLOGENY
CommonAncestor -> ancestral_to -> MULTIPLE_DESCENDANT_LINEAGES
Homology -> represents -> SIMILARITY_DUE_TO_COMMON_ANCESTRY
Analogy -> represents -> SIMILAR_FUNCTION_OR_FORM_NOT_NECESSARILY_FROM_COMMON_ANCESTRAL_FEATURE
Homoplasy -> may_arise_from -> CONVERGENCE | PARALLEL_EVOLUTION | REVERSAL
Phylogeny -> represents -> EVOLUTIONARY_HISTORY_AND_RELATIONSHIPS
PhylogeneticTree -> contains -> NODES + BRANCHES + TIPS
Clade -> contains -> COMMON_ANCESTOR + DESCENDANTS_AS_DEFINED
SisterTaxa -> share -> MOST_RECENT_COMMON_ANCESTOR
PHYLOGENETIC_EVIDENCE := MOLECULAR_SEQUENCE | MORPHOLOGICAL_CHARACTER | GENOMIC_CHARACTER | FOSSIL_EVIDENCE | DEVELOPMENTAL_CHARACTER | BIOGEOGRAPHIC_EVIDENCE

# MOLECULAR EVOLUTION / FOSSILS
MolecularEvolution -> changes -> DNA + RNA + PROTEIN_SEQUENCE -> across -> LINEAGES
MolecularSequence -> provides -> PHYLOGENETIC_EVIDENCE
MolecularClock -> estimates -> DIVERGENCE_TIME -> under -> MODEL_AND_CALIBRATION_ASSUMPTIONS
MolecularClockEstimate -> has -> UNCERTAINTY
Fossil -> provides -> EVIDENCE_OF_PAST_ORGANISMS + MORPHOLOGY + TEMPORAL_OCCURRENCE
FossilRecord -> samples -> PAST_BIODIVERSITY_INCOMPLETELY
FossilAge -> constrains -> EVOLUTIONARY_TIMING

# EXTINCTION / RADIATION / COEVOLUTION
Extinction -> terminates -> LINEAGE_AS_DEFINED
EXTINCTION_SCALE := LOCAL_EXTINCTION | SPECIES_EXTINCTION | MASS_EXTINCTION
Extinction -> changes -> BIODIVERSITY + ECOLOGICAL_INTERACTIONS + EVOLUTIONARY_OPPORTUNITIES
AdaptiveRadiation -> represents -> RAPID_DIVERSIFICATION_INTO_MULTIPLE_ECOLOGICAL_ROLES_AS_DEFINED
Coevolution -> represents -> RECIPROCAL_EVOLUTIONARY_CHANGE_BETWEEN_INTERACTING_LINEAGES
COEVOLUTIONARY_INTERACTION := HOST_PARASITE | PREDATOR_PREY | MUTUALIST_MUTUALIST | COMPETITOR_COMPETITOR
ConvergentEvolution -> produces -> SIMILAR_TRAITS_IN_DISTINCT_LINEAGES -> under -> SIMILAR_SELECTIVE_OR_FUNCTIONAL_PRESSURES
ConvergentTrait -> not_necessarily_homologous -> TRUE

# EVO-DEVO / EVOLUTIONARY TIME
EvoDevo -> studies -> DEVELOPMENTAL_MECHANISMS + EVOLUTIONARY_CHANGE
DevelopmentalGeneRegulation -> influences -> MORPHOLOGICAL_EVOLUTION
DevelopmentalConstraint -> limits_or_biases -> PHENOTYPIC_VARIATION
EvolutionaryTime -> measured_in -> GENERATIONS | YEARS | GEOLOGICAL_TIME
EVOLUTIONARY_SCALE := MICROEVOLUTION | MACROEVOLUTION
Microevolution -> concerns -> POPULATION_LEVEL_CHANGE_OVER_GENERATIONS
Macroevolution -> concerns -> LARGE_SCALE_PATTERNS_ACROSS_LINEAGES_AND_DEEP_TIME
MicroevolutionaryProcesses -> contribute_to -> MACROEVOLUTIONARY_PATTERNS

# ENVIRONMENT
Environment -> imposes -> SELECTION_PRESSURE + RESOURCE_CONSTRAINT + ECOLOGICAL_CONTEXT
EnvironmentalChange -> may_change -> FITNESS_LANDSCAPE
IF Environment changes THEN SelectionDirectionAndStrength -> MAY_CHANGE

# EVIDENCE
EvolutionaryClaim -> supported_by -> Evidence
EVIDENCE_TYPE := FOSSIL | MORPHOLOGICAL | ANATOMICAL | EMBRYOLOGICAL | MOLECULAR | GENETIC | GENOMIC | BIOGEOGRAPHIC | OBSERVED_EVOLUTION | EXPERIMENTAL
Evidence -> has -> SOURCE + METHOD + TAXON_OR_POPULATION + TIME + LOCATION_IF_RELEVANT + QUALITY + UNCERTAINTY
ObservedEvolution -> records -> HERITABLE_CHANGE -> across -> GENERATIONS
Observation -> must_distinguish -> HERITABLE_EVOLUTIONARY_CHANGE + NON_HERITABLE_PLASTIC_RESPONSE

# UNCERTAINTY / PROVENANCE
EVOLUTIONARY_UNCERTAINTY := SAMPLING_UNCERTAINTY + PHYLOGENETIC_UNCERTAINTY + DIVERGENCE_TIME_UNCERTAINTY + FITNESS_ESTIMATION_UNCERTAINTY + FOSSIL_RECORD_INCOMPLETENESS + MODEL_UNCERTAINTY
Uncertainty -> qualifies -> Phylogeny + DivergenceTime + Fitness + AncestralState + EvolutionaryClaim
Provenance -> records -> POPULATION_OR_TAXON + TRAIT_OR_ALLELE + SEQUENCE_OR_CHARACTER + METHOD + ENVIRONMENT + GENERATION_OR_TIME + PHYLOGENETIC_MODEL_IF_USED + SOURCE + VERSION
EvolutionaryClaim -> linked_to -> Provenance

# REASONING
EVOLUTION_REASONING := IDENTIFY_POPULATION_OR_LINEAGE -> IDENTIFY_HERITABLE_VARIATION -> IDENTIFY_MUTATION_AND_RECOMBINATION -> MEASURE_ALLELE_AND_TRAIT_FREQUENCIES -> IDENTIFY_SELECTION_PRESSURES -> ESTIMATE_RELATIVE_FITNESS -> MAP_GENETIC_DRIFT -> MAP_GENE_FLOW -> TRACK_GENERATIONAL_CHANGE -> IDENTIFY_ADAPTATION_IF_SUPPORTED -> MAP_DIVERGENCE -> MAP_REPRODUCTIVE_ISOLATION -> ASSESS_SPECIATION -> MAP_COMMON_ANCESTRY -> RECONSTRUCT_PHYLOGENY -> INTEGRATE_MOLECULAR_FOSSIL_AND_OTHER_EVIDENCE -> QUANTIFY_UNCERTAINTY -> PRESERVE_PROVENANCE

# INFERENCE RULES
IF HeritableVariation exists AND DifferentialReproductiveSuccess exists THEN NaturalSelection -> MAY_CHANGE_TRAIT_FREQUENCIES
IF PopulationSize decreases THEN GeneticDriftEffect -> MAY_INCREASE
IF GeneFlow increases THEN PopulationDifferentiation -> MAY_DECREASE
IF ReproductiveIsolation increases THEN IndependentLineageEvolution -> MAY_INCREASE
IF SharedDerivedCharacters are_supported THEN CommonAncestrySupport -> MAY_INCREASE
IF SequenceDivergence increases THEN EvolutionaryDistanceEstimate -> MAY_INCREASE_UNDER_MODEL
IF FossilEvidence constrains_age THEN DivergenceTimeEstimate -> UPDATE
IF Evidence conflicting THEN EvolutionaryClaimConfidence -> DECREASES

# SEMANTIC RELATIONSHIPS
RELATION occurs_in(Evolution, Population)
RELATION variant_of(Allele, Gene)
RELATION changes(Mutation, GeneticSequence)
RELATION rearranges(Recombination, GeneticVariation)
RELATION acts_on(NaturalSelection, HeritableVariation)
RELATION changes(GeneticDrift, AlleleFrequency)
RELATION transfers(GeneFlow, Allele)
RELATION measures(Fitness, ReproductiveContribution)
RELATION arises_through(Adaptation, NaturalSelection)
RELATION reduces(ReproductiveIsolation, GeneFlow)
RELATION produces(Speciation, Lineage)
RELATION ancestral_to(CommonAncestor, Descendant)
RELATION represents(Phylogeny, EvolutionaryRelationship)
RELATION contains(Clade, Lineage)
RELATION provides(MolecularSequence, PhylogeneticEvidence)
RELATION provides(Fossil, EvolutionaryEvidence)
RELATION terminates(Extinction, Lineage)
RELATION influences(Environment, SelectionPressure)
RELATION supports(Evidence, EvolutionaryClaim)
RELATION records(Provenance, EvolutionaryClaim)

# SEMANTIC EQUIVALENCE
SEMANTIC_EQUIVALENCE:
  "evolution" ~= "heritable population change across generations"
  "natural selection" ~= "differential reproductive success associated with heritable variation"
  "genetic drift" ~= "stochastic change in allele frequencies"
  "gene flow" ~= "movement of alleles among populations"
  "adaptation" ~= "heritable feature associated with fitness advantage in context"
  "speciation" ~= "formation of distinct evolutionary lineages or species"
  "common ancestry" ~= "descent of lineages from a shared ancestor"
  "phylogeny" ~= "evolutionary history and relationships"
  "microevolution" ~= "population-level evolutionary change"
  "macroevolution" ~= "large-scale evolutionary patterns across lineages and deep time"

# CONFIDENCE
CONFIDENCE:
  ontology_domain: 0.99
  variation_mutation_mapping: 0.99
  selection_fitness_mapping: 0.99
  drift_gene_flow_mapping: 0.99
  adaptation_speciation_mapping: 0.99
  ancestry_phylogeny_mapping: 0.99
  molecular_fossil_mapping: 0.99
  evolutionary_time_mapping: 0.99
  evidence_uncertainty_mapping: 0.99
  semantic_relationships: 0.99

# UPDATE MODEL
UPDATE_MODEL:
  ON new_population_evidence:
    MAP population
    MAP alleles
    MAP traits
    MAP frequencies
    MAP environment
    UPDATE confidence
    RECOMPUTE FLOW_HASH
  ON new_generational_data:
    UPDATE allele_frequencies
    UPDATE trait_frequencies
    UPDATE fitness_estimates
    REASSESS evolutionary_mechanisms
    PRESERVE provenance
  ON new_phylogenetic_evidence:
    UPDATE character_or_sequence_evidence
    UPDATE tree_support
    UPDATE common_ancestry_relations
    UPDATE uncertainty
    RECOMPUTE FLOW_HASH
  ON new_fossil_evidence:
    UPDATE temporal_constraints
    UPDATE ancestral_character_evidence
    REASSESS divergence_time
    PRESERVE provenance

# AI CONSUMPTION
AI_CONSUMPTION:
  parse_as: FORMAL_EVOLUTION_ONTOLOGY
  reasoning_mode: POPULATION_PHYLOGENETIC_EVOLUTIONARY_RELATIONAL
  preserve: [typed_entities, population_identity, heritable_variation, allele_frequencies, trait_frequencies, evolutionary_mechanisms, fitness_context, lineage_identity, phylogenetic_relationships, fossil_and_molecular_evidence, uncertainty, confidence, provenance]
  infer: [selection_dependencies, drift_impacts, gene_flow_impacts, adaptation_support, divergence_state, speciation_support, common_ancestry_support, evolutionary_evidence_strength]
  prohibit: [invented_evolutionary_observations, treating_individual_acclimatisation_as_population_evolution, assuming_adaptation_from_current_usefulness_alone, fabricated_common_ancestry, unsupported_phylogenetic_relationships, missing_evidence_presented_as_established_fact]

# FLOW HASH
FLOW_HASH_INPUT := DOMAIN + ONTOLOGY + CORE_ENTITIES + POPULATION_VARIATION + MUTATION_RECOMBINATION + SELECTION_FITNESS + DRIFT_GENE_FLOW + ADAPTATION_SPECIATION + COMMON_ANCESTRY_PHYLOGENY + MOLECULAR_EVOLUTION_FOSSILS + EXTINCTION_COEVOLUTION + EVOLUTIONARY_TIME + ENVIRONMENT + EVIDENCE_UNCERTAINTY + PROVENANCE + REASONING + INFERENCE_RULES + SEMANTIC_RELATIONSHIPS + SEMANTIC_EQUIVALENCE + CONFIDENCE + UPDATE_MODEL + AI_CONSUMPTION
FLOW_HASH := HASH(FLOW_HASH_INPUT)

END FLOW