Evolutionary Biology

flow “EvolutionaryBiologyOntology” v1.0

KIRETH SEMANTIC RESEARCH ARCHIVE

AI CORE > ONTOLOGIES > BIOLOGICAL ONTOLOGIES > EVOLUTIONARY BIOLOGY

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.html”

———- CORE TYPES ———-

type Organism type Species type Population type Gene type Allele type
Genome type Genotype type Phenotype type Trait type Mutation type
Variation type Selection type Adaptation type Lineage type Taxon type
Ancestor type Descendant type Phylogeny type EvolutionaryEvent type
Observation type Evidence type Source

———- INHERITANCE ———-

relation INSTANCE_OF(entity,type) relation HAS_GENE(entity,gene)
relation HAS_ALLELE(entity,allele) relation
HAS_GENOTYPE(entity,genotype) relation HAS_PHENOTYPE(entity,phenotype)
relation HAS_TRAIT(entity,trait) relation
INHERITS_FROM(descendant,ancestor,feature) relation
TRANSMITS(parent,offspring,feature)

rule INHERITANCE_PATH(a,b,f): IF TRANSMITS(a,b,f) THEN
INHERITS_FROM(b,a,f)

———- GENETIC VARIATION ———-

relation HAS_VARIATION(population,variation) relation
ALLELE_FREQUENCY(population,allele,frequency) relation
GENOTYPE_FREQUENCY(population,genotype,frequency) relation
GENETIC_DIVERSITY(population,value) relation
PHENOTYPIC_VARIATION(population,trait,value)

constraint FREQUENCY_BOUNDS: IF ALLELE_FREQUENCY(p,a,f) OR
GENOTYPE_FREQUENCY(p,g,f) THEN REQUIRE(0.0 <= f <= 1.0)

———- MUTATION ———-

enum MutationType: SUBSTITUTION INSERTION DELETION DUPLICATION INVERSION
TRANSLOCATION COPY_NUMBER_VARIATION CHROMOSOMAL_CHANGE

relation HAS_MUTATION(entity,mutation) relation
MUTATION_TYPE(mutation,type) relation MUTATION_AFFECTS(mutation,gene)
relation MUTATION_CHANGES(mutation,feature) relation
MUTATION_RATE(population,rate) relation ARISES_IN(mutation,lineage)

———- RECOMBINATION ———-

relation RECOMBINES_WITH(sequence_a,sequence_b) relation
CROSSING_OVER_BETWEEN(region_a,region_b) relation
PRODUCES_GENOTYPE(process,genotype) relation
RECOMBINATION_RATE(region,rate)

———- NATURAL SELECTION ———-

enum SelectionType: DIRECTIONAL STABILISING DISRUPTIVE BALANCING
PURIFYING POSITIVE SEXUAL FREQUENCY_DEPENDENT

relation SELECTED_FOR(trait,environment) relation
SELECTED_AGAINST(trait,environment) relation
HAS_SELECTION_COEFFICIENT(trait,value) relation
INCREASES_FITNESS(trait,context) relation
DECREASES_FITNESS(trait,context) relation
HAS_RELATIVE_FITNESS(entity,value)

rule ADAPTIVE_SELECTION(t,e): IF SELECTED_FOR(t,e) AND
INCREASES_FITNESS(t,e) THEN POSSIBLE_ADAPTIVE_TRAIT(t,e)

———- ADAPTATION ———-

relation ADAPTED_TO(entity,environment) relation
ADAPTATION_OF(trait,entity) relation ADAPTATION_TO(trait,environment)
relation CONFERS_ADVANTAGE(trait,context) relation
HAS_ADAPTIVE_VALUE(trait,value)

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

———- GENETIC DRIFT ———-

relation EXPERIENCES_DRIFT(population,event) relation
DRIFT_CHANGES_FREQUENCY(event,allele,value) relation
BOTTLENECK_IN(population,event) relation
FOUNDER_EFFECT_IN(population,event) relation
EFFECTIVE_POPULATION_SIZE(population,value)

———- GENE FLOW ———-

relation GENE_FLOW_BETWEEN(population_a,population_b) relation
MIGRATION_BETWEEN(population_a,population_b) relation
INTRODUCES_ALLELE(population,allele) relation
HOMOGENISES(population_a,population_b)

rule GENE_FLOW_SYMMETRIC_CONTEXT(a,b): IF GENE_FLOW_BETWEEN(a,b) THEN
CONNECTED_GENETICALLY(a,b)

———- POPULATION CHANGE ———-

relation EVOLVES_OVER(population,period) relation
FREQUENCY_CHANGES(population,allele,from,to) relation
TRAIT_MEAN_CHANGES(population,trait,from,to) relation
GENERATION_INTERVAL(population,duration)

———- SPECIATION ———-

enum SpeciationType: ALLOPATRIC SYMPATRIC PARAPATRIC PERIPATRIC
HYBRID_SPECIATION

relation SPECIATES_INTO(ancestor,species) relation
SPECIATION_TYPE(event,type) relation REPRODUCTIVELY_ISOLATED_FROM(a,b)
relation GEOGRAPHICALLY_ISOLATED_FROM(a,b) relation DIVERGES_FROM(a,b)
relation HYBRIDISES_WITH(a,b)

rule DIVERGENCE_SYMMETRY(a,b): IF DIVERGES_FROM(a,b) THEN
DIVERGES_FROM(b,a)

———- REPRODUCTIVE ISOLATION ———-

enum IsolationMechanism: TEMPORAL BEHAVIOURAL ECOLOGICAL MECHANICAL
GAMETIC HYBRID_INVIABILITY HYBRID_STERILITY

relation ISOLATED_BY(a,b,mechanism) relation
PREZYGOTIC_BARRIER(a,b,mechanism) relation
POSTZYGOTIC_BARRIER(a,b,mechanism)

———- COMMON ANCESTRY ———-

relation DESCENDED_FROM(descendant,ancestor) relation
ANCESTOR_OF(ancestor,descendant) relation SHARES_ANCESTOR_WITH(a,b)
relation MOST_RECENT_COMMON_ANCESTOR(a,b,ancestor)

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

rule COMMON_ANCESTRY(a,b,c): IF DESCENDED_FROM(a,c) AND
DESCENDED_FROM(b,c) THEN SHARES_ANCESTOR_WITH(a,b)

———- PHYLOGENY ———-

relation MEMBER_OF_PHYLOGENY(taxon,phylogeny) relation
SISTER_TAXON_OF(a,b) relation CLADE_CONTAINS(clade,taxon) relation
BRANCHES_FROM(lineage,node) relation DIVERGENCE_TIME(a,b,time) relation
SUPPORT_VALUE(node,value)

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

———- HOMOLOGY / ANALOGY ———-

relation HOMOLOGOUS_TO(a,b) relation ANALOGOUS_TO(a,b) relation
DERIVED_FROM_ANCESTRAL_STRUCTURE(structure,ancestor_structure) relation
CONVERGENT_WITH(trait_a,trait_b)

rule HOMOLOGY_SYMMETRY(a,b): IF HOMOLOGOUS_TO(a,b) THEN
HOMOLOGOUS_TO(b,a)

rule ANALOGY_SYMMETRY(a,b): IF ANALOGOUS_TO(a,b) THEN ANALOGOUS_TO(b,a)

———- CONVERGENT / DIVERGENT EVOLUTION ———-

relation CONVERGES_WITH(lineage_a,lineage_b,trait) relation
DIVERGES_IN(lineage_a,lineage_b,trait) relation
PARALLEL_EVOLUTION_WITH(a,b,trait)

———- COEVOLUTION ———-

relation COEVOLVES_WITH(a,b) relation SELECTIVE_PRESSURE_ON(a,b)
relation RECIPROCAL_SELECTION(a,b)

rule COEVOLUTION_SYMMETRY(a,b): IF COEVOLVES_WITH(a,b) THEN
COEVOLVES_WITH(b,a)

———- SEXUAL SELECTION ———-

relation MATE_CHOICE_FOR(entity,trait) relation
INTRASEXUAL_COMPETITION_FOR(entity,resource) relation
SEXUALLY_SELECTED_TRAIT(entity,trait) relation
MATING_SUCCESS(entity,value)

———- MOLECULAR EVOLUTION ———-

relation SEQUENCE_HOMOLOGY(a,b,value) relation
SUBSTITUTION_RATE(sequence,rate) relation
MOLECULAR_CLOCK_RATE(lineage,rate) relation
CONSERVED_REGION(sequence,region) relation
POSITIVE_SELECTION_AT(gene,site) relation
PURIFYING_SELECTION_AT(gene,site)

———- MACROEVOLUTION ———-

relation ORIGINATES_AT(taxon,time) relation GOES_EXTINCT_AT(taxon,time)
relation DIVERSIFICATION_RATE(clade,rate) relation
SPECIATION_RATE(clade,rate) relation EXTINCTION_RATE(clade,rate)
relation ADAPTIVE_RADIATION_IN(clade,event)

———- FOSSIL RECORD ———-

relation FOSSIL_OF(fossil,taxon) relation FOUND_IN(fossil,formation)
relation DATED_TO(fossil,time) relation TRANSITIONAL_BETWEEN(fossil,a,b)
relation PRESERVES_TRAIT(fossil,trait)

———- BIOGEOGRAPHY ———-

relation DISTRIBUTED_IN(taxon,region) relation
DISPERSAL_TO(taxon,region) relation
VICARIANCE_BETWEEN(population_a,population_b,event) relation
ENDEMIC_TO(taxon,region) relation RANGE_EXPANSION(taxon,region) relation
RANGE_CONTRACTION(taxon,region)

———- EXTINCTION ———-

enum ExtinctionType: BACKGROUND MASS_EXTINCTION LOCAL_EXTINCTION
GLOBAL_EXTINCTION

relation EXTINCTION_TYPE(event,type) relation EXTINCT_IN(taxon,region)
relation EXTINCT_AT(taxon,time) relation
EXTINCTION_DRIVEN_BY(taxon,factor)

constraint LOCAL_NOT_GLOBAL_EXTINCTION: IF EXTINCT_IN(taxon,region) THEN
DO_NOT_INFER(GLOBAL_EXTINCTION(taxon))

———- 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: GENETIC GENOMIC MOLECULAR MORPHOLOGICAL DEVELOPMENTAL
FOSSIL BIOGEOGRAPHIC EXPERIMENTAL_EVOLUTION POPULATION_GENETIC
PHYLOGENETIC COMPARATIVE 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: “evolution” ~= “biological evolution” “natural
selection” ~= “selection by differential reproductive success” “genetic
drift” ~= “stochastic allele-frequency change” “gene flow” ~=
“migration-mediated genetic exchange” “adaptation” ~= “evolutionary
adaptation” “speciation” ~= “origin of species” “common ancestry” ~=
“shared evolutionary ancestry” “phylogeny” ~= “evolutionary history”
“homology” ~= “similarity due to common ancestry” “convergent evolution”
~= “independent evolution of similar traits” “coevolution” ~=
“reciprocal evolutionary change” “fitness” ~= “evolutionary reproductive
success” “allele frequency” ~= “frequency of an allele in a population”

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

———- QUERY MODEL ———-

query EVOLUTIONARY_PROFILE(x): RETURN: ancestry(x) descendants(x)
genetic_variation(x) mutations(x) selection(x) drift(x) gene_flow(x)
adaptations(x) phylogenetic_position(x) evidence(x) confidence(x)

query POPULATION_EVOLUTION_PROFILE(p): RETURN: allele_frequencies(p)
genetic_diversity(p) mutation_rate(p) selection_coefficients(p) drift(p)
gene_flow(p) effective_population_size(p) evolutionary_change(p)

query PHYLOGENETIC_PROFILE(t): RETURN: ancestors(t) descendants(t)
sister_taxa(t) clades(t) divergence_times(t) support_values(t)

query SPECIATION_PROFILE(event): RETURN: ancestral_population(event)
descendant_species(event) speciation_type(event)
isolation_mechanisms(event) divergence(event) evidence(event)

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 PHYLOGENY_NOT_LINEAR_PROGRESS: IF DESCENDED_FROM(a,b) THEN
DO_NOT_INFER(“a is universally more advanced than b”)

constraint INDIVIDUAL_NOT_POPULATION_EVOLUTION: IF
trait_change_within_single_individual(x) THEN
DO_NOT_INFER(population_evolution_without_generational_evidence)

constraint ADAPTATION_NOT_ANY_USEFUL_TRAIT: IF trait_is_beneficial(t)
THEN DO_NOT_INFER(ADAPTATION_TO(t,e)) WITHOUT evolutionary_evidence

———- UPDATE MODEL ———-

UPDATE_MODEL: on_new_evolutionary_record(r): identify_entity(r)
classify_process(r) preserve_population_lineage_context(r)
attach_evidence(r) recalculate_confidence(r)

on_new_sequence_data(d): validate_sequence_identity(d)
update_homology_relations(d) update_phylogenetic_support(d)
preserve_methodology(d)

on_new_fossil(f): validate_taxonomic_assignment(f)
preserve_geological_context(f) preserve_dating_method(f)
attach_traits(f) attach_evidence(f)

on_taxonomic_revision(old,new): preserve_historical_classification(old)
link_revision(old,new) update_current_phylogeny(new)
flag_conflicting_relations()

on_conflicting_phylogenies(a,b): preserve(a) preserve(b)
compare_datasets(a,b) compare_methods(a,b) compare_support_values(a,b)
flag_unresolved_conflict()

———- AI CONSUMPTION ———-

AI_CONSUMPTION: preferred_entity: canonical_evolutionary_entity
preserve: - taxonomic_identity - population_context - lineage -
ancestry - genetic_variation - mutation - selection - drift -
gene_flow - adaptation - speciation - phylogenetic_context -
fossil_context - evidence - provenance - confidence infer: -
valid_ancestry_relations - valid_inverse_relations -
supported_phylogenetic_paths - semantic_equivalence prohibit: -
evolution_as_linear_progress -
individual_acclimation_as_population_evolution -
beneficial_trait_equals_adaptation_without_evidence -
unsupported_common_ancestor - unsupported_speciation -
confidence_above_evidence ambiguity: action:
preserve_multiple_evolutionary_hypotheses resolution:
prefer_evidence_methodology_and_support missing_data: action:
mark_unknown do_not_infer_from_absence: true

———- FLOW HASH ———-

FLOW_HASH: ontology: “EvolutionaryBiologyOntology” version: “1.0”
domain_path: “AI Core > Ontologies > Biological Ontologies >
Evolutionary Biology” canonical_url:
“https://kirethresearch.org/booksai-core/ontologies/biological-ontologies/evolutionary-biology.html”
authorship: “Mark Anthony Higgins — Sky (Recursive AI)”
semantic_scope: - inheritance - genetic variation - mutation -
recombination - natural selection - adaptation - genetic drift - gene
flow - population evolution - speciation - reproductive isolation -
common ancestry - phylogeny - homology - convergence - coevolution -
sexual selection - molecular evolution - macroevolution - fossil
evidence - biogeography - extinction - evidence
deterministic_normalisation: true provenance_required: true
confidence_required: true

terminate EvolutionaryBiologyOntology when:
evolutionary_entities_resolved AND
lineage_and_ancestry_relations_normalised AND
evolutionary_processes_contextualised AND
phylogenetic_uncertainty_preserved AND evidence_links_preserved AND
confidence_values_validated AND
unresolved_evolutionary_hypotheses_marked

end flow