Class PopulationGenetics

java.lang.Object

org.episteme.natural.biology.genetics.PopulationGenetics

public final class PopulationGenetics
extends Object

Models population genetics and evolutionary equilibrium.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static final record	PopulationGenetics.AlleleFrequencies
static final record	PopulationGenetics.GenotypeFrequencies

Method Summary

Modifier and Type	Method	Description
static PopulationGenetics.GenotypeFrequencies	calculateHardyWeinberg(PopulationGenetics.AlleleFrequencies alleles)	Hardy-Weinberg Equilibrium: p² + 2pq + q² = 1.
static Real	driftVariance(PopulationGenetics.AlleleFrequencies alleles, int populationSize)	Checks for genetic drift probability using Wright-Fisher model.
static PopulationGenetics.AlleleFrequencies	estimateAlleles(PopulationGenetics.GenotypeFrequencies observed)	Estimates allele frequencies from observed genotypes using maximum likelihood.
static Real	inbreedingCoefficient(double expectedHet, double observedHet)	Calculates Inbreeding Coefficient (F).
static Real	selectionCoefficient(double fitness)	Calculates the Selection Coefficient 's'.
static List<PopulationGenetics.AlleleFrequencies>	simulateSelection(PopulationGenetics.AlleleFrequencies initial, double wAA, double wAa, double waa, int generations)	Projects allele frequency change due to selection.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

calculateHardyWeinberg

public static PopulationGenetics.GenotypeFrequencies calculateHardyWeinberg(PopulationGenetics.AlleleFrequencies alleles)

Hardy-Weinberg Equilibrium: p² + 2pq + q² = 1. Calculates genotype frequencies from allele frequencies.

estimateAlleles

public static PopulationGenetics.AlleleFrequencies estimateAlleles(PopulationGenetics.GenotypeFrequencies observed)

Estimates allele frequencies from observed genotypes using maximum likelihood.

selectionCoefficient

public static Real selectionCoefficient(double fitness)

Calculates the Selection Coefficient 's'. Fitness W = 1 - s.

simulateSelection

public static List<PopulationGenetics.AlleleFrequencies> simulateSelection(PopulationGenetics.AlleleFrequencies initial,
 double wAA,
 double wAa,
 double waa,
 int generations)

Projects allele frequency change due to selection. Δp = (p * q * [p(w11-w12) + q(w12-w22)]) / W_mean

inbreedingCoefficient

public static Real inbreedingCoefficient(double expectedHet,
 double observedHet)

Calculates Inbreeding Coefficient (F). F = (He - Ho) / He

driftVariance

public static Real driftVariance(PopulationGenetics.AlleleFrequencies alleles,
 int populationSize)

Checks for genetic drift probability using Wright-Fisher model. Variance in allele frequency Δp = p*q / 2N