JW - genetics bad

Additive Effect (a)

A quantitative measure defined as half the difference between the phenotypic values of the two homozygotes; represents the clean, step-wise phenotypic change per allele substitution.

Dominant Effect (d)

The deviation of the heterozygote’s phenotypic value from the exact mid-parental average of the two homozygotes.

Complete Dominance

A genetic pattern where $|a| = |d| \neq 0$; the heterozygote displays a phenotype identical to one of the homozygotes.

Partial Dominance

A genetic pattern where $|a| > |d| > 0$; the heterozygote's phenotype falls closer to one homozygote than the other, but not identically.

Co-dominance

A genetic pattern where $|a| \neq 0$ and $d = 0$; the heterozygote's phenotype is the exact mathematical average of the two homozygotes.

Overdominance

A genetic pattern where $|a| < d$ and $d > 0$; the phenotype of the heterozygote is more extreme (e.g., larger or more robust) than either homozygote.

Underdominance

A genetic pattern where $d < 0$ and either $|a| < |d|$ or $a = 0$; the phenotype of the heterozygote is significantly lower than either of the homozygotes.

Neutral Variation

An allelic variation ($a = d = 0$) where different alleles exist at a locus but do not contribute to any phenotypic differences in the trait.

Average Effect of an Allele Substitution (α)

The average change in phenotype that occurs when one allele is randomly replaced by the alternative allele in a population; mathematically expressed as $\alpha = a + d(q - p)$.

Breeding Value

The value of an individual judged by the mean phenotypic value of its offspring; it represents the sum of the average effects ($\alpha$) of the alleles an individual possesses and determines heritable variation.

Additive Genetic Variance (VA)

The component of genetic variance due to the additive effects of alleles; it drives resemblance between parents and offspring and is calculated as $V_A = 2pq[a + d(q - p)]^2$.

Dominance Variance (VD)

The component of genetic variance arising from the interaction between alleles at a single locus; it represents non-heritable genetic variation that does not contribute to parent-offspring resemblance.

Univariate vs. Multivariate Analysis

Univariate focuses on a single trait at a time, whereas multivariate simultaneously examines multiple traits to capture their structural and genetic interdependencies.

Covariance

A statistical measure of how two variables change together; a positive value means they tend to increase together, while a negative value means one increases as the other decreases.

Correlation

A standardized measure of association ranging from -1 to 1, calculated by dividing covariance by the product of the individual standard deviations, making it unitless and comparable.

Genetic Covariance/Correlation

An association between two traits driven by a shared genetic basis, meaning the same genes or tightly linked genes influence both traits across different genotypes.

Environmental Covariance/Correlation

An association between two traits arising because the environmental factors that alter one trait jointly affect the other trait within individuals of the same genotype.

Linkage Disequilibrium (LD)

The non-random association of alleles at different loci within a population; alleles are inherited together more or less frequently than expected by chance.

Pleiotropy

A genetic phenomenon where a single locus or gene simultaneously influences multiple, seemingly distinct phenotypic traits.

Antagonistic Pleiotropy

A form of pleiotropy where an allele has beneficial effects on one trait but detrimental effects on another, often creating evolutionary trade-offs (e.g., high early fecundity vs. reduced longevity).

G Matrix (Genetic Variance-Covariance Matrix)

A matrix that organizes the pattern of additive genetic variation within traits (on the diagonal) and the genetic covariances between pairs of traits (off the diagonal) across a population.

Evolutionary Constraint

A limitation on the direction or rate of evolutionary change caused by genetic correlations; selection cannot easily optimize one trait if it is negatively correlated with another crucial trait.

Epistasis

A genetic interaction where the phenotypic effect of alleles at one locus depends entirely on the specific genotype present at one or more other loci in the genome.

Background Dependence

The phenomenon where the clinical or physical expression (penetrance/severity) of a genetic mutation changes based on the wider genetic background of the individual organism.

Physiological Epistasis

The physical, mechanistic interaction between proteins, biochemical pathways, or molecular networks inside a single organism where genes interact to produce a phenotype.

Statistical Epistasis

The population-level variance ($V_I$) that can be mathematically attributed to epistatic interactions; it requires genetic variation to be present at both interacting loci simultaneously.

Missing Heritability

The discrepancy where the specific genetic variants identified in large-scale studies (like GWAS) fail to account for the total heritability calculated from family or twin studies, often caused by complex epistasis.

Fitness Landscape

A conceptual or mathematical model mapping combinations of genotypes (or phenotypes) to their corresponding reproductive fitness, often featuring multiple peaks and valleys.

Outbreeding Depression (Hybrid Dysgenesis)

A reduction in fitness observed in the offspring of crosses between two genetically differentiated populations, caused by the breakup of co-adapted gene complexes via recombination.

Co-adapted Alleles

A suite of specific alleles across different loci that have evolved together because their combined epistatic interaction yields high fitness.