Population Genetics Vocabulary

Vocabulary flashcards covering key concepts, equations, and terms in Population Genetics.

Allele

One version of a gene.

Genotype

The allele combination that an individual possesses (for example, $AA$, $Aa$, or $aa$).

Homozygote

An individual possessing two identical alleles at a given locus (for example, $AA$ or $aa$).

Heterozygote

An individual possessing two different alleles at a given locus (for example, $Aa$, $AB$, or $AC$).

Genotypic frequency

The proportion of individuals in a population with a specific genotype, calculated as $\text{genotype count} \times \text{total number of individuals}^{-1}$.

Allele frequency

The proportion of all allele copies in a population represented by a particular allele, where $p + q = 1$ for a two-allele system.

Hardy-Weinberg Equilibrium (HWE)

An ideal model predicting genotype frequencies using $p^2 + 2pq + q^2 = 1$, where $p^2 = \text{frequency of } AA$, $2pq = \text{frequency of } Aa$, and $q^2 = \text{frequency of } aa$.

Observed heterozygosity ($H_O$)

The proportion of sampled individuals that are actually heterozygous, calculated as $\text{observed heterozygous individuals} \times \text{total individuals}^{-1}$.

Expected heterozygosity ($H_E$)

The amount of heterozygosity expected in a population based on allele frequencies, calculated as $H_E = 1 - \frac{\text{d}}{\text{d}x}\big(\text{sum of squared allele frequencies}\big) = 1 - \frac{\text{d}}{\text{d}x}\big(\text{values}\big)$ or $H_E = 1 - \big(p_1^2 + p_2^2 + \frac{\text{d}}{\text{d}x}\big)$.

Fixation Index ($F_{ST}$)

A measure of population differentiation and genetic structure among subpopulations relative to the total population, ranging from $0$ to $1$.

Linkage equilibrium

The state in which alleles at different loci are associated randomly in proportions expected from their separate individual frequencies.

Linkage disequilibrium (LD)

The non-random association between alleles at different loci, calculated as $D = P(AB) - p(A)p(B)$.

Assortative mating

A mating pattern in which individuals with similar phenotypes or genotypes preferentially mate with one another.

Disassortative mating

A mating pattern in which individuals with different phenotypes or genotypes preferentially mate with one another.

Wahlund effect

The deficit of heterozygotes produced relative to HWE expectations when multiple genetically different subpopulations are combined into a single sample.

Effective population size ($N_e$)

The size of an idealized population that would experience the same amount of genetic drift or inbreeding as the population being studied.

Allelic diversity

The total amount of variation in alleles present within a population.

Haplotype diversity

The probability that two randomly chosen haplotypes from a population sample are different.

Allelic richness

The count of different alleles in a population, commonly standardized to account for sample size differences.

XY system

The sex-determination system typical of mammals, in which females are $XX$ and males are $XY$.

ZW system

The sex-determination system typical of birds, in which males are $ZZ$ and females are $ZW$.

Exon

A region of the genome that is retained in mature mRNA following RNA processing and splicing.

Intron

An intervening region of the genome that is removed during RNA processing and splicing.

Microsatellite

A short tandem repeat (STR) consisting of very short repeated DNA motifs.

Minisatellite

A tandemly repeated DNA sequence with repeat units generally longer than those found in microsatellites.

Sanger sequencing

A DNA sequencing method using dideoxynucleotide ($\text{ddNTP}$) chain termination combined with fluorescence detection.

qPCR

Quantitative or real-time PCR, a technology that tracks DNA amplification continuously during the reaction using fluorescence.

Mutation

A change in a DNA sequence that serves as the ultimate source of new genetic variation.

Muller's ratchet

The stochastic and irreversible accumulation of deleterious mutations in an asexual population that occurs when the least-mutated class is lost by drift.

Substitution

A genetic change or mutation that eventually becomes fixed within a population, replacing the original allele.

Molecular clock

A technique that uses accumulated genetic differences along with an estimated rate of molecular change to estimate divergence times between lineages.

Generation time

The average duration between the birth of an individual and the birth of its offspring.

Island model

A model of population structure assuming gene flow occurs via broad, random exchange among all populations.

Stepping-stone model

A model of population structure in which gene flow occurs primarily between adjacent, neighboring populations.

Maximum likelihood

A statistical method for identifying the parameter value or hypothesis that makes the observed data most probable.