Molecular Evolution and Population Genetic

Punnett square

Diagram predicting offspring genotype frequencies from parental cross. Significance: Teaches Mendelian inheritance patterns.

Homozygote

Individual with two identical alleles at a locus. Significance: Breed true for that trait.

Heterozygote

Individual with two different alleles at a locus. Significance: Can maintain recessive alleles.

Diploid

Having two sets of chromosomes (one from each parent). Significance: Standard for most animals.

Haploid

Having one set of chromosomes. Significance: Gametes and some organisms (e.g., male bees).

Polyploidy

Having more than two sets of chromosomes (common in plants). Significance: Can cause immediate reproductive isolation (instant speciation).

Hardy-Weinberg equations

p + q = 1 (allele frequencies); p² + 2pq + q² = 1 (genotype frequencies). Significance: Null hypothesis for detecting evolution.

p² + 2pq + q²

p² = frequency of homozygous dominant; 2pq = heterozygous; q² = homozygous recessive. Significance: Predicts genotype frequencies under Hardy-Weinberg equilibrium.

Assumptions of Hardy-Weinberg equilibrium

1) No selection; 2) No mutation; 3) No migration; 4) Infinite population size (no drift); 5) Random mating. Significance: Violation of any assumption means evolution is occurring.

Overdominance

Heterozygote has higher fitness than both homozygotes (e.g., sickle-cell trait). Significance: Maintains genetic variation (balanced polymorphism).

Frequency-dependent selection

Fitness depends on allele frequency. Negative (rare advantage) maintains variation; positive (common advantage) drives fixation. Significance: Explains many polymorphisms.

Mutation-selection balance

Equilibrium frequency of deleterious mutation = mutation rate / selection coefficient. Significance: Explains persistence of harmful alleles.

Gene flow and small populations

Gene flow introduces new alleles, counteracts drift, and reduces genetic differentiation. In small populations, even low gene flow can prevent divergence. Significance: Opposes local adaptation and speciation.

Founder effects

Small group establishes new population, carrying only a subset of original genetic diversity. Significance: Causes rapid genetic drift and possible speciation.

Genetic drift

Random changes in allele frequency due to sampling error, especially in small populations. Significance: Nonadaptive evolution; reduces diversity; key in neutral theory.

Migration-selection balance (gene flow–selection balance)

Equilibrium between gene flow (homogenizing) and selection (adaptive divergence). Significance: Explains how locally adapted traits persist despite migration.

Inbreeding

Mating between relatives. Significance: Increases homozygosity, often reduces fitness (inbreeding depression).

Hitchhiking (genetic)

Selection on one allele drags linked alleles to high frequency. Significance: Reduces genetic diversity in genome regions.

Clines

Gradual change in trait or allele frequency across geographic space. Significance: Shows natural selection or gene flow gradient.

Linkage disequilibrium (LD)

Non-random association of alleles at different loci. Significance: Indicates selection, admixture, or recent mutation.

Factors promoting LD

Admixture (mixing populations), genetic drift (small populations), selection (especially on haplotypes). Significance: LD signals evolutionary processes.

Relationship between LD and recombination

Recombination breaks down LD; without recombination, LD persists. Significance: High recombination = low LD; low recombination = high LD.

Recombination

DNA exchange during meiosis; shuffles alleles on same chromosome. Significance: Breaks down linkage disequilibrium.

Meiosis

Cell division producing haploid gametes; crossing over occurs. Significance: Generates genetic variation via recombination.

Crossing over

Exchange of genetic material between homologous chromosomes during meiosis. Significance: Creates new allele combinations; breaks LD.

Age of Earth

4.5 billion years (determined by radiometric dating of meteorites). Significance: Provides sufficient time for evolution to occur.

DNA substitution

Permanent change in DNA sequence fixed in a population. Significance: Raw material for molecular evolution.

Transitions

Purine to purine (A↔G) or pyrimidine to pyrimidine (C↔T). Significance: More common than transversions.

Transversions

Purine to pyrimidine or vice versa (A↔C, A↔T, G↔C, G↔T). Significance: Less frequent than transitions; used in molecular evolution studies.

Synonymous mutation

Silent mutation; no amino acid change. Significance: Often neutral; evolves by drift.

Non-synonymous mutation

Replacement mutation; changes amino acid. Significance: Often subject to selection (purifying or positive).

Types of mutations

Point (single base), frameshift (insertion/deletion), silent (no amino acid change), missense (amino acid change), nonsense (stop codon). Significance: Effects range from none to severe.

Homologous genes

Genes that share a common ancestry (includes orthologs and paralogs). Significance: Evidence of common descent.

Orthologous genes

Homologous genes in different species that diverged after speciation event. Significance: Used to build phylogenetic trees.

Paralogous genes

Homologous genes related by gene duplication within a genome (e.g., globin gene family). Significance: Indicates functional divergence after duplication.