Lecture 8

• Phenotype


  Observable trait(s) of an organism
• Genotype


  Set of alleles possessed by an organism at one or more loci of interest
• Locus


  Site on a chromosome
• Allele


  One of several alternate forms of DNA sequence at the same locus
• Phenotypic variation among individuals is common
• Variation in phenotypes is partially caused by variation in genotypes
• Relationships between phenotype and genotype range from simple to complex

  
• Relationships between phenotype and genotype

  • Some phenotypes vary due to alleles of a single gene
  • Some genotypes can produce different phenotypes if exposed to different environments
• Phenotypic variance (VP)


  Can be decomposed into three main sources: genetic variance (VG), environmental variance (VE), and genotype-by-environment interaction variance (VG×E)
• Genetic variance (VG)


  Caused by differences in genotypes among individuals
• Environmental variance (VE)


  Caused by different individuals experiencing different environments
• Genotype-by-environment interaction variance (VG×E)


  Caused by genotypes having different effects on phenotype in different environments
• Genetic variation and genotype-by-environment interaction variation are (partially) heritable and form the raw material for evolution by natural selection
• Variation in human skin colour

  • Newborns vary in skin colour because of genetic variation
  • Identical twins may differ in skin colour if one spends more time in the sun
  • If two people with identical skin tones go to the beach, one may tan easily, while the other doesn't (due to genetic differences)
• Genetic variance


  Differences among individuals that are encoded in the genome and transmitted from parents to offspring
• For quantitative traits (e.g., height), genetic variance is generally caused by allelic variation at many loci
• Environmental variance


  Differences among individuals due to exposure to different environments
• Environment can influence phenotype by altering gene expression
• Genotype-by-environment interactions


  Genetic differences among individuals in the way the environment influences phenotype
• If genotypes differ in their reaction norms, these differences are heritable and could be subject to selection
• DNA is the genetic material for all organisms (excluding RNA viruses, etc.)
• DNA replicates semi-conservatively


  Strands separate, and each becomes a template for a new strand

  
• Components of the genome

  • Coding regions (protein-coding genes)
  • Non-coding regions (e.g., regulatory regions, introns, pseudogenes, transposable elements)
• From DNA to protein

  1. DNA sequence is transcribed to mRNA

  2. mRNA is translated in sets of three nucleotides (codon triplets) into an amino acid sequence

  3. Proteins consist of amino acid chains that are folded into specific three-dimensional structures

  
• Mutation


  Change in the DNA sequence of an organism's genome

  
• Types of mutations


  • Somatic mutations (occur in somatic cells, not heritable)
  • Germline mutations (occur in sperm or eggs, heritable to offspring)

  
• Mutation is the ultimate source of all heritable genetic variation

  
• Point mutation


  Substitution of one nucleotide base for another
• Types of point mutations

  • Transitions (purine↔purine or pyrimidine↔pyrimidine)
  • Transversions (purine↔pyrimidine)

  
• Effects of point mutations in coding DNA

  • Silent (synonymous, no amino acid change)
  • Missense (non-synonymous, amino acid change)
  • Nonsense (introduce a premature stop codon)

  
• Insertions and deletions


  Caused by misalignment during DNA replication, can cause frameshift mutations

  
• Gene duplications


  Can create new genes through unequal crossing over or retrotransposition

  
• Gene duplication is important for evolution
• Gene families


  Formed by repeated gene duplication events, where each copy evolves separately and may diverge in function

  
• Unequal crossing over


  Homologous chromosomes align incorrectly during meiosis; crossover removes a region from one and adds it to the other

  
• Duplication by retrotransposition


  DNA gene is transcribed to RNA, reverse transcribed to RNA, then reintegrated into the genome

  
• Duplication by retrotransposition usually creates nonfunctional pseudogenes because regulatory elements are missing
• Increase in copy number may be adaptive
• Duplication followed by divergence in function generates gene families

  
• Gene families


  After a gene duplication, each copy evolves separately; gene copies diverge, one may evolve a new function; repeated gene duplication generates a gene family