Genomes and Their Evolution

Genomes and Their Evolution

• Genome: Entire set of DNA from an organism.
• Human Genome Project (1990-2003): Determined complete nucleotide sequence of each chromosome.
• Eukaryotes generally have larger genomes and more genes than prokaryotes.
• Larger multicellular eukaryote genomes have lower gene density.
• Human genome:
  • 1.5 \% exons (protein/RNA encoding).
  • 5 \% regulatory sequences.
  • 20 \% introns.
  • 44 \% intergenic repetitive DNA (mostly transposable elements).
  • 6 \% large segment duplications.
• Transposons: Mobile genetic elements that move DNA around the genome (copy & paste or cut & paste).
• Retrotransposons: Mobile genetic elements that use an RNA intermediate and reverse transcriptase for transposition (copy & paste only).

Descent with Modification: A Darwinian View of Life

• Evolution: Descent with modification; changes in the genetic composition of a population over time.
• Natural selection: A process where individuals with certain heritable traits survive and reproduce at a higher rate.
• Key influences on Darwin:
  • Hutton: Gradualism (profound geologic changes are cumulative, slow, continuous processes).
  • Lyell: Uniformitarianism (geologic processes have not changed throughout Earth’s history).
• Evidence for evolution:
  • Direct observation of natural selection.
  • Fossil record.
  • Homology (similarity due to common ancestry).
  • Biogeography (geographic distribution of species).

The Evolution of Populations

• Microevolution: Change in allele frequencies in a population over time.
• Mechanisms of microevolution:
  • Natural selection.
  • Genetic drift.
  • Gene flow.
• New genes and alleles originate from mutation.
• Genetic variation origins:
  • Mutation.
  • Gene duplication.
  • Sexual reproduction.
• Chromosome mutations: Duplication, translocation, deletion, inversion.
• Mutation: the ultimate source of new alleles; can be detrimental, harmless, or occasionally beneficial.
• Population genetics: Describes the genetic composition of a population and how it changes.
• Hardy-Weinberg Principle: Describes the gene pool of a non-evolving population; allele frequencies remain constant.
• Hardy-Weinberg equilibrium conditions:
  1. No mutations.
  2. Random mating.
  3. No natural selection.
  4. Large population size.
  5. No gene flow.
• Hardy-Weinberg equation: p^2 + 2pq + q^2 = 1, where p and q are allele frequencies.
• Genetic drift: Random fluctuations in allele frequencies, especially in small populations (e.g., founder effect, bottleneck effect).
• Gene flow: Transfer of alleles into or out of a population due to movement of individuals or gametes.
• Natural selection acts on phenotype directly.
• Modes of natural selection:
  • Directional selection.
  • Disruptive selection.
  • Stabilizing selection.
• Sexual selection: Selection for mating success, resulting in sexual dimorphism.
  • Intrasexual selection (competition within one sex).
  • Intersexual selection (mate choice).