EO

Mutation and Molecular Evolution

Evolution of Genes and Genomes

  • Genes and genomes mutate through various mechanisms.
  • Understanding their evolution is crucial for studying genetic material.
  • Genomic functions are influenced by size and complexity.

Genomes and Evolution

  • The genome comprises all genes and non-coding DNA regions.
  • In viruses, genomic material is often RNA.
  • In eukaryotes, genes are found in chromosomes, mitochondria, and chloroplasts.
  • Mitochondrial and chloroplast genes are maternally inherited.

Case Study: The Orangutan

  • The orangutan genome illustrates the complexity of genetic structures.
  • Gene positions and sequences are variable due to mutational changes.
  • Differences between Sumatran and Bornean orangutans were identified through chromosome analysis, particularly in chromosome 2.
  • Wild populations exhibit homozygosity for specific genomic morphs, whereas zoo populations have heterozygotes due to captive breeding practices.

Mutation and Mutagenesis

  • Evolution of nucleic acids and proteins is driven by mutations.
  • Nucleotide substitutions can lead to amino acid changes, affecting protein structure and function.

Types of Mutations

  • Endogenous Causes:
    • Replication errors, base mismatches, oxidative damage, and DNA methylation.
  • Exogenous Causes:
    • Ionizing radiation, UV damage, and toxins (e.g., Aflatoxin B1).

DNA Sequencing Techniques

  • Sanger Sequencing: A classic method using chain-termination to determine DNA sequences.
  • Illumina Sequencing: A modern high-throughput method, involving fragmentation and adapter ligation of DNA.

Substitutions in Genetic Sequences

  • Sequence comparisons reveal minimum differences, underestimating actual substitutions.
  • Types of substitutions include:
    • Multiple Substitutions: More than one change at a position.
    • Coincident Substitutions: Different changes in different lineages.
    • Parallel Substitutions: Same change independently in different lineages.
    • Back Substitutions: Changes revert to original forms.

Mutation Rates

  • Transitions (A↔G; C↔T) occur more frequently than transversions (A↔C; A↔T).
  • The rate of transitions compared to transversions is approximately 2:1 or 3:1.

Homologous Features

  • Homologous sequences facilitate comparisons and evolutionary studies.
  • Techniques include alignment of nucleotide sequences, accounting for deletions and insertions.

Sequence Alignment Example

  • Cytochrome c is compared across species to identify invariant positions and variations.

Mutation and Function

  • Silent Mutations: Do not affect amino acid sequence.
  • Nonsynonymous Substitutions: Change the amino acid and may be neutral or deleterious.
  • Synonymous substitutions are five times more common than nonsynonymous ones.

Evolutionary Processes

  • Evolutionary players can be distinguished by gene sequence comparisons to reveal historical divergence and gene function.
  • Example: Lysozyme gene differently selected in fermenters vs. non-fermenters reveals insights into evolutionary pressures.

Genome Size and Complexity

  • Genome size varies across taxa, correlating with organism complexity.
  • Size is more consistent when only protein-coding genes are considered.
  • Non-coding elements play significant roles: satellite DNA, retrotransposons, and lateral gene transfers.

Gene Duplication and Function Maintenance

  • Gene duplication leads to gene families, which can evolve alongside each other.
  • Example: Hemoglobin and myoglobin demonstrate divergence and functional evolution.

Gene Trees and Relationships

  • Gene trees depict relationships of genes across species; distinguishes orthologs (from speciation) from paralogs (due to duplication) for understanding evolutionary lineage.