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.