Molecular Biology

1. Molecular Evolution
   1. Evolution of Genes and Genomes
      1. Gene Duplication and Divergence
         1. Mechanisms of gene duplication
            1. Unequal crossing over
            2. Retrotransposition
         2. Outcomes of gene duplication
            1. Neo-functionalization
            2. Sub-functionalization
            3. Pseudo-functionalization
      2. Horizontal Gene Transfer
         1. Mechanisms in prokaryotes
            1. Transformation
            2. Transduction
            3. Conjugation
         2. Impact on genome evolution
            1. Genetic diversity
            2. Antibiotic resistance spread
      3. Genome Reduction and Streamlining
         1. Evolutionary pressures in symbiotic and parasitic organisms
         2. Case studies in bacteria and organelles (e.g., mitochondria, chloroplasts)
         3. Consequences on metabolic capabilities and host interactions
   2. Molecular Phylogenetics
      1. Phylogenetic Tree Construction
         1. Data types used
            1. DNA sequence data
            2. Protein sequence data
            3. Morphological data
         2. Methods of construction
            1. Distance-based (e.g., neighbor-joining)
            2. Character-based (e.g., maximum parsimony, maximum likelihood)
         3. Model selection and evaluation
      2. Molecular Clock Hypothesis
         1. Concept and assumptions of a molecular clock
         2. Methods to estimate divergence times
            1. Calibration using fossil records
            2. Relative rate tests
      3. Ancestral Sequence Reconstruction
         1. Techniques for inferring ancestral states
         2. Applications in understanding evolutionary pathways and lost functions
   3. Population Genetics in Molecular Evolution
      1. Genetic Drift and Bottlenecks
         1. Impact on small populations
         2. Founder effects and population bottlenecks
         3. Consequences for genetic variation
      2. Natural Selection at the Molecular Level
         1. Positive selection and adaptive evolution
         2. Purifying selection
         3. Balancing selection
      3. Neutral Theory of Molecular Evolution
         1. Concept of neutral mutations
         2. Molecular signatures of neutrality
         3. Debates and implications for evolution
   4. Speciation and Molecular Evolution
      1. Genetic Basis of Speciation
         1. Role of genetic incompatibilities
         2. Hybrid zones and reinforcement
      2. Molecular markers in identifying species boundaries
         1. Use of mitochondrial DNA
         2. Single nucleotide polymorphisms (SNPs) in speciation studies
      3. Evolution of reproductive isolation
         1. Pre-zygotic barriers
         2. Post-zygotic barriers
   5. Co-evolution and Molecular Arms Races
      1. Host-pathogen interactions
         1. Molecular mechanisms of immune evasion
         2. Evolution of pathogenicity
      2. Plant-insect interactions
         1. Evolution of plant defenses
         2. Insect counter-adaptations
      3. Symbiotic relationships and co-evolutionary dynamics
         1. Mutualistic associations
         2. Parasitic interactions
   6. Molecular Evolutionary Innovations
      1. Origin of novel genes and functions
         1. Exaptation and innovation
         2. Role of transposable elements
      2. Adaptive Radiations
         1. Molecular basis of rapid diversification
         2. Case studies in adaptive radiations (e.g., finches, cichlids)
      3. Evolution of Developmental Pathways (Evo-Devo)
         1. Changes in gene regulatory networks
         2. Hox genes and body plan evolution