Evolutionary Biology

1. Evolutionary Genetics
   1. Population Genetics
      1. Hardy-Weinberg Equilibrium
         1. Assumptions and Conditions
            1. No Mutation
            2. Large Population Size
            3. Random Mating
            4. No Selection
            5. No Gene Flow
         2. Mathematical Model
         3. Deviations from Equilibrium
      2. Allele Frequency
         1. Calculation and Estimation
         2. Factors Affecting Allele Frequencies
            1. Mutation Rates
            2. Selection Pressure
            3. Mating Patterns
         3. Genetic Drift Impact
         4. Applications in Studies of Genetic Variation
      3. Genetic Variation within Populations
         1. Sources of Genetic Variation
         2. Measurement and Analysis Techniques
         3. Importance in Adaptation and Survival
   2. Molecular Evolution
      1. DNA Sequencing and Phylogenetics
         1. Techniques of DNA Sequencing
         2. Construction of Phylogenetic Trees
         3. Analyzing Evolutionary Relationships
         4. Homology vs. Analogy in Genetic Sequences
      2. Molecular Clocks
         1. Concept and Development
         2. Rate of Genetic Change Over Time
         3. Calibration Methods
         4. Use in Dating Divergence Events
      3. Protein Evolution
         1. Amino Acid Substitution Models
         2. Structural and Functional Constraints
         3. Adaptive vs. Neutral Evolution of Proteins
      4. Horizontal Gene Transfer
         1. Mechanisms of Transfer
         2. Impact on Genetic Diversity
         3. Role in Evolutionary Novelty
   3. Genomics and Evolution
      1. Comparative Genomics
         1. Genome Size and Content
         2. Gene Duplication and Loss
         3. Synteny Analysis
      2. Evolution of Genome Architecture
         1. Mobile Genetic Elements
         2. Evolution of Gene Regulatory Networks
         3. Chromosomal Rearrangements
      3. Evolutionary Developmental Genetics
         1. Genetic Basis of Morphological Evolution
         2. Homeotic and Other Developmental Genes
         3. Insights from Model Organisms
      4. Ancient DNA and Paleogenomics
         1. Techniques for DNA Recovery
         2. Insights into Extinct Species
         3. Implications for Understanding Human Evolution
   4. Genetic Basis of Adaptation
      1. Identifying Adaptive Genes
      2. Experimental Evolution Approaches
      3. Role of Epigenetics in Evolutionary Adaptation
      4. Case Studies in Natural Populations
   5. Evolution of Genetic Systems
      1. Sex and Recombination
         1. Costs and Benefits of Sexual Reproduction
         2. Evolution of Mating Systems
         3. Genetic Consequences of Recombination
      2. Polyploidy and Hybridization
         1. Effects on Genetic Diversity
         2. Speciation Events
         3. Examples in Plant and Animal Kingdoms
      3. Genetic Load and Inbreeding
         1. Consequences for Population Viability
         2. Identification and Management in Conservation
   6. Population Genomics
      1. Genome-wide Association Studies (GWAS)
         1. Methodology and Applications
         2. Challenges and Limitations
      2. Genomic Patterns of Selection
         1. Signatures of Positive and Negative Selection
         2. Statistical Tools for Detection
      3. Ecological Genomics
         1. Adaptations to Environmental Changes
         2. Genomic Basis of Ecological Interactions
         3. Case Studies
   7. Adaptation and Speciation in Genetic Context
      1. Evolutionary Dynamics of Speciation Genes
      2. Role of Hybrid Zones in Speciation
      3. Genomic Islands of Divergence
      4. Integration with Evolutionary Ecology