Genetics and Genomics

  1. Population and Evolutionary Genetics
    1. Population Genetics Foundations
      1. Gene Pool Concept
        1. Allele Diversity
          1. Population Boundaries
            1. Effective Population Size
            2. Allele Frequency Calculations
              1. Counting Method
                1. Hardy-Weinberg Method
                  1. Sampling Considerations
                  2. Genotype Frequency Determination
                    1. Direct Counting
                      1. Hardy-Weinberg Predictions
                        1. Deviation Analysis
                      2. Hardy-Weinberg Principle
                        1. Equilibrium Conditions
                          1. No Mutations
                            1. No Selection
                              1. No Migration
                                1. Large Population Size
                                  1. Random Mating
                                  2. Mathematical Formulation
                                    1. p + q = 1
                                      1. p² + 2pq + q² = 1
                                        1. Multi-Allele Extensions
                                        2. Applications and Testing
                                          1. Allele Frequency Estimation
                                            1. Genotype Prediction
                                              1. Equilibrium Testing
                                                1. Medical Applications
                                              2. Evolutionary Forces
                                                1. Natural Selection
                                                  1. Fitness Concepts
                                                    1. Absolute Fitness
                                                      1. Relative Fitness
                                                        1. Selection Coefficients
                                                        2. Selection Types
                                                          1. Directional Selection
                                                            1. Stabilizing Selection
                                                              1. Disruptive Selection
                                                                1. Balancing Selection
                                                                2. Selection Models
                                                                  1. Selection Against Recessives
                                                                    1. Selection Against Dominants
                                                                      1. Heterozygote Advantage
                                                                    2. Genetic Drift
                                                                      1. Random Sampling Effects
                                                                        1. Drift Strength Factors
                                                                          1. Fixation Probability
                                                                            1. Bottleneck Effects
                                                                              1. Population Crashes
                                                                                1. Recovery Patterns
                                                                                2. Founder Effects
                                                                                  1. Colonization Events
                                                                                    1. Genetic Consequences
                                                                                  2. Gene Flow
                                                                                    1. Migration Models
                                                                                      1. One-Way Migration
                                                                                        1. Bidirectional Migration
                                                                                          1. Stepping-Stone Model
                                                                                          2. Migration Effects
                                                                                            1. Allele Frequency Changes
                                                                                              1. Homogenization
                                                                                                1. Local Adaptation
                                                                                              2. Mutation Pressure
                                                                                                1. Forward Mutation
                                                                                                  1. Back Mutation
                                                                                                    1. Mutation-Selection Balance
                                                                                                      1. Neutral Mutations
                                                                                                      2. Non-Random Mating
                                                                                                        1. Assortative Mating
                                                                                                          1. Positive Assortment
                                                                                                            1. Negative Assortment
                                                                                                            2. Inbreeding Effects
                                                                                                              1. Inbreeding Coefficient
                                                                                                                1. Homozygosity Increase
                                                                                                                  1. Inbreeding Depression
                                                                                                              2. Molecular Evolution
                                                                                                                1. Molecular Clock Hypothesis
                                                                                                                  1. Rate Constancy
                                                                                                                    1. Calibration Methods
                                                                                                                      1. Clock Violations
                                                                                                                      2. Sequence Evolution
                                                                                                                        1. Synonymous Substitutions
                                                                                                                          1. Non-Synonymous Substitutions
                                                                                                                            1. Ka/Ks Ratios
                                                                                                                            2. Phylogenetic Analysis
                                                                                                                              1. Tree Construction Methods
                                                                                                                                1. Distance Methods
                                                                                                                                  1. Parsimony Methods
                                                                                                                                    1. Maximum Likelihood
                                                                                                                                      1. Bayesian Methods
                                                                                                                                      2. Tree Interpretation
                                                                                                                                        1. Bootstrap Analysis
                                                                                                                                        2. Genome Evolution
                                                                                                                                          1. Gene Duplication
                                                                                                                                            1. Gene Loss
                                                                                                                                              1. Horizontal Gene Transfer
                                                                                                                                                1. Genome Rearrangements

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                                                                                                                                            6. Mutation, Variation, and DNA Repair

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                                                                                                                                            8. Genomics and Bioinformatics