1. Correlation and Causation
2. Pattern and Process
   1. Pattern
   2. Process
      1. Proximate Process
      2. Ultimate Process
3. Tactics
   1. Observation
   2. Theory
      1. Hypothesis
      2. Mathematical Model
   3. Experiment
      1. Controls
      2. Independent Variables
      3. Dependent Variables
      4. Pseudoreplication
   4. Observation->Theory->Experiment
4. Evolution
   1. Evidence
      1. Origin of Species
         1. Organisms change over time.
      2. Fossil Record
         1. Stratigraphy
            1. The Great Unconformity
      3. Homology of Parts
         1. Functional Parts
         2. Imperfect Design
         3. Vestigial Parts 退化
      4. Embryology
         1. Morphology
         2. Genetic homology
      5. Hierarchical classification of organisms
      6. Biogeography
         1. Relatives on mainland & isolated islands
         2. Gondwanan Formation
      7. Artificial Selection
      8. Rapid evolution in nature
         1. Peppered moth
   2. Mechanism
      1. Natural Selection
      2. Genetic Drift
      3. Mutation
      4. Gene Flow (Migration)
   3. Molecular Evolution
      1. Neutral theory
      2. Mutation Rate (μ)
      3. Rate of Fixation (1/(2N))
      4. Molecular Clock
      5. Divergence (K)
         1. Ka: Divergence at a Nonsynonymous site.
         2. Ks: Divergence at a Synonymous Site.
5. Natural Selection
   1. Phenotypic variation
   2. Consequences
      1. Genetic Variation
      2. Environmental variation
      3. Polymorphism 多态性
      4. Quantitative Variation
   3. Molecular Level Variation
      1. Synonymous mutation (Silent)
      2. Antonymous mutation
      3. Nonsense Mutation (Replacement, i.e., stop codon)
   4. Measuring sequence variation
      1. Theta
      2. Pi
   5. Stabilizing and Purifying Selection
   6. Heterosis 杂种优势
   7. Conditions
      1. Variations among individuals in some phenotypic trait.
      2. Variation is Heritable
      3. Non-random differences in survival and fertility
   8. Consequence
      1. Differential representation in the next generation
      2. Divergence of different populations
   9. Types
      1. Phenotypic Level
         1. Stabilizing Selection
         2. Directional Selection
         3. Disruptive Selection
      2. Genetic Level
         1. Purifying Selection
         2. Positive Selection
         3. Diversifying Selection
      3. Genotype-Phenotype Mapping
   10. Note-worthy
       1. Selection Without Evolution
          1. Frequency Dependent Selection
             1. Positive Selection
             2. Negative Selection
       2. One species does not evolve just for the benefit of another species.
       3. Selection sometimes are not beneficial or the species in long term.
       4. Selection happens at several levels.
          1. Kin selection
       5. Selection is not just the survival of the fittest.
       6. Selection does not anticipate the future.
       7. selection does not achieve the optimal phenotype for all traits.
          1. Pleiotropic effect
   11. Genetic Linkage
   12. Levels (Units) of Selection
       1. Gene
          1. Meiotic Drive
          2. Retrotransposon
       2. Cell
       3. Organism
       4. Group
       5. Species
6. Sexual selection
   1. Anisogamy 异配生殖
   2. Type
      1. Male-male competition
      2. Female choice
   3. Sexual Dimorphism
      1. Good gene hypothesis
      2. Runaway sexual hypothesis
7. Genetics
   1. Population Genetics
   2. Mendelian Genetics
      1. Law of Segregation
      2. Law of Independent Assortment
      3. Law of Dominance
   3. Allele
      1. Allele Frequency
         1. Hardy Weinberg Equilibrium
            1. Assumption: No Evolutionary Forces
         2. With natural selection
            1. Mean fitness w
8. Species and Speciation
   1. Species
      1. Concept
         1. Morphological
         2. Biological
   2. Speciation
      1. Geography
         1. Allopatric
            1. Colonization
            2. Vicariance
         2. Parapatric
         3. Sympatric
      2. Isolating Mechanism
         1. Pre-mating
            1. Habitat Segregation
            2. Seasonal Isolation
            3. Behavioral Isolation
         2. Post-mating, Pre-zygotic
            1. Mechanical
            2. Gametic Isolation
            3. Sperm Competition
            4. Post-mating sexual selection
            5. Wind Pollinated plant
         3. Post-mating, post-zygotic
            1. Hybrid Inviability
            2. Hybrid Sterility
      3. Dobzhansky-Muller Model
      4. Reinforcement
9. Phylogenetics
   1. Taxonomy
   2. Systematics
   3. Phylogeny
      1. Ingroup
      2. Outgroup
      3. Clade
      4. Root
      5. Node
      6. Branch
   4. Homologous Trait
      1. Ancestral Trait
      2. Derived Trait
   5. Phylogenetic Tree
      1. Monophyletic
      2. Paraphyletic
      3. Polyphyletic
   6. Phylogenetically Informative
      1. Shared Derived Traits
   7. Phylogenetically Uninformative
      1. Unique Derived Traits
      2. Ancestral Traits
      3. Homoplasy 趋同性
      4. Polytomy
   8. Methods
      1. Parsimony 简约法
      2. Maximum Likelihood
      3. Distance method