Evolutionary Biology

1. Phylogenetics and Systematics
   1. Introduction to Phylogenetics
      1. Definition and Scope
      2. Importance in Biological Sciences
      3. Historical Development
   2. Methods of Phylogenetic Reconstruction
      1. DNA Sequencing Technologies
         1. Sanger Sequencing
         2. Next-Generation Sequencing
         3. Third-Generation Sequencing
      2. Morphological Data Analysis
         1. Collection and Measurement
         2. Use of Morphological Characters
      3. Molecular and Genetic Markers
         1. Mitochondrial DNA
         2. Ribosomal RNA Genes
         3. Nuclear Genes
      4. Computational Tools and Software
         1. Phylogenetic Analysis Software
         2. Bioinformatics Approaches
      5. Statistical Methods
         1. Maximum Parsimony
         2. Maximum Likelihood
         3. Bayesian Inference
   3. Cladistics and Taxonomy
      1. Principles of Cladistics
         1. Definition of Clades
         2. Cladistic Analysis
         3. Synapomorphies and Autapomorphies
      2. Hierarchical Classification
         1. Linnaean System
         2. Modern Nomenclature Codes
      3. Phylogenetic Trees
         1. Construction and Interpretation
         2. Tree Topologies
         3. Rooted vs. Unrooted Trees
      4. Monophyly, Paraphyly, and Polyphyly
         1. Definitions and Examples
         2. Implications for Classification
   4. Evolutionary Relationships
      1. Inferring Ancestral Traits
         1. Methods for Ancestral Character Estimation
         2. Limitations and Uncertainties
      2. Phylogenetic Signals
         1. Measuring and Testing Phylogenetic Signal
         2. Homology vs. Homoplasy
      3. Coalescent Theory
         1. Genetic Lineage Tracing
         2. Impact on Phylogenetic Inference
   5. Applications of Phylogenetics
      1. Biodiversity and Conservation
         1. Identifying Evolutionary Distinct Lineages
         2. Conservation Prioritization
      2. Epidemiology and Infectious Diseases
         1. Tracing Pathogen Evolution
         2. Outbreak Source Analysis
      3. Agriculture and Breeding
         1. Domestication Studies
         2. Genetic Improvement Programs
      4. Understanding Human Ancestry
         1. Human Migration Patterns
         2. Comparative Analysis with Other Primates
   6. Challenges and Limitations
      1. Incomplete Lineage Sorting
      2. Horizontal Gene Transfer
      3. Limited Fossil Record
      4. Rapid Radiation and Their Consequences
   7. Future Directions
      1. Advances in Sequencing and Analysis
      2. Integrating Multi-level Data
      3. Impact of Emerging Genomic Technologies
      4. Development of More Robust Phylogenetic Models