Five stages of phylogenetic analysis

Stage 1. Sequence Acquisition

• For phylogeny, DNA can be more informative
  • The protein-coding portion of DNA has synonymous and nonsynonymous substitutions
  • Thus, some DNA changes do not have corresponding protein changes

Stage 2. Multiple Sequence Alignment (MSA)

• The fundamental basis of a phylogenetic tree
• Include misalignment, nonhomologous sequence → It will still be possible to generate a tree
  1. Confirm that all sequences are homologous
  2. Adjust gap creation and extension penalties as needed to optimize the alignment
  3. Restrict phylogenetic analysis to regions of the MSA for which data are available for all taxa

Stage 3. Models of DNA and Amino Acid Substitution

DNA models

1. Jukes and Cantor model
2. Kimura model
3. Tamura and Nei model

Protein models

개념 정리

• Substitution models
• DNA substitution mutations
  • Transition : Interchanges of two-ring purines (A, G) or of one-ring pyrimidines (C, T) / Involve bases of smilar shape
  • Transconversion : Interchanges of purine for pyrimidine bases / Involve exchange of one-ring & two-ring structures

Stage 4. Tree-Building Methods

• Tree

• Phylogenetic tree construction
  • Input: a set of n species, a method for computing a score for a labeled tree
  • Output: labeled tree with the optimal score
• Distance-based methods
  • UPGMA (Unweighted Pair Group Method with Arithmetic mean)
    • Input: Distance matrix showing distances between sequences
    • Idea: Combine the two closest sequences, then iterate until reach a single cluster
    • Distance $dij$ between two clusters Ci and Cj is defined as the average distance between pairs of sequences from each other
    • |Ci|, |Cj| : the number of sequences
    • Neighbor-joining
• : involve a distance metric (e.g. the number of amio acid changes between the sequences, distance score)
• Character-based methods
  • Maximum parsimony
  • Maximum likelihood
  • Bayesian