Phylogenetic Tree Building
One-Sentence Definition
Phylogenetic tree building infers evolutionary relationships among sequences by fitting a branching model to aligned characters (nucleotides, amino acids, or alleles).
Simple Explanation
Turn sequence differences into a family tree, then judge how much to trust each branch.
Detailed Scientific Explanation
| Method | Idea | Notes |
|---|---|---|
| Distance (NJ) | Cluster by pairwise distances | Fast, less accurate |
| Maximum parsimony | Fewest changes | Sensitive to long-branch attraction |
| Maximum likelihood (IQ-TREE, RAxML) | Best fit under substitution model | Standard for genomics |
| Bayesian (MrBayes, BEAST) | Posterior distributions | Adds time/priors — see Phylodynamics |
Practical points:
- Substitution model selection (e.g., GTR+G) matters
- Support values: bootstrap / ultrafast bootstrap / posterior probabilities
- Rooting: outgroup, midpoint, or molecular clock
- Recombination distorts trees — mask with Gubbins/ClonalFrameML in recombinogenic species
Mechanism
Alignment → model → search tree space to maximize likelihood → assess support by resampling.
Clinical Importance
- Trees underlie outbreak claims; poor support ⇒ weak transmission conclusions
Research Importance
- Taxonomy (Carl Woese lineage of thought), evolution of resistance lineages
Diagnostic Relevance
- Public-health genomics reporting
AMR Relevance
- Distinguishes vertical spread of a resistant clone from repeated horizontal acquisition
Related MOCs
Active Recall Questions
- Why is maximum likelihood preferred over neighbor-joining for genomics?
- What do bootstrap values express?
- Why mask recombination before tree building?