Phylodynamics

One-Sentence Definition

Phylodynamics combines pathogen genome phylogenies with sampling dates and epidemiological models to estimate timing, transmission dynamics, and population history of outbreaks.

Simple Explanation

Trees plus dates: when did this lineage emerge, how fast is it spreading, where did it come from?

Detailed Scientific Explanation

• Molecular clock: substitutions accumulate roughly with time → time-scaled trees (BEAST, TreeTime)
• Estimates: time to most recent common ancestor (tMRCA), effective population size trajectories, R₀-like growth parameters
• Phylogeography: discrete/continuous trait models to infer geographic spread
• Requires temporal signal (root-to-tip regression) — bacteria with slow clocks and dense recombination are harder than RNA viruses
• Sampling bias is the dominant practical limitation

Mechanism

Bayesian inference jointly over tree, clock rate, and population model, conditioned on dated tips.

Clinical Importance

• Was this hospital cluster imported once and spread locally, or repeatedly introduced? Different interventions follow.

Research Importance

• Pandemic-scale genomic epidemiology (widely used for SARS-CoV-2, influenza); emergence of resistant lineages

Diagnostic Relevance

• Public health rather than individual diagnostics

AMR Relevance

• Dates emergence and expansion of resistant clones and plasmid lineages

Related MOCs

• MOC - Bioinformatics in Microbiology · MOC - Antimicrobial Resistance (AMR) · MOC - Virology

Active Recall Questions

1. What is tMRCA?
2. How do you check for temporal signal?
3. Why is sampling bias so damaging in phylodynamics?

Connections

• Phylogenetic Tree Building · Phylogenomics and Outbreak Typing · AI for Outbreak Detection