Phylodynamics

How pathogens
evolve and spread

CZI journal club 2019-03-28

Metagenomics, intrahost evolution

Phylodynamics,
genomic epidemiology

car

cat

Reconstructing evolution is a lot like "telephone"

zebra

....

car

cat

Reconstructing evolution is a lot like "telephone"

zebra

Reconstructing evolution is a lot like "telephone"

ACG

AGG

AGT

Evolution provides context

to viral outbreaks

Where did this virus come from?

When did interesting traits change?

ACG

AGG

AGT

A note about sampling

ACG

AGG

AGT

Most models make strong assumptions about sampling (e.g., sparse, equal sampling or complete sampling)

A note about sampling

Context is everything.

Tree clustering is NOT necessarily direct transmission.

  • Evolve quickly

  • Small, simple genomes

  • Some classes: only vertical gene transfer

  • Analytical models,
    prediction and epidemiological inference

  • Evolve more slowly

  • Larger, complex genomes

  • Horizontal gene transfer (reticulate evolutionary history)

  • Descriptive models, retrospective

 

Sidebar:

"Erm, did you forget all the other pathogens?"

Core concepts
& types of questions

Molecular Clock

Ancestral state reconstruction

Demographic history

Molecular clocks

Example: dating epidemiological events

Ancestral state reconstruction

Model trait as an evolving site

Model trait as an evolving site

Model trait as an evolving site

Use continuous time markov chain (CTMC) to estimate pairwise rate of transition between states

Example: phylogeography

Example: phylogeography

Example: epidemiological inference

Example: inferring

cross-species transmission

Demographic history

'Skyline' demographic models estimate population size in windows of time

Example: inferring epidemiological dynamics

Rambaut 2008

Effective population size

Questions?

learning-hour-phylodynamics-overview

By Sidney Bell

learning-hour-phylodynamics-overview

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