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.
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Evolve quickly
-
Small, simple genomes
-
Some classes: only vertical gene transfer
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Analytical models,
prediction and epidemiological inference
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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