Lecture 12
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Biological populations often have some internal —–.
structure
What is a structured population?
A population is structured if its members possess one or more traits that affects their phylodynamic parameters.
In geographic/spatial structuring, gene flow is limited by —/—
spatial or geographic segregation of subpopulations.
What does the impact of structure depend on in geographic structuring?
It depends on the rate of migration across boundaries relative to local birth rate
What is an example of geographic structuring?
A population spanning an archipelago
How could populations that are spatially mixed be structured in other ways?
-pathogens are generally composed of many within host sub populations. -pathogen sub populations may possess traits affecting reproductive success -infected individuals may be in different epidemiological states -sampled animals may be members of different species between which there may be (extremely rare) horizontal gene transfer
——- can play an important role in shaping the phylogenetic relationships between samples
population structure
If we dont account for existing structures analysis could be —–.
biased
What are features of BiSSE?
It allows for 2 states affecting birth and death rates, assumes complete present day sampling
What are features of MuSSE?
It allows for more than two states, allows for incomplete present day sampling
What are features of MTBD?
it allows for more than 2 states, allows for both incomplete present day and through time sampling.
In slide 14,what does each term represent?
slide 14
In a simple structured model, what could different compartments represent?
pathogen strains, geographic locations, hot risk groups, etc
What does B_i_j, y_i-_j show?
represents the rate at which individuals of type I produce individuals of type j, while y_ij is the rate at which individuals of type I become type j
Do multi type birth death models have an analytical solution?
no, they must solved numerically to compute structured phylodynamic likelihood
What is the phylogenetic posterior of a multi type birth death model?
slide 16
For coloured trees, what should we use? what is its + and -?
MCMC should be perform on the expanded state. +: posterior distribution for ancestral types are directly available -: analysis is much more computationally demanding
When does the problem of unknown leaf types/locations get more challenging?
when the number of types/locations are unknown
Structure coalescent models have type specific —–.
population sizes