Introduction to the Coalescent Theory - Lecture 3

Third Bangalore School on Population Genetics and Evolution
Introduction to the coalescent theory
Selection and the coalescent
The ancestral selection graph
The Moran model
The biased voter model
The dual process
The ancestral selection graph
The conditional structured coalescent
Balancing selection
A peak of polymorphism is expected. .
Positive directional selection
Example: maize and teosinte
Purifying selection
Why purifying selection may reduce Ne
Summary
What is it good for?
Detecting selection
Allele frequency distribution
Polymorphism & divergence
Haplotype sharing
Standard approach 80's-90's
Plants vs flies
The CCR5-32 AIDS-
This approach is now dead
Sample size over time
You too, Drosophila!
"It is difficult to get a man to understand something when his salary depends upon his not understanding it.
Two possible ways out
Forget about p-values
Calibrating background models
But no model fits Arabidopsis...
Testing for local adaptation
Field experiments Schmitt et al
Alleles associated with fitness advantage are local
Schmitt et al
"The method has been shown to be robust to demography..."
"The method has been sh to be robust co
etched has been
"No evidence for population structure was found..."
evidence for ture was found...
Moral of the story
I'm not depressed
Gene trees & species trees
A. haller
The pairwise sequentially Markovian coalescent model
Problem: the ARG is not Markovian...
"Effective population size" over time ...