Introduction to Coalescent Theory - Lecture 1

Explore the foundations of coalescent theory in this comprehensive lecture from the Third Bangalore School on Population Genetics and Evolution. Delve into the neutral Wright-Fisher model, examine the structure and implications of coalescence trees, and learn how to interpret polymorphism data. Investigate key concepts such as mitochondrial Eve, ancient Neanderthal mtDNA, and mutation rates. Gain insights into estimating parameters under the infinite-sites model and detecting deviations from standard evolutionary models. Ideal for advanced PhD students and researchers in biology, mathematics, and related fields seeking to deepen their understanding of population genetics and evolutionary processes.

Third Bangalore School on Population Genetics and Evolution
Introduction to the coalescent theory
The Gregor Mendel Institute
The Coming of Data
"We cranked the handle and nothing came genome chromosome 21
Example: Polymorphism in the human genome chromosome 21
Making sense of sequence data
The neutral model
History
Importance
Three insights
Some English
The neutral Wright-Fisher model
The Wright-Fisher model
Summary
The coalescent and classical population genetics
Implications for how we should view polymorphism data
Example: mitochondrial Eve
The coalescent
Topology & branch lengths
Distribution of the branch lengths
Scale time so that one unit of scaled time corresponds to N generations.
Let Tk be the
Summary
What do coalescence trees look like?
Deep branches often dominate
Example: How big a sample is needed to include the MRCA of everyone?
What do larger coalescence trees look like?
Distribution of the topology
Example: ancient Neanderthal mtDNA
The mutation rate
The probability of "identity by descent"
Superimposing mutations
The expected number of mutations is:
Note that
Mutation models
Estimating 0 under the infinite-sites model
segregating polymorphic sites, S.:
Both are unbiased, however,
How do we detect deviations from the standard model e.g., growth?