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

Introduction to Coalescent Theory - Lecture 1

International Centre for Theoretical Sciences
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#Science #Biology #Genetics #Population Genetics #Evolutionary Biology #Phylogenetics #Genetic Drift
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Third Bangalore School on Population Genetics and Evolution