666.06 - Coalescent Models With Recombination Biostatistics...

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Coalescent Models With Recombination Biostatistics 666 Lecture 6
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So far … z Basic Properties of the Coalescent MRCA Coalescence times Number of mutations z Frequency spectrum of polymorphisms z Predicting number of variants in a sample
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Today … z Further refining the coalescent Recombination Migration z Discussion of potential applications
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Recombination … z No recombination Single genealogy z Free recombination Two independent genealogies Same population history z Intermediate case Correlated genealogies
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The History of Two Sequences Sequence A Sequence B Let’s consider the potential history of two sequences, but this time… with a twist!
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The History of Two Sequences Before we reach a common ancestor … we find that sequence B is actually the result of recombination between two ancestral sequences
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The History of Two Sequences The next event we encounter is a coalescence event, as expected …
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The History of Two Sequences Final event is again a coalescence event. ..
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Potential Consequences … z Different portions of the sequence have different coalescence times z Different portions of the sequence will show more or less variation
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Another Consequence … z Recombination and recurrent mutation can produce similar outcomes … Figure from McVean et al ( Genetics, 2001)
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Simulating the Coalescent with Recombination z Assume the various alternative events are rare z Time until the next event is approximately exponentially distributed z Conditional on something happening, figure out whether it was: Recombination Coalescence
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This note was uploaded on 12/26/2011 for the course BIO 666 taught by Professor Staff during the Fall '06 term at University of Michigan.

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666.06 - Coalescent Models With Recombination Biostatistics...

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