The neutral coalescent process for recent gene duplications and copy number variants
Kevin R. Thornton 1*
1 University of California, Irvine
* To whom correspondence should be addressed. E-mail: krthornt{at}uci.edu.
Submitted on April 24, 2007
Revised on June 18, 2007
Accepted on 6 August 2007
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Abstract |
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I describe a method for simulating samples from gene families of size two under a neutral coalescent process, for the case where the duplicate gene has either fixed recently in the population, or is still segregating. When a duplicate locus has recently fixed by genetic drift, diversity in the new gene is expected to be reduced, and an excess of rare alleles is expected, relative to the predictions of the standard coalescent model. The expected patterns of polymorphism in segregating duplicates (``copy-number variants'') depend both on the frequency of the duplicate in the sample, and the recombination rate between the two loci. When the recombination rate between the ancestral gene and the copy-number variant is low, the expected pattern of variability in the ancestral gene will be similar to the predictions of models of either balancing or positive selection, if the frequency of the duplicate in the sample is intermediate or high, respectively. Simulations are used to invgestigate the effect of recombination between loci, and gene conversion between copies, on levels of variability and the site-frequency spectrum.
Key Words:
coalescent theory, copy number variation, gene duplication, population genetics
