- THIS ARTICLE
- Full Text
- Full Text (PDF)
-
All Versions of this Article:
genetics.107.074948v1
177/2/987 most recent - Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Thornton, K. R.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Thornton, K. R.
Originally published as Genetics Published Articles Ahead of Print on August 24, 2007.
Genetics, Vol. 177, 987-1000, October 2007, Copyright © 2007
doi:10.1534/genetics.107.074948
The Neutral Coalescent Process for Recent Gene Duplications and Copy-Number Variants
Kevin R. Thornton1
Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697
1 Address for correspondence: Department of Ecology and Evolutionary Biology, 321 Steinhaus Hall, University of California, Irvine, CA 92697.
E-mail: krthornt{at}uci.edu
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 either has 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 on the rate of crossing over between the two loci. When the crossover 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 investigate the effect of crossing over between loci, and gene conversion between the duplicate loci, on levels of variability and the site-frequency spectrum.
This article has been cited by other articles:
 |
|
 |
|
  C. Fan, Y. Chen, and M. Long Recurrent Tandem Gene Duplication Gave Rise to Functionally Divergent Genes in Drosophila Mol. Biol. Evol., July 1, 2008; 25(7): 1451 - 1458. [Abstract] [Full Text] [PDF]
|
|