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Originally published as Genetics Published Articles Ahead of Print on November 19, 2005.
Genetics, Vol. 172, 2441-2448, April 2006, Copyright © 2006
doi:10.1534/genetics.104.040311
Relative Influences of Crossing Over and Gene Conversion on the Pattern of Linkage Disequilibrium in Arabidopsis thaliana
Vincent Plagnol*,1,2,
Badri Padhukasahasram*,2,
Jeffrey D. Wall*,
Paul Marjoram
and
Magnus Nordborg*
* Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089 and Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089
1 Corresponding author: University of Southern California, 1050 Childs Way, MCB 413L, Los Angeles, CA 90089-2910.
E-mail: vincent.plagnol{at}normalesup.org
In this article we infer the rates of gene conversion and crossing over in Arabidopsis thaliana from population genetic data. Our data set is a genomewide survey consisting of 1347 fragments of length 600 bp sequenced in 96 accessions. It has several orders of magnitude more markers than any previous nonhuman study. This allows for more accurate inference as well as a detailed comparison between theoretical expectations and observations. Our methodology is specifically set to account for deviations such as recurrent mutations or a skewed frequency spectrum. We found that even if some components of the model clearly do not fit, the pattern of LD conforms to theoretical expectations quite well. The ratio of gene conversion to crossing over is estimated to be around one. We also find evidence for fine-scale variations of the crossing-over rate.
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