Genetics. Published Articles Ahead of Print: April 19, 2006, Copyright © 2006
doi:10.1534/genetics.105.054502


A more recent version of this article appeared on July 1, 2006.

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Estimating the contribution of mutation, recombination, and gene conversion in the generation of haplotypic diversity

Peter L Morrell 1, Donna M. Toleno 1, Karen E. Lundy 1 and Michael T. Clegg 1*

1 University of California, Irvine

* To whom correspondence should be addressed. E-mail: mclegg{at}uci.edu.

Submitted on December 16, 2005
Revised on February 21, 2006
Accepted on 11 April 2006


Abstract

Recombination occurs through both homologous crossing over and homologous gene conversion during meiosis. The contribution of recombination relative to mutation is expected to be dramatically reduced in inbreeding organisms. We report coalescent-based estimates of the recombination parameter ({rho}) relative to estimates of the mutation parameter ({vartheta}) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp spontaneum. Estimates of {rho}/{vartheta} are much greater than expected, with a mean estimated {rho}/{vartheta} {approx} 1.5; similar to estimates from outcrossing species. We also estimate with and without the contribution of gene conversion. Genotyping errors can mimic the effect of gene conversion, upwardly biasing estimates of the role of conversion. Thus we report a novel method for identifying genotyping errors in nucleotide sequence data sets. We show that there is evidence for gene conversion in many large nucleotide sequence data sets including our data that have been purged of all detectable sequencing errors and in data sets from Drosophila melanogaster, D. simulans, and Zea mays. In total, 13 of 27 data sets show evidence of gene conversion. For these loci, gene conversion is estimated to contribute an average of twice as much as crossing over to total recombination.

Key Words: Hordeum, coalescent theory, gene conversion, population genetics, recombination




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