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

Genetics
Peter L MorrellMichael T Clegg

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 (theta) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp. spontaneum. Estimates of rho/theta are much greater than expected, with a mean rho/theta approximately 1.5, similar to estimates from outcrossing species. We also estimate rho 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 loci show evidence of gene conversion. For these loci, gene conversion is estimated to contribute a...Continue Reading

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Citations

Sep 23, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hanan SelaTzion Fahima
Jan 10, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Patrick A ReevesChristopher M Richards
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Jul 31, 2013·The Journal of Heredity·Zhou FangPeter L Morrell
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Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Peter L Morrell, Michael T Clegg
Dec 31, 2011·Nature Reviews. Genetics·Peter L MorrellJeffrey Ross-Ibarra
May 10, 2013·Scientific Reports·Christopher M RobinsonJames Chodosh
Dec 17, 2008·PLoS Genetics·Naoki Osada, Hideki Innan
Jun 16, 2016·Molecular Biology and Evolution·Thomas J Y KonoPeter L Morrell
Oct 28, 2019·Genetics·Thomas J Y KonoPeter L Morrell
Jun 21, 2014·Genetics·Michael LynchBernhard Haubold
Apr 25, 2014·G3 : Genes - Genomes - Genetics·Zhou FangPeter L Morrell
Dec 1, 2019·Genetics·Thomas J Y KonoPeter L Morrell

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