TY - JOUR
T1 - Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity
AU - Morrell, Peter L.
AU - Toleno, Donna M.
AU - Lundy, Karen E.
AU - Clegg, Michael T.
PY - 2006
Y1 - 2006
N2 - 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 (r) relative to estimates of the mutation parameter (θ) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp. spontaneum. Estimates of θ/θ are much greater than expected, with a mean ρr/θ ≈ 1.5, similar to estimates from outcrossing species. We also estimate ρ 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 an average of twice as much as crossing over to total recombination.
AB - 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 (r) relative to estimates of the mutation parameter (θ) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp. spontaneum. Estimates of θ/θ are much greater than expected, with a mean ρr/θ ≈ 1.5, similar to estimates from outcrossing species. We also estimate ρ 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 an average of twice as much as crossing over to total recombination.
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U2 - 10.1534/genetics.105.054502
DO - 10.1534/genetics.105.054502
M3 - Article
C2 - 16624913
AN - SCOPUS:33746464543
SN - 0016-6731
VL - 173
SP - 1705
EP - 1723
JO - Genetics
JF - Genetics
IS - 3
ER -