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Genetics, Vol. 167, 2097-2109, August 2004, Copyright © 2004
doi:10.1534/genetics.103.021535
Maximum-Likelihood Estimation of Rates of Recombination Within Mating-Type Regions
Naoki Takebayashi*,1,
Ed Newbigin
and
Marcy K. Uyenoyama*,2
* Department of Biology, Duke University, Durham, North Carolina 27708-0338
School of Botany, University of Melbourne, Victoria 3010, Australia
2 Corresponding author: Department of Biology, Box 90338, Duke University, Durham, NC 27708-0338.
E-mail: marcy{at}duke.edu
Features common to many mating-type regions include recombination suppression over large genomic tracts and cosegregation of genes of various functions, not necessarily related to reproduction. Model systems for homomorphic self-incompatibility (SI) in flowering plants share these characteristics. We introduce a method for the exact computation of the joint probability of numbers of neutral mutations segregating at the determinant of mating type and at a linked marker locus. The underlying Markov model incorporates strong balancing selection into a two-locus coalescent. We apply the method to obtain a maximum-likelihood estimate of the rate of recombination between a marker locus, 48A, and S-RNase, the determinant of SI specificity in pistils of Nicotiana alata. Even though the sampled haplotypes show complete allelic linkage disequilibrium and recombinants have never been detected, a highly significant deficiency of synonymous substitutions at 48A compared to S-RNase suggests a history of recombination. Our maximum-likelihood estimate indicates a rate of recombination of perhaps 3 orders of magnitude greater than the rate of synonymous mutation. This approach may facilitate the construction of genetic maps of regions tightly linked to targets of strong balancing selection.
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