Estimating the rates of crossover and gene conversion from individual genomes

Recombination can occur either as a result of crossover or gene conversion events. Population genetic methods for inferring the rate of recombination from patterns of linkage disequilibrium generally assume a simple model of recombination that only involves crossover events and ignore gene conversion. However, distinguishing the 2 processes is not only necessary for a complete description of recombination, but also essential for understanding the evolutionary consequences of inversions and other genomic partitions in which crossover (but not gene conversion) is reduced. We present heRho, a simple composite likelihood scheme for coestimating the rate of crossover and gene conversion from individual diploid genomes. The method is based on analytic results for the distance-dependent probability of heterozygous and homozygous states at 2 loci. We apply heRho to simulations and data from the house mouse Mus musculus castaneus, a well-studied model. Our analyses show (1) that the rates of crossover and gene conversion can be accurately coestimated at the level of individual chromosomes and (2) that previous estimates of the population scaled rate of recombination ρ=4Ner under a pure crossover model are likely biased.