Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic Diversity

By Morrell, Peter L.; Toleno, Donna M. et al. | Genetics, July 2006 | Go to article overview

Estimating the Contribution of Mutation, Recombination and Gene Conversion in the Generation of Haplotypic Diversity


Morrell, Peter L., Toleno, Donna M., Lundy, Karen E., Clegg, Michael T., Genetics


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 (ρ) 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 ρ/θ are much greater than expected, with a mean ρ /θ [asymptotically =] 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.

THERE are two sources of genetic diversity, mutation and recombination. Mutation, broadly defined here as novel heritable change in nucleotide state, introduces new variants while recombination reassorts the variants along a chromosome into novel combinations or haplotypes. Recombination can occur through both homologous crossover and homologous (intralocus) gene conversion, processes that occur as part of meiosis in diploid (or higher ploidy) organisms (WIUF and HEIN 2000). Under the Holliday junction model (HOLLIDAY 1964), homologous gene conversion is thought to occur when only a short tract of the alternate chromosome (usually a few hundred base pairs) is incorporated during meiotic exchange (e.g., STAHL 1994).

Inbreeding dramatically reduces the role of recombination. Recurrent inbreeding can rapidly increase homozygosity; the recombination process continues to exchange chromosomal segments during gamete formation but with little effective recombination of mutations. Thus the primary impact of inbreeding is expected to be a reduction of the contribution of recombination, relative to mutation, to total genetic diversity.

Under coalescent theory and assuming a standard neutral model, the impact of inbreeding can be measured as a reduction in the ratio of the recombination parameter ρ to themutation parameter θ, i.e., ρ/θ (where ρ = 4N^sub e^r and θ4N^sub e^µ and where N^sub e^ is the effective population size, r is the rate of recombination, and µ is the rate of mutation) (symbols used are listed in Table 1). It is predicted that both ρ and θ are reduced by inbreeding, but the impact on recombination is expected to be much greater (NORDBORG 2000). NORDBORG (2000) showed that ρ is predicted to be reduced under partial self-fertilization based on the relationship ρ^sub s^ = ρ(1 - s), where s is the selfing rate; θ will be affected as θ^sub s^ = θ/(1 + (s/(2 - s))). As inbreeding approaches maximal values, i.e., 98-99%, the value of ρ is reduced by 40- to 50-fold, while θ is reduced by only 2-fold relative to that expected under outcrossing.

The relative roles of gene conversion and crossing over are important because they influence the degree of the association among segregating sites, particularly at the intragenic level. The gene conversion process results in the exchange of small tracts of a chromosome, creating a mosaic sequence. At the population level, gene conversion interrupts linkage disequilibrium (LD, the association among segregating sites) in a very localized manner while long-distance LD remains largely unaffected (ANDOLFATTO and NORDBORG 1998). This can result in a reduction in LDamong closely linked markers, while flanking markers remain in complete association. …

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