Is intragenic recombination a factor in the maintenance of genetic variation in natural populations?

Abstract

INTRAGENIC recombination between two different existing alleles in a population can create new alleles. The role of this process in maintaining variation in a natural population has been investigated¹ by assuming that a gene consists of two sites, each of which can mutate to an infinite number of unique ‘alleles’ (the infinite allele model of Kimura and Crow²). Using this model it was shown that if the product of the population size, N, and the mutation rate, μ, is ⩾1, and the recombination rate, r, is the same order of magnitude as the mutation rate, then intragenic recombination significantly increases the number of alleles maintained in a finite population. Moreover, this is not equivalent to an increase in the mutation rate as the variance of homozygosity and the variance of the number of alleles are larger. This implies that the sampling theory of neutral alleles developed by Ewens³ does not apply to the situation where intragenic recombination is important in maintaining variation⁴. Application of these results to the study of intragenic recombination in natural populations would require a large number of independent samples in order to estimate the variance of homozygosity and the variance of the number of alleles. However, data from natural populations usually consist of the number of alleles and their frequencies in a single sample. Therefore, for the effect of intragenic recombination to be observable, there must be a detectable change in the distribution of the allele frequencies in a sample which contains k alleles. We present here the results of Monte Carlo simulation which show that intragenic recombination in the equilibrium population increases the frequency of the most common allele, increases the number of alleles which occur only once in the sample, and increases the homozygosity.