High fraction of silent recombination in a finite population two-locus neutral birth-death-mutation model

A precise estimate of allele and haplotype polymorphism is of great interest in theoretical population genetics, but also has practical applications, such as bone marrow registries management. Allele polymorphism is driven mainly by point mutations, while haplotype polymorphism is also affected by recombination. Current estimates treat recombination as mutations in an infinite site model. We here show that even in the simple case of two loci in a haploid individual, for a finite population, most recombination events produce existing haplotypes, and as such are silent. Silent recombination considerably reduces the total number of haplotypes expected from the infinite site model for populations that are not much larger than one over the mutation rate. Moreover, in contrast with mutations, the number of haplotypes does not grow linearly with the population size. We hence propose a more accurate estimate of the total number of haplotypes that takes into account silent recombination. We study large-scale Human Leukocyte Antigen (HLA) haplotype frequencies from human populations to show that the current estimated recombination rate in the HLA region is underestimated.