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A precise estimate of allele and haplotype polymorphism is of great interestin theoretical population genetics, but also has practical applications, suchas bone marrow registries management. Allele polymorphism is driven mainly bypoint mutations, while haplotype polymorphism is also affected byrecombination. Current estimates treat recombination as mutations in aninfinite site model. We here show that even in the simple case of two loci in ahaploid individual, for a finite population, most recombination events produceexisting haplotypes, and as such are silent. Silent recombination considerablyreduces the total number of haplotypes expected from the infinite site modelfor populations that are not much larger than one over the mutation rate.Moreover, in contrast with mutations, the number of haplotypes does not growlinearly with the population size. We hence propose a more accurate estimate ofthe total number of haplotypes that takes into account silent recombination. Westudy large-scale Human Leukocyte Antigen (HLA) haplotype frequencies fromhuman populations to show that the current estimated recombination rate in theHLA region is underestimated.

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