PMID- 36109958
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20220916
IS  - 2470-0053 (Electronic)
IS  - 2470-0045 (Linking)
VI  - 106
IP  - 2-1
DP  - 2022 Aug
TI  - High fraction of silent recombination in a finite-population two-locus neutral 
      birth-death-mutation model.
PG  - 024409
LID - 10.1103/PhysRevE.106.024409 [doi]
AB  - 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.
FAU - Melka, A B
AU  - Melka AB
AD  - Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel.
FAU - Louzoun, Y
AU  - Louzoun Y
AD  - Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel.
AD  - Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Phys Rev E
JT  - Physical review. E
JID - 101676019
SB  - IM
EDAT- 2022/09/17 06:00
MHDA- 2022/09/17 06:01
CRDT- 2022/09/16 01:05
PHST- 2021/06/26 00:00 [received]
PHST- 2022/07/25 00:00 [accepted]
PHST- 2022/09/16 01:05 [entrez]
PHST- 2022/09/17 06:00 [pubmed]
PHST- 2022/09/17 06:01 [medline]
AID - 10.1103/PhysRevE.106.024409 [doi]
PST - ppublish
SO  - Phys Rev E. 2022 Aug;106(2-1):024409. doi: 10.1103/PhysRevE.106.024409.