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Genetics. May 2003; 164(1): 407–417.
PMCID: PMC1462539

A coalescent model of recombination hotspots.

Abstract

Recent experimental findings suggest that the assumption of a homogeneous recombination rate along the human genome is too naive. These findings point to block-structured recombination rates; certain regions (called hotspots) are more prone than other regions to recombination. In this report a coalescent model incorporating hotspot or block-structured recombination is developed and investigated analytically as well as by simulation. Our main results can be summarized as follows: (1) The expected number of recombination events is much lower in a model with pure hotspot recombination than in a model with pure homogeneous recombination, (2) hotspots give rise to large variation in recombination rates along the genome as well as in the number of historical recombination events, and (3) the size of a (nonrecombining) block in the hotspot model is likely to be overestimated grossly when estimated from SNP data. The results are discussed with reference to the current debate about block-structured recombination and, in addition, the results are compared to genome-wide variation in recombination rates. A number of new analytical results about the model are derived.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Hudson RR. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol. 1983 Apr;23(2):183–201. [PubMed]
  • Hudson RR, Kaplan NL. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics. 1985 Sep;111(1):147–164. [PMC free article] [PubMed]
  • Jeffreys AJ, Kauppi L, Neumann R. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet. 2001 Oct;29(2):217–222. [PubMed]
  • Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, et al. Haplotype tagging for the identification of common disease genes. Nat Genet. 2001 Oct;29(2):233–237. [PubMed]
  • Kaplan N, Hudson RR. The use of sample genealogies for studying a selectively neutral m-loci model with recombination. Theor Popul Biol. 1985 Dec;28(3):382–396. [PubMed]
  • McPeek MS, Speed TP. Modeling interference in genetic recombination. Genetics. 1995 Feb;139(2):1031–1044. [PMC free article] [PubMed]
  • Myers Simon R, Griffiths Robert C. Bounds on the minimum number of recombination events in a sample history. Genetics. 2003 Jan;163(1):375–394. [PMC free article] [PubMed]
  • Nachman MW. Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 2001 Sep;17(9):481–485. [PubMed]
  • Rosenberg Noah A, Nordborg Magnus. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet. 2002 May;3(5):380–390. [PubMed]
  • Simonsen KL, Churchill GA. A Markov Chain Model of Coalescence with Recombination. Theor Popul Biol. 1997 Aug;52(1):43–59. [PubMed]
  • Wall JD. A comparison of estimators of the population recombination rate. Mol Biol Evol. 2000 Jan;17(1):156–163. [PubMed]
  • Watterson GA. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975 Apr;7(2):256–276. [PubMed]
  • Wiuf C. A coalescence approach to gene conversion. Theor Popul Biol. 2000 Jun;57(4):357–367. [PubMed]
  • Wiuf C, Hein J. The coalescent with gene conversion. Genetics. 2000 May;155(1):451–462. [PMC free article] [PubMed]
  • Zhang Kui, Deng Minghua, Chen Ting, Waterman Michael S, Sun Fengzhu. A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci U S A. 2002 May 28;99(11):7335–7339. [PMC free article] [PubMed]
  • Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet. 2001 Oct;29(2):229–232. [PubMed]
  • Fearnhead P, Donnelly P. Estimating recombination rates from population genetic data. Genetics. 2001 Nov;159(3):1299–1318. [PMC free article] [PubMed]
  • Gabriel Stacey B, Schaffner Stephen F, Nguyen Huy, Moore Jamie M, Roy Jessica, Blumenstiel Brendan, Higgins John, DeFelice Matthew, Lochner Amy, Faggart Maura, et al. The structure of haplotype blocks in the human genome. Science. 2002 Jun 21;296(5576):2225–2229. [PubMed]

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