Home LiteratureArticle Details
PMID: 15208713 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

Absence of the TAP2 human recombination hotspot in chimpanzees.

PLoS biology ·Vol. 2 ·No. 6 ·2004-06-00 ·Pages e155

Ptak SE, Roeder AD, Stephens M, Gilad Y, Pääbo S, Przeworski M

Abstract

Recent experiments using sperm typing have demonstrated that, in several regions of the human genome, recombination does not occur uniformly but instead is concentrated in "hotspots" of 1-2 kb. Moreover, the crossover asymmetry observed in a subset of these has led to the suggestion that hotspots may be short-lived on an evolutionary time scale. To test this possibility, we focused on a region known to contain a recombination hotspot in humans, TAP2, and asked whether chimpanzees, the closest living evolutionary relatives of humans, harbor a hotspot in a similar location. Specifically, we used a new statistical approach to estimate recombination rate variation from patterns of linkage disequilibrium in a sample of 24 western chimpanzees (Pan troglodytes verus). This method has been shown to produce reliable results on simulated data and on human data from the TAP2 region. Strikingly, however, it finds very little support for recombination rate variation at TAP2 in the western chimpanzee data. Moreover, simulations suggest that there should be stronger support if there were a hotspot similar to the one characterized in humans. Thus, it appears that the human TAP2 recombination hotspot is not shared by western chimpanzees. These findings demonstrate that fine-scale recombination rates can change between very closely related species and raise the possibility that rates differ among human populations, with important implications for linkage-disequilibrium based association studies.

MeSH Terms
ATP Binding Cassette Transporter, Subfamily B, Member 3 ATP-Binding Cassette Transporters/genetics Animals Base Sequence Computer Simulation Evolution, Molecular Genetic Variation Haplotypes/genetics Humans Linkage Disequilibrium/genetics Models, Genetic Molecular Sequence Data Mutation/genetics Pan troglodytes/genetics Polymorphism, Single Nucleotide/genetics Recombination, Genetic/genetics Sequence Analysis, DNA
Chemicals
ATP Binding Cassette Transporter, Subfamily B, Member 3 ATP-Binding Cassette Transporters TAP2 protein, human
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Ptak Susan E
Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
Roeder Amy D
Stephens Matthew
Gilad Yoav
Pääbo Svante
Przeworski Molly
Conflict of Interest

The authors have declared that no conflicts of interest exist.

References (45)
45 references, click to expand
  1. Distribution of meiotic recombination sites.
    Trends Genet. 2003 Sep;19(9):514-22 PMID: 12957545
  2. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
    Genetics. 1989 Nov;123(3):585-95 PMID: 2513255
  3. On the number of segregating sites in genetical models without recombination.
    Theor Popul Biol. 1975 Apr;7(2):256-76 PMID: 1145509
  4. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data.
    Genetics. 2003 Dec;165(4):2213-33 PMID: 14704198
  5. Natural selection on the olfactory receptor gene family in humans and chimpanzees.
    Am J Hum Genet. 2003 Sep;73(3):489-501 PMID: 12908129
  6. High-resolution mapping of crossovers in human sperm defines a minisatellite-associated recombination hotspot.
    Mol Cell. 1998 Aug;2(2):267-73 PMID: 9734365
  7. Linkage disequilibrium in humans: models and data.
    Am J Hum Genet. 2001 Jul;69(1):1-14 PMID: 11410837
  8. Estimating the recombination parameter of a finite population model without selection.
    Genet Res. 1987 Dec;50(3):245-50 PMID: 3443297
  9. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis.
    Bioinformatics. 1999 Feb;15(2):174-5 PMID: 10089204
  10. A comparison of bayesian methods for haplotype reconstruction from population genotype data.
    Am J Hum Genet. 2003 Nov;73(5):1162-9 PMID: 14574645
  11. Meiotic DNA breaks at the S. pombe recombination hot spot M26.
    Mol Cell. 2002 Apr;9(4):847-55 PMID: 11983175
  12. Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved.
    Am J Hum Genet. 2003 Jul;73(1):5-16 PMID: 12772086
  13. Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot.
    Nat Genet. 2002 Jul;31(3):267-71 PMID: 12089523
  14. Comparative analyses of multi-species sequences from targeted genomic regions.
    Nature. 2003 Aug 14;424(6950):788-93 PMID: 12917688
  15. Direct measurement of the male recombination fraction in the human beta-globin hot spot.
    Hum Mol Genet. 2002 Feb 1;11(3):207-15 PMID: 11823440
  16. Meiotic recombination hot spots and cold spots.
    Nat Rev Genet. 2001 May;2(5):360-9 PMID: 11331902
  17. The roles of REV3 and RAD57 in double-strand-break-repair-induced mutagenesis of Saccharomyces cerevisiae.
    Genetics. 2002 Nov;162(3):1063-77 PMID: 12454056
  18. High resolution localization of recombination hot spots using sperm typing.
    Nat Genet. 1994 Jul;7(3):420-4 PMID: 7920662
  19. High-resolution patterns of meiotic recombination across the human major histocompatibility complex.
    Am J Hum Genet. 2002 Oct;71(4):759-76 PMID: 12297984
  20. High levels of Y-chromosome nucleotide diversity in the genus Pan.
    Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):43-8 PMID: 11756656
  21. Genomewide comparison of DNA sequences between humans and chimpanzees.
    Am J Hum Genet. 2002 Jun;70(6):1490-7 PMID: 11992255
  22. A genetic linkage map of the baboon (Papio hamadryas) genome based on human microsatellite polymorphisms.
    Genomics. 2000 Aug 1;67(3):237-47 PMID: 10936045
  23. The structure of haplotype blocks in the human genome.
    Science. 2002 Jun 21;296(5576):2225-9 PMID: 12029063
  24. Variation in recombination rate across the genome: evidence and implications.
    Curr Opin Genet Dev. 2002 Dec;12(6):657-63 PMID: 12433578
  25. Estimating recombination rates from population genetic data.
    Genetics. 2001 Nov;159(3):1299-318 PMID: 11729171
  26. High-resolution sperm typing of meiotic recombination in the mouse MHC Ebeta gene.
    EMBO J. 2003 Mar 17;22(6):1389-97 PMID: 12628931
  27. High resolution analysis of haplotype diversity and meiotic crossover in the human TAP2 recombination hotspot.
    Hum Mol Genet. 2000 Mar 22;9(5):725-33 PMID: 10749979
  28. Haplotype blocks and linkage disequilibrium in the human genome.
    Nat Rev Genet. 2003 Aug;4(8):587-97 PMID: 12897771
  29. Amplification and analysis of DNA sequences in single human sperm and diploid cells.
    Nature. 1988 Sep 29;335(6189):414-7 PMID: 3419517
  30. Crossover breakpoint mapping identifies a subtelomeric hotspot for male meiotic recombination.
    Hum Mol Genet. 2000 May 1;9(8):1239-44 PMID: 10767349
  31. Kin selection, social structure, gene flow, and the evolution of chimpanzees.
    Science. 1994 Aug 26;265(5176):1193-201 PMID: 7915048
  32. Differences in crossover frequency and distribution among three sibling species of Drosophila.
    Genetics. 1996 Feb;142(2):507-23 PMID: 8852849
  33. Linkage limits the power of natural selection in Drosophila.
    Proc Natl Acad Sci U S A. 2002 Oct 15;99(21):13616-20 PMID: 12370444
  34. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex.
    Nat Genet. 2001 Oct;29(2):217-22 PMID: 11586303
  35. A high-resolution recombination map of the human genome.
    Nat Genet. 2002 Jul;31(3):241-7 PMID: 12053178
  36. Recombination breakpoints in the human beta-globin gene cluster.
    Blood. 1998 Dec 1;92(11):4415-21 PMID: 9834248
  37. A new statistical method for haplotype reconstruction from population data.
    Am J Hum Genet. 2001 Apr;68(4):978-89 PMID: 11254454
  38. High-resolution haplotype structure in the human genome.
    Nat Genet. 2001 Oct;29(2):229-32 PMID: 11586305
  39. The hotspot conversion paradox and the evolution of meiotic recombination.
    Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):8058-63 PMID: 9223314
  40. The International HapMap Project.
    Nature. 2003 Dec 18;426(6968):789-96 PMID: 14685227
  41. Evidence for a complex demographic history of chimpanzees.
    Mol Biol Evol. 2004 May;21(5):799-808 PMID: 14963091
  42. Evolutionary dynamics of non-coding sequences within the class II region of the human MHC.
    J Mol Biol. 1996 Jan 12;255(1):1-13 PMID: 8568858
  43. Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates.
    Am J Hum Genet. 2003 Dec;73(6):1330-40 PMID: 14628290
  44. Haplotype tagging for the identification of common disease genes.
    Nat Genet. 2001 Oct;29(2):233-7 PMID: 11586306
  45. A neutral explanation for the correlation of diversity with recombination rates in humans.
    Am J Hum Genet. 2003 Jun;72(6):1527-35 PMID: 12740762
Article Info
Journal
PLoS biology
Abbr.
PLoS Biol
ISSN
1545-7885
DOI
10.1371/journal.pbio.0020155
Published
2004-06-00
Epub
2004-00-15
Pages
e155
Language
English
Region
United States
NLM ID
101183755
PMCID
PMC423135
Subset
IM
Grants
NHGRI NIH HHS · 1R01HG/LM02585-01 · United States
Databases
GENBANK
AY559252, AY559253, AY559254, AY559255, AY559256, AY559257, AY559258, AY559259, AY559260, AY559261, AY559262, AY559263, AY559264, AY559265, AY559266, AY559267, AY559268, AY559269, AY559270, AY559271, AY559272, AY559273, AY559274, AY559275, AY559276, AY559277, AY559278, AY559279, AY559280, AY559281, AY559282, AY559283, AY559284, AY559285, AY559286, AY559287, AY559288, AY559289, AY559290, AY559291, AY559292, AY559293, AY559294, AY559295, AY559296, AY559297, AY559298, AY559299, X87344
External Links
PubMed source DOI: 10.1371/journal.pbio.0020155 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2