Recombination hotspots and population structure in Plasmodium falciparum

PLoS Biology

Volumn 3, Issue 10, 2005, Pages

  Mu, Jianbing ^a   Awadalla, Philip ^b   Duan, Junhui ^a   McGee, Kate M ^b   Joy, Deirdre A ^a   McVean, Gilean A T ^c   Su, Xin Zhuan ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; CONTROLLED STUDY; FEASIBILITY STUDY; GENE CLUSTER; GENE ISOLATION; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; NONHUMAN; PLASMODIUM FALCIPARUM; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; SUPERINFECTION; AFRICA; ANIMAL; CENTRAL AMERICA; DRUG RESISTANCE; GENE LINKAGE DISEQUILIBRIUM; GENETICS; PAPUA NEW GUINEA; PHYSIOLOGY; POPULATION GENETICS; SOUTH AMERICA; SOUTHEAST ASIA;

PLASMODIUM FALCIPARUM;

AFRICA; ANIMALS; ASIA, SOUTHEASTERN; CENTRAL AMERICA; DRUG RESISTANCE; GENETICS, POPULATION; LINKAGE DISEQUILIBRIUM; PAPUA NEW GUINEA; PLASMODIUM FALCIPARUM; POLYMORPHISM, SINGLE NUCLEOTIDE; RECOMBINATION, GENETIC; SOUTH AMERICA;

EID: 26444574740     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030335     Document Type: Article

References (42)

1. WHO (2000) WHO Expert Committee on Malaria. World Health Organ Tech Rep Ser 892: 1-74.
2. Tishkoff SA, Varkonyi R, Cahinhinan N, Abbes S, Argyropoulos G, et al (2001) Haplotype diversity and linkage disequilibrium at human G6PD: Recent origin of alleles that confer malarial resistance. Science 293: 455-462.
3. Ohashi J, Naka I, Patarapotikul J, Hananantachai H, Brittenham G, et al. (2004) Extended linkage disequilibrium surrounding the hemoglobin E variant due to malarial selection. Am J Hum Genet 74: 1198-1208.
4. Conway DJ, Cavanagh DR, Tanabe K, Roper C, Mikes ZS, et al. (2000) A principal target of human immunity to malaria identified by molecular population genetic and immunological analyses. Nat Med 6: 689-692.
5. Wootton JC, Feng X, Ferdig MT, Cooper RA, Mu J, et al. (2002) Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum. Nature 418: 320-323.
6. Nair S, Williams JT, Brockman A, Paiphun L, Mayxay M, et al. (2003) A selective sweep driven by pyrimethamine treatment in southeast asian malaria parasites. Mol Biol Evol 20: 1526-1536.
7. Roper C, Pearce R, Bredenkamp B, Gumede J, Drakeley C, et al. (2003) Antifolate antimalarial resistance in southeast Africa: A population-based analysis. Lancet 361: 1174-1181.
8. Anderson TJ (2004) Mapping drug resistance genes in Plasmodium falciparum by genome-wide association. Curr Drug Targets Infect Disord 4: 65-78.
9. Hill WG, Babiker HA, Ranford-Cartwright LC, Walliker D (1995) Estimation of inbreeding coefficients from genotypic data on multiple alleles, and application to estimation of clonality in malaria parasites. Genet Res 65: 53-61.
10. Paul RE, Packer MJ, Walmsley M, Lagog M, Ranford-Cartwright LC, et al. (1995) Mating patterns in malaria parasite populations of Papua New Guinea. Science 269: 1709-1711.
11. Babiker HA, Lines J, Hill WG, Walliker D (1997) Population structure of Plasmodium falciparum in villages with different malaria endemicity in east Africa. Am J Trop Med Hyg 56: 141-147.
12. Conway DJ, Roper C, Oduola AM, Arnot DE, Kremsner PG, et al. (1999) High recombination rate in natural populations of Plasmodium falciparum. Proc Natl Acad Sci U S A 96: 4506-4511.
13. Anderson TJ, Haubold B, Williams JT, Estrada-Franco JG, Richardson L, et al. (2000) Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Mol Biol Evol 17: 1467-1482.
14. Su X, Ferdig MT, Huang Y, Huynh CQ, Liu A, et al. (1999) A genetic map and recombination parameters of the human malaria parasite Plasmodium falciparum. Science 286: 1351-1353.
15. Mu J, Duan J, Makova K, Joy DA, Huynh CQ, et al. (2002) Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature 418: 323-326.
16. Chakravarti A, Buetow KH, Antonarakis SE, Waber PG, Boehm CD, et al. (1984) Nonuniform recombination within the human beta-globin gene cluster. Am J Hum Genet 36: 1239-1258.
17. Jeffreys AJ, Kauppi L, Neumann R (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 29: 217-222.
18. Petes TD (2001) Meiotic recombination hot spots and cold spots. Nat Rev Genet 2: 360-369.
19. McVean GA, Myers SR, Hunt S, Deloukas P, Bentley DR, et al. (2004) The fine-scale structure of recombination rate variation in the human genome. Science 304: 581-584.
20. Jeffreys AJ, Neumann R (2002) Reciprocal crossover asymmetry and meiotic drive in a human recombination hot spot. Nat Genet 31: 267-271.
21. Pollak E (1987) On the theory of partially inbreeding finite populations. I. Partial selfing. Genetics 117: 353-360.
22. Pritchard JK, Przeworski M (2001) Linkage disequilibrium in humans: Models and data. Am J Hum Genet 69: 1-14.
23. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat Genet 36: 512-517.
24. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
25. Schneider S, Roessli D, Excoffier L (2000) Arlequin: A software for population genetics data analysis. Version 2.000. Genetics and Biometry Lab, Department of Anthropology, University of Geneva. Available: http://lgb.unige.ch/arlequin/software/2.000/doc/faq/faqlist.htm. Accessed 4 August 2005.
26. Mu J, Ferdig MT, Feng X, Joy DA, Duan J, et al. (2003) Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol Microbiol 49: 977-989.
27. McVean G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
28. Myers SR, Griffiths RC (2003) Bounds on the minimum number of recombination events in a sample history. Genetics 163: 375-394.
29. Nordborg M (2000) Linkage disequilibrium, gene trees and selfing: An ancestral recombination graph with partial self-fertilization. Genetics 154: 923-929.
30. Hill WG, Babiker HA (1995) Estimation of numbers of malaria clones in blood samples. Proc R Soc Lond B Biol Sci 262: 249-257.
31. Nicholson G, Smith AV, Jónsson F, Gústafsson Ó, Stefánsson K, et al. (2002) Assessing population differentiation and isolation from single-nucleotide polymorphism data. J Royal Stat Soc Series B 64: 695-716.
32. Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, et al. (2002) A high-resolution recombination map of the human genome. Nat Genet 31: 241-247.
33. Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
34. Bowman S, Lawson D, Basham D, Brown D, Chillingworth T, et al. (1999) The complete nucleotide sequence of Chromosome 3 of Plasmodium falciparum. Nature 400: 532-538.
35. Volkman SK, Hartl DL, Wirth DF, Nielsen KM, Choi M, et al. (2002) Excess polymorphisms in genes for membrane proteins in Plasmodium falciparum. Science 298: 216-218.
36. Otto SP, Barton NH (1997) The evolution of recombination: Removing the limits to natural selection. Genetics 147: 879-906.
37. Hill WG (1974) Disequilibrium among several linked neutral genes in finite population. II. Variances and covariances of disequilibria. Theor Popul Biol 6: 184-198.
38. Weir BS, Hill WG (1986) Nonuniform recombination within the human beta-globin gene cluster. Am J Hum Genet 38: 776-781.
39. Dye C, Williams BG (1997) Multigenic drug resistance among inbred malaria parasites. Proc Biol Sci 264: 61-67.
40. Awadalla P (2003) The evolutionary genomics of pathogen recombination. Nat Rev Genet 4: 50-60.
41. Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
42. Zhang K, Deng M, Chen T, Waterman MS, Sun F (2002) A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci U S A 99: 7335-7339.