Apparent high recombination rates in clonal parasitic organisms due to inappropriate sampling design

Heredity

Volumn 104, Issue 2, 2010, Pages 135-140

  Prugnolle, F ^a   De Meeus, T ^a,b  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^b CIRAD   (France)

Author keywords

Clonality; Linkage disequilibrium; Molecular markers; Population genetics; Sampling design

Indexed keywords

CLONAL ORGANISM; GENETIC MARKER; GENETIC VARIATION; GENOTYPE; LIFE CYCLE; RECOMBINATION; SAMPLING; SUBPOPULATION;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CANDIDA ALBICANS; CANDIDIASIS; COMPUTER SIMULATION; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETICS; GENOTYPE; GROWTH, DEVELOPMENT AND AGING; HOST PATHOGEN INTERACTION; HUMAN; LIFE CYCLE; MALARIA; METHODOLOGY; MICROBIOLOGY; PARASITOLOGY; PLASMODIUM;

ANIMALS; CANDIDA ALBICANS; CANDIDIASIS; COMPUTER SIMULATION; GENOTYPE; HOST-PATHOGEN INTERACTIONS; HUMANS; LIFE CYCLE STAGES; LINKAGE DISEQUILIBRIUM; MALARIA; MODELS, GENETIC; PLASMODIUM; RECOMBINATION, GENETIC; RESEARCH DESIGN;

EID: 75549088664     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2009.128     Document Type: Article

References (39)

1. Agapow PM, Burt A (2001). Indices of multilocus linkage disequilibrium. Mol Ecol Notes 1: 101-102.
2. Akaike H (1974). A new look at the statistical model identification. IEEE Trans Automat Contr 19: 716-723.
3. Balloux F (2001). EASYPOP (version 1.7): a computer program for population genetics simulations. J Hered 92: 301-302.
4. Balloux F, Lehmann L, de Meeus T (2003). The population genetics of clonal and partially clonal diploids. Genetics 164: 1635-1644.
5. Beck-Sague CM, Jarvis WR (1993). Secular trends in the epidemiology of nosocomial fungal infections in the United-States, 1980-1990. J Infect Dis 167: 1247-1251.
6. Berman J, Sudbery PE (2002). Candida albicans: a molecular revolution built on lessons from budding yeast. Nat Rev Genet 3: 918-930.
7. Boerlin P, BoerlinPetzold F, Goudet J, Durussel C, Pagani JL, Chave JP et al. (1996). Typing Candida albicans oral isolates from human immunodeficiency virus-infected patients by multilocus enzyme electrophoresis and DNA fingerprinting. J Clin Microb 34: 1235-1248.
8. Bougnoux ME, Aanensen DM, Morand S, Théraud M, Spratt BG, d0Enfert C (2004). Multilocus sequence typing of Candida albicans: strategies, data exchange and applications. Inf Genet Evol 4: 243-252.
9. Bush AO, Lafferty KD, Lotz JM, Shostak AW (1997). Parasitology meets ecology on its own terms: Margolis et al. revisited. J Parasitol 83: 575-583.
10. Criscione CD (2008). Parasite co-structure: broad and local scale approaches. Parasite 15: 439-443.
11. Criscione CD, Blouin MS (2005). Effective sizes of macroparasite populations: a conceptual model. Trends Parasitol 21: 212-217.
12. Criscione CD, Blouin MS (2006). Minimal selfing, few clones, and no among-host genetic structure in a hermaphroditic parasite with asexual larval propagation. Evolution 60: 553-562.
13. Criscione CD, Poulin R, Blouin MS (2005). Molecular ecology of parasites: elucidating ecological and microevolutionary processes. Mol Ecol 14: 2247-2257.
14. de Freitas JM, Augusto-Pinto L, Pimenta JR, Bastos-Rodrigues L, Gonçalves VF, Teixeira SMR et al. (2006). Ancestral genomes, sex, and the population structure of Trypanosoma cruzi. PLoS Pathog 2: 226-235.
15. De Meeus T, Lehmann L, Balloux F (2006). Molecular epidemiology of clonal diploids: a quick overview and a short DIY (do it yourself) notice. Inf Genet Evol 6: 163-170.
16. de Meeus T, Prugnolle F, Agnew P (2007). Asexual reproduction: genetics and evolutionary aspects. Cell Mol Life Sci 64: 1355-1372.
17. Goudet J (1995). Fstat (vers.1.2): a computer program to calculate F-statistics. J Hered 86: 485-486.
18. Haukisalmi V, Henttonen H (1993). Coexistence in Helminths of the Bank Vole Clethrionomys-Glareolus.2. Intestinal distribution and interspecific interactions. J Anim Ecol 62: 230-238.
19. Hull CM, Raisner RM, Johnson AD (2000). Evidence for mating of the''asexual''yeast Candida albicans in a mammalian host. Science 289: 307-310.
20. Koffi M, Solano P, Barnabé C, De Meeûs T, Bucheton B, N'Dri L et al. (2007). Genetic characterisation of Trypanosoma brucei ssp by microsatellite typing: new perspectives for the molecular epidemiology of human African trypanosomosis. Inf Genet Evol 7: 675-684.
21. Kuhls K, Keilonat L, Ochsenreither S, Schaar M, Schweynoch C, Presber W et al. (2007). Multilocus microsatellite typing (MLMT) reveals genetically isolated populations between and within the main endemic regions of visceral leishmaniasis. Microbes Infect 9: 334-343.
22. MacLeod A, Tweedie A, Welburn SC, Maudlin I, Turner CMR, Tait A (2000). Minisatellite marker analysis of Trypanosoma brucei: reconciliation of clonal, panmictic, and epidemic population genetic structures. Proc Natl Acad Sci USA 97: 13442-13447.
23. Maynard Smith J, Smith NH, O'Rourke M, Spratt BG (1993). How clonal are bacteria? Proc Natl Acad Sci USA 90: 4384-4390.
24. McVean G, Awadalla P, Fearnhead P (2002). A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
25. Mulvey M, Aho JM, Lydeard C, Leberg PL, Smith MH (1991). Comparative population genetic structure of a parasite (Fascioloides magna) and its definitive host. Evolution 45: 1628-1640.
26. Mzilahowa T, McCall PJ, Hastings IM (2007).'Sexual'population structure and genetics of the malaria agent P.falciparum. PLoS ONE 2: e613.
27. Nebavi F, Ayala FJ, Renaud F, Bertout S, Eholie S, Moussa K et al. (2006). Clonal population structure and genetic diversity of Candida albicans in AIDS patients from Abidjan (Cote d'Ivoire). Proc Natl Acad Sci USA 103: 3663-3668.
28. Nei M, Li WH (1973). Linkage disequilibrium in subdivided populations. Genetics 75: 213-219.
29. Nejsum P, Frydenberg J, Roepstorff A, Parker Jr ED (2005). Population structure in Ascaris suum (Nematoda) among domestic swine in Denmark as measured by whole genome DNA fingerprinting. Hereditas 142: 7-14.
30. Prugnolle F, Choisy M, de Meeus T (2008). Clonality V.0.4: a randomization-based program to test for heterozygositygenet size relationships in clonal organisms. Mol Ecol Resour 8: 954-956.
31. Prugnolle F, Liu H, de Meeus T, Balloux F (2005a). Population genetics of complex life-cycle parasites: an illustration with trematodes. Int J Parasitol 35: 255-263.
32. Prugnolle F, Roze D, Theron A, DE Meeûs T (2005b). F-statistics under alternation of sexual and asexual reproduction: a model and data from schistosomes (platyhelminth parasites). Mol Ecol 14: 1355-1365.
33. Pujol C, Reynes J, Renaud F, Raymond M, Tibayrenc M, Ayala FJ et al. (1993). The yeast Candida albicans has a clonal mode of reproduction in a population of infected human immunodeficiency virus-positive patients. Proc Natl Acad Sci USA 90: 9456-9459.
34. R Development-core-team (2008). R Foundation for Statistical Computing, Vienna, Austria http://www.R-project.org, ISBN 3-900051-07-0.
35. Razakandrainibe FG, Durand P, Koella JC, De Meeus T, Rousset F, Ayala FJ et al. (2005).'Clonal'population structure of the malaria agent Plasmodium falciparum in high-infection regions. Proc Natl Acad Sci USA 102: 17388-17393.
36. Swidsinski A, Loening-Baucke V, Lochs H, Hale L-P (2005). Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice. World J Gastroenterol 11: 1131-1140.
37. Tibayrenc M, Ayala FJ (2002). The clonal theory of parasitic protozoa: 12 years on. Trends Parasitol 18: 405-410.
38. Wahlund S (1928). Zuzammensetzung von populationen und korrelation-serscheiunungen von standpunkt der vererbungslehre aus betrachtet. Hereditas 11: 65-106.
39. Weir BS, Cockerham CC (1984). Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.