New Insights into Clonality and Panmixia in Plasmodium and Toxoplasma

Agrawal, 2006, Evolution of sex: why do organisms shuffle their genotypes?, Curr. Biol., 16, R696, 10.1016/j.cub.2006.07.063 Anderson, 2000, Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum, Mol. Biol. Evol., 17, 1467, 10.1093/oxfordjournals.molbev.a026247 Annan, 2007, Population genetic structure of Plasmodium falciparum in the two main African vectors, Anopheles gambiae and Anopheles funestus, Proc. Natl. Acad. Sci. U.S.A., 104, 7987, 10.1073/pnas.0702715104 Arnott, 2012, Understanding the population genetics of Plasmodium vivax is essential for malaria control and elimination, Malar. J., 11, 14, 10.1186/1475-2875-11-14 Avise, 2004, Molecular markers, Natural History and Evolution Beck, 2009, Molecular approaches to diversity of populations of apicomplexan parasites, Int. J. Parasitol., 39, 175, 10.1016/j.ijpara.2008.10.001 Ben Abderrazak, 1999, Plasmodium falciparum: population genetic analysis by multilocus enzyme electrophoresis and other molecular markers, Exp. Parasitol., 92, 232, 10.1006/expr.1999.4424 Boothroyd, 2009, Toxoplasma gondii: 25 years and 25 major advances for the field, Int. J. Parasitol., 39, 935, 10.1016/j.ijpara.2009.02.003 Branch, 2011, Plasmodium falciparum genetic diversity maintained and amplified over 5 years of a low transmission endemic in the Peruvian Amazon, Mol. Biol. Evol., 28, 1973, 10.1093/molbev/msq311 Chenet, 2012, Local population structure of Plasmodium: impact on malaria control and elimination, Malar. J., 11, 412, 10.1186/1475-2875-11-412 Conway, 2007, Molecular epidemiology of malaria, Clin. Microbiol. Rev., 20, 188, 10.1128/CMR.00021-06 da Silva, 2011, Genotypic characterization of Toxoplasma gondii in sheep from Brazilian slaughterhouses: new atypical genotypes and the clonal type II strain identified, Vet. Parasitol., 175, 173, 10.1016/j.vetpar.2010.09.021 De Meeûs, 2007, Population genetics and molecular epidemiology or how to “débusquer la bête”, Infect. Genet. Evol., 7, 308, 10.1016/j.meegid.2006.07.003 Dubey, 2011, Genetic characterisation of Toxoplasma gondii in wildlife from North America revealed widespread and high prevalence of the fourth clonal type, Int. J. Parasitol., 41, 1139, 10.1016/j.ijpara.2011.06.005 Duval, 2010, African apes as reservoirs of Plasmodium falciparum and the origin and diversification of the Laverania subgenus, Proc. Natl. Acad. Sci. U.S.A., 23, 10561, 10.1073/pnas.1005435107 Dye, 1990, When are parasites clonal?, Nature, 348, 120, 10.1038/348120b0 Ferreira, 2007, Population structure and transmission dynamics of Plasmodium vivax in rural Amazonia, J. Infect. Dis., 195, 1218, 10.1086/512685 Griffing, 2011, South American Plasmodium falciparum after the malaria eradication era: clonal population expansion and survival of the fittest hybrids, PLoS One, 6, e23486, 10.1371/journal.pone.0023486 Grigg, 2009, Sexual recombination punctuated by outbreaks and clonal expansions predicts Toxoplasma gondii population genetics, Int. J. Parasitol., 39, 925, 10.1016/j.ijpara.2009.02.005 Gupta, 2012, Inferring the evolutionary history of Indian Plasmodium vivax from population genetic analyses of multilocus nuclear DNA fragments, Mol. Ecol., 21, 1597, 10.1111/j.1365-294X.2012.05480.x Heitman, 2006, Sexual reproduction and the evolution of microbial pathogens, Curr. Biol., 16, R711, 10.1016/j.cub.2006.07.064 Imwong, 2006, Microsatellite variation, repeat array length, and population history of Plasmodium vivax, Mol. Biol. Evol., 23, 1016, 10.1093/molbev/msj116 Imwong, 2007, Contrasting genetic structure in Plasmodium vivax populations from Asia and South America, Int. J. Parasitol., 37, 1013, 10.1016/j.ijpara.2007.02.010 Iwagami, 2012, Population structure and transmission dynamics of Plasmodium vivax in the Republic of Korea based on microsatellite DNA analysis, PLoS Negl. Trop. Dis., 6, e1592, 10.1371/journal.pntd.0001592 Iwagami, 2009, Genetic diversity and population structure of Plasmodium falciparum in the Philippines, Malar. J., 8, 96, 10.1186/1475-2875-8-96 Karunaweera, 2008, Extensive microsatellite diversity in the human malaria parasite Plasmodium vivax, Gene, 410, 105, 10.1016/j.gene.2007.11.022 Khan, 2011, Genetic analyses of atypical Toxoplasma gondii strains reveal a fourth clonal lineage in North America, Int. J. Parasitol., 41, 645, 10.1016/j.ijpara.2011.01.005 Khan, 2009, Selection at a single locus leads to widespread expansion of Toxoplasma gondii lineages that are virulent in mice, PLoS Genet., 5, e1000404, 10.1371/journal.pgen.1000404 Lehmann, 2004, Variation in the structure of Toxoplasma gondii and the roles of selfing, drift, and epistatic selection in maintaining linkage disequilibria, Infect. Genet. Evol., 4, 107, 10.1016/j.meegid.2004.01.007 Lehmann, 2006, Globalization and the population structure of Toxoplasma gondii, Proc. Natl. Acad. Sci. U.S.A., 103, 11423, 10.1073/pnas.0601438103 Liu, 2010, Origin of the human malaria parasite Plasmodium falciparum in gorillas, Nature, 467, 420, 10.1038/nature09442 Manske, 2012, Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing, Nature, 487, 375, 10.1038/nature11174 Mercier, 2011, Human impact on genetic diversity of Toxoplasma gondii: example of the anthropized environment from French Guiana, Infect. Genet. Evol., 11, 1378, 10.1016/j.meegid.2011.05.003 Mercier, 2010, Additional haplogroups of Toxoplasma gondii out of Africa: population structure and mouse-virulence of strains from Gabon, PLoS Negl. Trop. Dis., 4, e876, 10.1371/journal.pntd.0000876 Minot, 2012, Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity, Proc. Natl. Acad. Sci. U.S.A., 109, 13458, 10.1073/pnas.1117047109 Mobegi, 2012, Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa, Malar. J., 11, 223, 10.1186/1475-2875-11-223 Mu, 2005, Recombination hotspots and population structure in Plasmodium falciparum, PLoS Biol., 3, e335, 10.1371/journal.pbio.0030335 Mzilahowa, 2007, “Sexual” population structure and genetics of the malaria agent P. falciparum, PLoS One, 2, e613, 10.1371/journal.pone.0000613 Neafsey, 2013, ‘Big data’ from shrinking pathogen populations, Mol. Ecol., 22, 271, 10.1111/mec.12175 Neafsey, 2008, Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence, Genome Biol., 9, R171, 10.1186/gb-2008-9-12-r171 Nkhoma, 2013, Population genetic correlates of declining transmission in a human pathogen, Mol. Ecol., 22, 273, 10.1111/mec.12099 Orjuela-Sánchez, 2010, Single-nucleotide polymorphism, linkage disequilibrium and geographic structure in the malaria parasite Plasmodium vivax: prospects for genome-wide association studies, BMC Genet., 11, 65, 10.1186/1471-2156-11-65 Prugnolle, 2010, African great apes are natural hosts of multiple related malaria species, including Plasmodium falciparum, Proc. Natl. Acad. Sci. U.S.A., 107, 1458, 10.1073/pnas.0914440107 Prugnolle, 2011, A fresh look at the origin of Plasmodium falciparum, the most malignant malaria agent, PLoS Pathog., 7, 1, 10.1371/journal.ppat.1001283 Prugnolle, 2011, African monkeys are infected by Plasmodium falciparum nonhuman primate-specific strains, Proc. Natl. Acad. Sci. U.S.A., 108, 11948, 10.1073/pnas.1109368108 Rajendran, 2012, Molecular genotyping of Toxoplasma gondii from Central and South America revealed high diversity within and between populations, Infect. Genet. Evol., 12, 359, 10.1016/j.meegid.2011.12.010 Rayner, 2011, A plethora of Plasmodium species in wild apes: a source of human infection?, Trends Parasitol., 27, 222, 10.1016/j.pt.2011.01.006 Razakandrainibe, 2005, “Clonal” population structure of the malaria agent Plasmodium falciparum in high-infection regions, Proc. Natl. Acad. Sci. U.S.A., 102, 17388, 10.1073/pnas.0508871102 Rezende, 2010, Microsatellite loci: determining the genetic variability of Plasmodium vivax, Trop. Med. Int. Health, 15, 718, 10.1111/j.1365-3156.2010.02535.x Schultz, 2010, Multilocus haplotypes reveal variable levels of diversity and population structure of Plasmodium falciparum in Papua New Guinea, a region of intense perennial transmission, Malar. J., 9, 336, 10.1186/1475-2875-9-336 Sibley, 2008, Population structure of Toxoplasma gondii: clonal expansion driven by infrequent recombination and selective sweeps, Annu. Rev. Microbiol., 62, 329, 10.1146/annurev.micro.62.081307.162925 Sibley, 1992, Virulent strains of Toxoplasma gondii comprise a single clonal lineage, Nature, 359, 82, 10.1038/359082a0 Smith, 2009, Tracking transmission of the zoonosis Toxoplasma gondii, Adv. Parasitol., 68, 139, 10.1016/S0065-308X(08)00606-4 Su, 2003, Recent expansion of Toxoplasma through enhanced oral transmission, Science, 299, 414, 10.1126/science.1078035 Su, 2006, Genotyping of Toxoplasma gondii by multilocus PCR-RFLP markers: a high resolution and simple method for identification of parasites, Int. J. Parasitol., 36, 841, 10.1016/j.ijpara.2006.03.003 Su, 2010, Moving towards an integrated approach to molecular detection and identification of Toxoplasma gondii, Parasitology, 137, 1, 10.1017/S0031182009991065 Su, 2012, Globally diverse Toxoplasma gondii isolates comprise six major clades originating from a small number of distinct ancestral lineages, Proc. Natl. Acad. Sci. U.S.A., 109, 5844, 10.1073/pnas.1203190109 Tibayrenc, 2012, Reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa, Proc. Natl. Acad. Sci. U.S.A., 109, E3305, 10.1073/pnas.1212452109 Tibayrenc, 2013, How clonal are Trypanosoma and Leishmania?, Trends Parasitol., 29, 264, 10.1016/j.pt.2013.03.007 Tibayrenc, 1990, A clonal theory of parasitic protozoa: the population structure of Entamoeba, Giardia, Leishmania, Naegleria, Plasmodium, Trichomonas and Trypanosoma, and its medical and taxonomical consequences, Proc. Natl. Acad. Sci. U.S.A., 87, 2414, 10.1073/pnas.87.7.2414 Tibayrenc, 1991, Are eukaryotic microorganisms clonal or sexual? A population genetics vantage, Proc. Natl. Acad. Sci. U.S.A., 88, 5129, 10.1073/pnas.88.12.5129 Urdaneta, 2001, Evidence for clonal propagation in natural isolates of Plasmodium falciparum from Venezuela, Proc. Natl. Acad. Sci. U.S.A., 98, 625, 10.1073/pnas.111144998 Valkiunas, 2011, A cautionary note concerning Plasmodium in apes, Trends Parasitol., 27, 231, 10.1016/j.pt.2011.02.008 Volkman, 2003, A game of cat and mouth, Science, 299, 353, 10.1126/science.1081278 Volkman, 2007, A genome-wide map of diversity in Plasmodium falciparum, Nat. Genet., 1, 113, 10.1038/ng1930 Volkman, 2012, Application of genomics to field investigations of malaria by the international centers of excellence for malaria research, Acta Trop., 121, 324, 10.1016/j.actatropica.2011.12.002 Volkman, 2012, Harnessing genomics and genome biology to understand malaria biology, Nat. Rev. Genet., 13, 315, 10.1038/nrg3187 Walliker, 1991, Malaria parasites: randomly interbreeding or “clonal” populations?, Parasitol. Today, 7, 232, 10.1016/0169-4758(91)90235-G Walliker, 1990, When are parasites clonal?, Nature, 348, 120, 10.1038/348120a0 Wendte, 2010, Self-mating in the definitive host potentiates clonal outbreaks of the apicomplexan parasites Sarcocystis neurona and Toxoplasma gondii, PLoS Genet., 6, 1, 10.1371/journal.pgen.1001261 Wendte, 2011, Population genetics of Toxoplasma gondii: new perspectives from parasite genotypes in wildlife, Vet. Parasitol., 182, 96, 10.1016/j.vetpar.2011.07.018 Zingales, 2012, The revised Trypanosoma cruzi subspecific nomenclature: rationale, epidemiological relevance and research applications, Infect. Genet. Evol., 12, 240, 10.1016/j.meegid.2011.12.009