D. Ajzenberg, A. L. Bañ-uls, C. Su, A. Dumè-tre, M. Demar et al., Genetic diversity, clonality and sexuality in Toxoplasma gondii, International Journal for Parasitology, vol.34, issue.10, pp.1185-1196, 2004.
DOI : 10.1016/j.ijpara.2004.06.007

D. Ajzenberg, A. L. Banuls, M. Tibayrenc, and M. L. Dardé, Microsatellite analysis of Toxoplasma gondii shows considerable polymorphism structured into two main clonal groups, International Journal for Parasitology, vol.32, issue.1, pp.27-38, 2002.
DOI : 10.1016/S0020-7519(01)00301-0

D. Ajzenberg, F. Collinet, A. Mercier, P. Vignoles, and M. L. Dardé, Isolates with 15 Microsatellite Markers in a Single Multiplex PCR Assay, Journal of Clinical Microbiology, vol.48, issue.12, pp.4641-4645, 2010.
DOI : 10.1128/JCM.01152-10

URL : https://hal.archives-ouvertes.fr/hal-00677196

D. Ajzenberg, H. Yera, P. Marty, L. Paris, F. Dalle et al., Isolates Associated with Toxoplasmosis in Immunocompromised Patients and Correlation with Clinical Findings, The Journal of Infectious Diseases, vol.199, issue.8, pp.1155-1167, 2009.
DOI : 10.1086/597477

URL : https://hal.archives-ouvertes.fr/hal-00374813

T. J. Anderson, B. Haubold, J. T. Williams, J. G. Estrada-franco, L. Richardson et al., Microsatellite Markers Reveal a Spectrum of Population Structures in the Malaria Parasite Plasmodium falciparum, Molecular Biology and Evolution, vol.17, issue.10, pp.1467-1482, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026247

J. J. Aramini, C. Stephen, and J. P. Dubey, Toxoplasma gondii in Vancouver Island Cougars (Felis concolor vancouverensis): Serology and Oocyst Shedding, The Journal of Parasitology, vol.84, issue.2, pp.438-440, 1998.
DOI : 10.2307/3284508

J. C. Boothroyd, Expansion of host range as a driving force in the evolution of Toxoplasma, Mem??rias do Instituto Oswaldo Cruz, vol.104, issue.2, pp.179-184, 2009.
DOI : 10.1590/S0074-02762009000200009

P. Bossi, L. Paris, E. Caumes, C. Katlama, M. Danis et al., Severe acute disseminated toxoplasmosis acquired by an immunocompetent patient in French Guiana. Scand, J. Infect. Dis, vol.34, pp.311-314, 2002.

R. Brosch, S. V. Gordon, M. Marmiesse, P. Brodin, C. Buchrieser et al., A new evolutionary scenario for the Mycobacterium tuberculosis complex, Proc. Natl. Acad. Sci. U. S. A. 99, pp.3684-3689, 2002.

N. Brucato, O. Cassar, L. Tonasso, P. Tortevoye, F. Migot-nabias et al., The imprint of the Slave Trade in an African American population: mitochondrial DNA, Y chromosome and HTLV-1 analysis in the Noir Marron of French Guiana, BMC Evolutionary Biology, vol.10, issue.1, p.314, 2010.
DOI : 10.1186/1471-2148-10-314

URL : https://hal.archives-ouvertes.fr/pasteur-00530132

B. Carme, C. Aznar, A. Motard, M. Demar, and B. De-thoisy, in Noncarnivorous Free-Ranging Neotropical Mammals in French Guiana, Vector-Borne and Zoonotic Diseases, vol.2, issue.1, pp.11-17, 2002.
DOI : 10.1089/153036602760260733

B. Carme, M. Demar, D. Ajzenberg, and M. L. Dardé, , French Guiana, Emerging Infectious Diseases, vol.15, issue.4, pp.656-658, 2009.
DOI : 10.3201/eid1504.081306

L. L. Cavalli-sforza and A. W. Edwards, Phylogenetic Analysis: Models and Estimation Procedures, Evolution, vol.21, issue.3, pp.233-257, 1967.
DOI : 10.2307/2406616

L. Chacin-bonilla, Y. Sanchez-chavez, F. Monsalve, and J. Estevez, Seroepidemiology of toxoplasmosis in amerindians from western Venezuela, Am. J. Trop. Med. Hyg, vol.65, pp.131-135, 2001.

F. S. Chapin-3rd, E. S. Zavaleta, V. T. Eviner, R. L. Naylor, P. M. Vitousek et al., Consequences of changing biodiversity, Nature, vol.405, issue.6783, pp.234-242, 2000.
DOI : 10.1038/35012241

M. L. Dardé, I. Villena, J. M. Pinon, and I. Beguinot, Severe toxoplasmosis caused by a Toxoplasma gondii strain with a new isoenzyme type acquired in French Guyana, J. Clin. Microbiol, vol.36, p.324, 1998.

B. De-thoisy, M. Demar, C. Aznar, and B. Carme, Ecologic Correlates of Toxoplasma gondii Exposure in Free-ranging Neotropical Mammals, Journal of Wildlife Diseases, vol.39, issue.2, pp.456-459, 2003.
DOI : 10.7589/0090-3558-39.2.456

M. Demar, D. Ajzenberg, D. Maubon, F. Djossou, D. Panchoe et al., Fatal Outbreak of Human Toxoplasmosis along the Maroni River: Epidemiological, Clinical, and Parasitological Aspects, Clinical Infectious Diseases, vol.45, issue.7, pp.88-95, 2007.
DOI : 10.1086/521246

URL : https://hal.archives-ouvertes.fr/hal-00349111

M. Demar, D. Ajzenberg, B. Serrurier, M. L. Dardé, and B. Carme, Atypical Toxoplasma gondii strain from a free-living jaguar (Panthera onca) in French Guiana, Am. J. Trop. Med. Hyg, vol.78, pp.195-197, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00337687

G. Desmonts and J. S. Remington, Direct agglutination test for diagnosis of Toxoplasma infection: method for increasing sensitivity and specificity, J. Clin. Microbiol, vol.11, pp.562-568, 1980.

O. Diaz-suarez, J. Estevez, M. Garcia, R. Cheng-ng, J. Araujo et al., Seroepidemiology of toxoplasmosis in a Yucpa Amerindian community of Sierra de Perija, Zulia State, Venezuela. Rev. Med. Chil, vol.131, pp.1003-1010, 2003.

J. P. Dubey, Toxoplasmosis of Animals and Humans, second ed, 2010.

J. P. Dubey, L. Applewhaite, N. Sundar, G. V. Velmurugan, L. A. Bandini et al., Molecular and biological characterization of Toxoplasma gondii isolates from free-range chickens from Guyana, South America, identified several unique and common parasite genotypes, Parasitology, vol.35, issue.11, pp.1559-1565, 2007.
DOI : 10.1016/j.vetpar.2006.03.023

J. P. Dubey, R. Chellaiah, L. Ferreira, O. Kwok, D. Sinnett et al., A New Atypical Highly Mouse Virulent Toxoplasma gondii Genotype Isolated from a Wild Black Bear in Alaska, Journal of Parasitology, vol.96, issue.4, 2010.
DOI : 10.1645/GE-2429.1

J. P. Dubey, L. T. Huong, B. W. Lawson, D. T. Subekti, P. Tassi et al., Seroprevalence and Isolation of Toxoplasma gondii from Free-Range Chickens in Ghana, Indonesia, Italy, Poland, and Vietnam, Journal of Parasitology, vol.94, issue.1, pp.68-71, 2008.
DOI : 10.1645/GE-1362.1

J. P. Dubey, L. T. Huong, N. Sundar, and C. Su, Genetic characterization of Toxoplasma gondii isolates in dogs from Vietnam suggests their South American origin, Veterinary Parasitology, vol.146, issue.3-4, pp.347-351, 2007.
DOI : 10.1016/j.vetpar.2007.03.008

J. P. Dubey, R. P. Rajapakse, R. R. Wijesundera, N. Sundar, G. V. Velmurugan et al., Prevalence of Toxoplasma gondii in dogs from Sri Lanka and genetic characterization of the parasite isolates, Veterinary Parasitology, vol.146, issue.3-4, pp.341-346, 2007.
DOI : 10.1016/j.vetpar.2007.03.009

J. P. Dubey, N. Sundar, S. M. Gennari, A. H. Minervino, N. A. Farias et al., Biologic and genetic comparison of Toxoplasma gondii isolates in free-range chickens from the northern Par?? state and the southern state Rio Grande do Sul, Brazil revealed highly diverse and distinct parasite populations, Veterinary Parasitology, vol.143, issue.2, pp.182-188, 2007.
DOI : 10.1016/j.vetpar.2006.08.024

J. P. Dubey, N. Sundar, C. A. Nolden, M. D. Samuel, G. V. Velmurugan et al., Characterization of Toxoplasma gondii from Raccoons (Procyon lotor), Coyotes (Canis latrans), and Striped Skunks (Mephitis mephitis) in Wisconsin Identified Several Atypical Genotypes, Journal of Parasitology, vol.93, issue.6, pp.1524-1527, 2007.
DOI : 10.1645/GE-1245.1

J. P. Dubey, X. Q. Zhu, N. Sundar, H. Zhang, O. C. Kwok et al., Genetic and biologic characterization of Toxoplasma gondii isolates of cats from China, Veterinary Parasitology, vol.145, issue.3-4, pp.352-356, 2007.
DOI : 10.1016/j.vetpar.2006.12.016

D. W. Duszynski, L. Couch, L. Upton, and S. J. , Coccidia (Eimeriidae) of Canidae and Felidae, 2000.

M. A. El and R. J. Petit, High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic to Morocco, 1996.

G. D. Etheredge, G. Michael, M. P. Muehlenbein, and J. K. Frenkel, The roles of cats and dogs in the transmission of Toxoplasma infection in Kuna and Embera children in eastern Panama, Revista Panamericana de Salud P??blica, vol.16, issue.3, pp.176-186, 2004.
DOI : 10.1590/S1020-49892004000900004

G. Evanno, S. Regnaut, and J. Goudet, Detecting the number of clusters of individuals using the software structure: a simulation study, Molecular Ecology, vol.16, issue.8, pp.2611-2620, 2005.
DOI : 10.1098/rspb.2001.1600

S. Garnier, P. Alibert, P. Audiot, B. Prieur, and J. Y. Rasplus, Isolation by distance and sharp discontinuities in gene frequencies: implications for the phylogeography of an alpine insect species, Carabus solieri, Molecular Ecology, vol.28, issue.7, pp.1883-1897, 2004.
DOI : 10.1111/j.1365-294X.2004.02212.x

J. Goudet, Fstat, A Program to Estimate and Test Gene Diversities and Fixation Indices Version 2, 2002.

M. E. Grigg, J. Ganatra, J. C. Boothroyd, and T. P. Margolis, Unusual Abundance of Atypical Strains Associated with Human Ocular Toxoplasmosis, The Journal of Infectious Diseases, vol.184, issue.5, pp.633-639, 2001.
DOI : 10.1086/322800

D. L. Hartl, The origin of malaria: mixed messages from genetic diversity, Nature Reviews MicroBiology, vol.19, issue.1, pp.15-22, 2004.
DOI : 10.1093/molbev/msg009

S. Holm, A simple sequentially rejective multiple test procedure, Scand. J. Statist, vol.6, pp.65-70, 1979.

D. K. Howe and L. D. Sibley, Toxoplasma gondii Comprises Three Clonal Lineages: Correlation of Parasite Genotype with Human Disease, Journal of Infectious Diseases, vol.172, issue.6, pp.1561-1566, 1995.
DOI : 10.1093/infdis/172.6.1561

M. L. Jewell, J. K. Frenkel, K. M. Johnson, V. Reed, and A. Ruiz, Development of Toxoplasma oocysts in neotropical felidae, Am. J. Trop. Med. Hyg, vol.21, pp.512-517, 1972.

T. Jombart, adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics, vol.24, issue.11, pp.1403-1405, 2008.
DOI : 10.1093/bioinformatics/btn129

URL : https://hal.archives-ouvertes.fr/hal-00428105

T. Jombart, S. Devillard, and F. Balloux, Discriminant analysis of principal components: a new method for the analysis of genetically structured populations, BMC Genetics, vol.11, issue.1, p.94, 2010.
DOI : 10.1186/1471-2156-11-94

URL : https://hal.archives-ouvertes.fr/hal-00539267

N. Keyghobadi, The genetic implications of habitat fragmentation for animals, National Research Council of Canada, 2007.

A. Khan, B. Fux, C. Su, J. P. Dubey, M. L. Dardé et al., Recent transcontinental sweep of Toxoplasma gondii driven by a single monomorphic chromosome, Proceedings of the National Academy of Sciences, vol.104, issue.37, pp.14872-14877, 2007.
DOI : 10.1073/pnas.0702356104

URL : https://hal.archives-ouvertes.fr/hal-00349107

F. T. Ledig, Human Impacts on Genetic Diversity in Forest Ecosystems, Oikos, vol.63, issue.1, 1992.
DOI : 10.2307/3545518

T. Lehmann, D. H. Graham, E. Dahl, C. Sreekumar, F. Launer et al., Transmission dynamics of Toxoplasma gondii on a pig farm, Infection, Genetics and Evolution, vol.3, issue.2, pp.135-141, 2003.
DOI : 10.1016/S1567-1348(03)00067-4

T. Lehmann, P. L. Marcet, D. H. Graham, E. R. Dahl, and J. P. Dubey, Globalization and the population structure of Toxoplasma gondii, Proceedings of the National Academy of Sciences, vol.103, issue.30, pp.11423-11428, 2006.
DOI : 10.1073/pnas.0601438103

D. S. Lindsay and J. P. Dubey, Toxoplasmosis in wild and domestic animals Toxoplasma gondii. The Model Apicomplexan: Perspectives and Methods, pp.133-152, 2007.

I. Lindströ-m-bontell, N. Hall, K. E. Ashelford, J. P. Dubey, J. P. Boyle et al., Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants, Genome Biology, vol.10, issue.5, p.53, 2009.
DOI : 10.1186/gb-2009-10-5-r53

N. Mantel, The detection of disease clustering and a generalized regression approach, Cancer Res, vol.27, pp.209-220, 1967.

A. Mercier, S. Devillard, B. Ngoubangoye, H. Bonnabau, A. L. Banuls et al., Additional Haplogroups of Toxoplasma gondii out of Africa: Population Structure and Mouse-Virulence of Strains from Gabon, PLoS Neglected Tropical Diseases, vol.123, issue.11, p.876, 2010.
DOI : 10.1371/journal.pntd.0000876.s004

URL : https://hal.archives-ouvertes.fr/hal-00539268

N. L. Miller, J. K. Frenkel, and J. P. Dubey, Oral Infections with Toxoplasma Cysts and Oocysts in Felines, Other Mammals, and in Birds, The Journal of Parasitology, vol.58, issue.5, pp.928-937, 1972.
DOI : 10.2307/3286588

M. Nei and R. K. Chesser, Estimation of fixation indices and gene diversities, Annals of Human Genetics, vol.15, issue.3, pp.253-259, 1983.
DOI : 10.1016/0040-5809(77)90014-4

J. Nunura, T. Vasquez, S. Endo, D. Salazar, A. Rodriguez et al., Disseminated toxoplasmosis in an immunocompetent patient from Peruvian Amazon, Revista do Instituto de Medicina Tropical de S??o Paulo, vol.52, issue.2, pp.107-110, 2010.
DOI : 10.1590/S0036-46652010000200008

O. 'brien, S. J. Johnson, W. Driscoll, C. Pontius, J. Pecon-slattery et al., State of cat genomics, Trends Genet, vol.24, pp.268-279, 2008.

H. F. Pena, S. M. Gennari, J. P. Dubey, and C. Su, Population structure and mouse-virulence of Toxoplasma gondii in Brazil, International Journal for Parasitology, vol.38, issue.5, pp.561-569, 2008.
DOI : 10.1016/j.ijpara.2007.09.004

E. Petersen and J. P. Dubey, Biology of Toxoplasma gondii Toxoplasmosis: A Comprehensive Clinical Guide, pp.1-42, 2001.

J. K. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, pp.945-959, 2000.

R. Development and C. Team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2009.

S. M. Rich, F. H. Leendertz, G. Xu, M. Lebreton, C. F. Djoko et al., The origin of malignant malaria, Proc. Natl. Acad. Sci. U. S. A. 106, pp.14902-14907, 2009.
DOI : 10.1073/pnas.0907740106

L. D. Sibley and J. W. Ajioka, : Clonal Expansion Driven by Infrequent Recombination and Selective Sweeps, Annual Review of Microbiology, vol.62, issue.1, pp.329-351, 2008.
DOI : 10.1146/annurev.micro.62.081307.162925

C. Su, D. Evans, R. H. Cole, J. C. Kissinger, J. W. Ajioka et al., Recent Expansion of Toxoplasma Through Enhanced Oral Transmission, Science, vol.299, issue.5605, pp.414-416, 2003.
DOI : 10.1126/science.1078035

K. Tamura, J. Dudley, M. Nei, and S. Kumar, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0, Molecular Biology and Evolution, vol.24, issue.8, pp.1596-1599, 2007.
DOI : 10.1093/molbev/msm092

K. Tanabe, T. Mita, T. Jombart, A. Eriksson, S. Horibe et al., Plasmodium falciparum Accompanied the Human Expansion out of Africa, Current Biology, vol.20, issue.14, pp.1283-1289, 2010.
DOI : 10.1016/j.cub.2010.05.053

A. M. Tenter, A. R. Heckeroth, and L. M. Weiss, Toxoplasma gondii: from animals to humans, International Journal for Parasitology, vol.30, issue.12-13, pp.1217-1258, 2000.
DOI : 10.1016/S0020-7519(00)00124-7

R. S. Waples, Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species, Journal of Heredity, vol.89, issue.5, pp.438-450, 1998.
DOI : 10.1093/jhered/89.5.438

S. Watts, Epidemics and History: Disease, Power and Imperialism, 1997.

S. Wright, THE GENETICAL STRUCTURE OF POPULATIONS, Annals of Eugenics, vol.31, issue.111, pp.323-354, 1951.
DOI : 10.1111/j.1469-1809.1949.tb02451.x

P. Zhou, H. Zhang, R. Q. Lin, D. L. Zhang, H. Q. Song et al., Genetic characterization of Toxoplasma gondii isolates from China, Parasitology International, vol.58, issue.2, pp.193-195, 2009.
DOI : 10.1016/j.parint.2009.01.006