P. Anderson, A. Cunningham, N. Patel, F. Morales, P. Epstein et al., Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers, Trends in Ecology & Evolution, vol.19, issue.10, pp.535-579, 2004.
DOI : 10.1016/j.tree.2004.07.021

R. Jones, Plant virus emergence and evolution: Origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control, Virus Research, vol.141, issue.2, pp.113-143, 2009.
DOI : 10.1016/j.virusres.2008.07.028

C. Malmstrom, U. Melcher, and N. Bosque-pérez, The expanding field of plant virus ecology: Historical foundations, knowledge gaps, and research directions, Virus Research, vol.159, issue.2, pp.84-94, 2011.
DOI : 10.1016/j.virusres.2011.05.010

C. Fauquet and D. Fargette, African Cassava Mosaic Virus: Etiology, Epidemiology, and Control, Plant Disease, vol.74, issue.6, pp.404-415, 1990.
DOI : 10.1094/PD-74-0404

P. Aerni, Mobilizing science and technology for development: the case of the cassava biotechnology network (CBN), AgBioforum, vol.9, pp.1-14, 2006.

J. Stanley and M. Gay, Nucleotide sequence of cassava latent virus DNA, Nature, vol.9, issue.5897, pp.260-262, 1983.
DOI : 10.1038/301260a0

K. Bock and R. Woods, Etiology of African Cassava Mosaic Disease, Plant Disease, vol.67, issue.9, pp.994-999, 1983.
DOI : 10.1094/PD-67-994

M. Swanson and B. Harrison, Properties, relationships and distribution of cassava mosaic geminiviruses, Trop Sci, vol.34, pp.15-25, 1994.

V. Fondong, J. Pita, C. Rey, R. Beachy, and C. Fauquet, First Report of the Presence of East African Cassava Mosaic Virus in Cameroon, Plant Disease, vol.82, issue.10, p.1172, 1998.
DOI : 10.1094/PDIS.1998.82.10.1172B

X. Zhou, D. Robinson, and B. Harrison, Types of variation in DNA-A among isolates of East African cassava mosaic virus from Kenya, Malawi and Tanzania., Journal of General Virology, vol.79, issue.11, pp.2835-2875, 1998.
DOI : 10.1099/0022-1317-79-11-2835

M. Maruthi, S. Seal, J. Colvin, R. Briddon, and S. Bull, East African cassava mosaic Zanzibar virus ? a recombinant begomovirus species with a mild phenotype, Archives of Virology, vol.149, issue.12, pp.2365-77, 2004.
DOI : 10.1007/s00705-004-0380-1

L. Berrie, K. Palmer, E. Rybicki, and M. Rey, Molecular characterisation of a distinct South African cassava infecting geminivirus, Archives of Virology, vol.143, issue.11, pp.2253-60, 1998.
DOI : 10.1007/s007050050457

S. Bull, R. Briddon, W. Sserubombwe, K. Ngugi, P. Markham et al., Genetic diversity and phylogeography of cassava mosaic viruses in Kenya, Journal of General Virology, vol.87, issue.10, pp.3053-65, 2006.
DOI : 10.1099/vir.0.82013-0

F. Tiendrébéogo, P. Lefeuvre, M. Hoareau, M. Harimalala, D. Bruyn et al., Evolution of African cassava mosaic virus by recombination between bipartite and monopartite begomoviruses, Virology Journal, vol.9, issue.1, p.67, 2012.
DOI : 10.1093/nar/gki352

M. Harimalala, P. Lefeuvre, D. Bruyn, A. Tiendrébéogo, F. Hoareau et al., A novel cassava-infecting begomovirus from Madagascar: cassava mosaic Madagascar virus, Archives of Virology, vol.2, issue.10, pp.2027-2057, 2012.
DOI : 10.1111/j.1744-7348.2002.tb00187.x

D. Barro, P. Liu, S. Boykin, L. Dinsdale, and A. , : A Statement of Species Status, Annual Review of Entomology, vol.56, issue.1, pp.1-19, 2011.
DOI : 10.1146/annurev-ento-112408-085504

O. Ariyo, M. Koerbler, A. Dixon, G. Atiri, and S. Winter, Molecular Variability and Distribution of Cassava Mosaic Begomoviruses in Nigeria, Journal of Phytopathology, vol.78, issue.4, pp.226-257, 2005.
DOI : 10.1099/0022-1317-78-8-2101

V. Fondong, J. Pita, M. Rey, A. De-kochko, R. Beachy et al., Evidence of synergism between African cassava mosaic virus and a new double-recombinant geminivirus infecting cassava in Cameroon, Journal of General Virology, vol.79, issue.1, pp.287-97, 2000.
DOI : 10.1099/0022-1317-79-11-2835

J. Pita, V. Fondong, A. Sangaré, R. Kokora, and C. Fauquet, Genomic and biological diversity of the African cassava geminiviruses, Euphytica, vol.120, issue.1, pp.115-140, 2001.
DOI : 10.1023/A:1017536512488

J. Pita, V. Fondong, A. Sangaré, G. Otim-nape, S. Ogwal et al., Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda, Journal of General Virology, vol.78, issue.3, pp.655-65, 2001.
DOI : 10.1099/0022-1317-78-8-2101

J. Busogoro, L. Masquellier, J. Kummert, O. Dutrecq, P. Lepoivre et al., Application of a Simplified Molecular Protocol to Reveal Mixed Infections with Begomoviruses in Cassava, Journal of Phytopathology, vol.79, issue.7-8, pp.452-459, 2008.
DOI : 10.1099/0022-1317-79-11-2835

M. Harimalala, F. Chiroleu, C. Giraud-carrier, M. Hoareau, I. Zinga et al., Molecular epidemiology of cassava mosaic disease in Madagascar, Plant Pathology, vol.78, issue.3
DOI : 10.1099/0022-1317-78-8-2101

URL : https://hal.archives-ouvertes.fr/hal-01456714

P. Lefeuvre, J. Lett, A. Varsani, and D. Martin, Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses, Journal of Virology, vol.83, issue.6, pp.2697-707, 2009.
DOI : 10.1128/JVI.02152-08

URL : http://jvi.asm.org/content/83/6/2697.full.pdf

M. Padidam, S. Sawyer, and C. Fauquet, Possible Emergence of New Geminiviruses by Frequent Recombination, Virology, vol.265, issue.2, pp.218-243, 1999.
DOI : 10.1006/viro.1999.0056

URL : https://doi.org/10.1006/viro.1999.0056

S. Bull, R. Briddon, W. Sserubombwe, K. Ngugi, P. Markham et al., Infectivity, pseudorecombination and mutagenesis of Kenyan cassava mosaic begomoviruses, Journal of General Virology, vol.88, issue.5, pp.1624-1657, 2007.
DOI : 10.1099/vir.0.82662-0

URL : http://jgv.microbiologyresearch.org/deliver/fulltext/jgv/88/5/1624.pdf?itemId=/content/journal/jgv/10.1099/vir.0.82662-0&mimeType=pdf&isFastTrackArticle=

X. Zhou, Y. Liu, L. Calvert, C. Munoz, G. Otim-nape et al., Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination., Journal of General Virology, vol.78, issue.8, pp.2101-2112, 1997.
DOI : 10.1099/0022-1317-78-8-2101

J. Legg, R. French, D. Rogan, G. Okao-okuja, and J. Brown, A distinct Bemisia tabaci (Gennadius) (Hemiptera: Sternorrhyncha: Aleyrodidae) genotype cluster is associated with the epidemic of severe cassava mosaic virus disease in Uganda, Molecular Ecology, vol.78, issue.7, pp.1219-1248, 2002.
DOI : 10.1099/0022-1317-78-8-2101

J. Colvin, C. Omongo, M. Maruthi, G. Otim-nape, and J. Thresh, Dual begomovirus infections and high Bemisia tabaci populations: two factors driving the spread of a cassava mosaic disease pandemic, Plant Pathology, vol.78, issue.5, pp.577-84, 2004.
DOI : 10.1099/0022-1317-78-8-2101

S. Duffy and E. Holmes, Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses, Journal of General Virology, vol.79, issue.11, pp.1539-1586, 2009.
DOI : 10.1099/0022-1317-79-11-2835

J. Legg and C. Fauquet, Cassava mosaic geminiviruses in Africa, Plant Molecular Biology, vol.79, issue.4, pp.585-99, 2004.
DOI : 10.1099/0022-1317-79-11-2835

B. Patil and C. Fauquet, Cassava mosaic geminiviruses: actual knowledge and perspectives, Molecular Plant Pathology, vol.2, issue.5, pp.685-701, 2009.
DOI : 10.1099/0022-1317-78-8-2101

A. De-bruyn, J. Villemot, P. Lefeuvre, E. Villar, M. Hoareau et al., East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus, BMC Evolutionary Biology, vol.12, issue.1, p.228, 2012.
DOI : 10.1093/oxfordjournals.molbev.a003872

URL : https://hal.archives-ouvertes.fr/hal-01456744

J. Ndunguru, J. Legg, T. Aveling, G. Thompson, and C. Fauquet, Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses, Virology Journal, vol.2, issue.1, p.21, 2005.
DOI : 10.1186/1743-422X-2-21

G. Cours, D. Fargette, G. Otim-nape, and J. Thresh, The epidemic of cassava mosaic virus disease in Madagascar in the 1930s-1940s: lessons for the current situation in Uganda, Trop Sci, vol.37, pp.238-286, 1997.

S. Ranomenjanahary, R. Rabindran, and D. Robinson, Occurrence of three distinct begomoviruses in cassava in Madagascar, Annals of Applied Biology, vol.78, issue.3, pp.315-323, 2002.
DOI : 10.1099/0022-1317-78-8-2101

J. Brown, F. Zerbini, J. Navas-castillo, E. Moriones, R. Ramos-sobrinho et al., Revision of Begomovirus taxonomy based on pairwise sequence comparisons, Archives of Virology, vol.153, issue.6, pp.1593-619, 2015.
DOI : 10.1007/s00705-008-0037-6

R. Briddon, B. Patil, B. Bagewadi, M. Nawaz-ul-rehman, and C. Fauquet, Distinct evolutionary histories of the DNA-A and DNA-B components of bipartite begomoviruses, BMC Evolutionary Biology, vol.10, issue.1, p.97, 2010.
DOI : 10.1186/1471-2148-10-97

P. Lefeuvre, D. Martin, M. Hoareau, F. Naze, H. Delatte et al., Begomovirus 'melting pot' in the south-west Indian Ocean islands: molecular diversity and evolution through recombination, Journal of General Virology, vol.88, issue.12, pp.3458-68, 2007.
DOI : 10.1099/vir.0.83252-0

D. Martin, E. Van-der-walt, D. Posada, and E. Rybicki, The Evolutionary Value of Recombination Is Constrained by Genome Modularity, PLoS Genetics, vol.16, issue.4, p.51, 2005.
DOI : 1367-4803(2000)016[0573:SAMCPF]2.0.CO;2

F. Escriu, A. Fraile, and F. Garcia-arenal, Constraints to Genetic Exchange Support Gene Coadaptation in a Tripartite RNA Virus, PLoS Pathogens, vol.29, issue.1, p.8, 2007.
DOI : 10.1371/journal.ppat.0030008.st004

A. Galli, M. Kearney, O. Nikolaitchik, S. Yu, M. Chin et al., Patterns of Human Immunodeficiency Virus Type 1 Recombination Ex Vivo Provide Evidence for Coadaptation of Distant Sites, Resulting in Purifying Selection for Intersubtype Recombinants during Replication, Journal of Virology, vol.84, issue.15, pp.7651-61, 2010.
DOI : 10.1128/JVI.00276-10

R. Kawuki, L. Herselman, M. Labuschagne, I. Nzuki, I. Ralimanana et al., Genetic diversity of cassava (Manihot esculenta Crantz) landraces and cultivars from southern, eastern and central Africa, Plant Genetic Resources, vol.34, issue.02, pp.170-81, 2013.
DOI : 10.1016/j.fcr.2011.03.006

D. Shepherd, D. Martin, P. Lefeuvre, A. Monjane, B. Owor et al., A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue, Journal of Virological Methods, vol.149, issue.1, pp.97-102, 2008.
DOI : 10.1016/j.jviromet.2007.12.014

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1799, 2004.
DOI : 10.1093/nar/gkh340

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei et al., MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, vol.141, issue.3, pp.2731-2740, 2011.
DOI : 10.1007/BF00160154

B. Muhire, A. Varsani, and D. Martin, SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation, PLoS ONE, vol.88, issue.(95), p.108277, 2014.
DOI : 10.1371/journal.pone.0108277.s002

M. Price, P. Dehal, and A. Arkin, FastTree 2 ??? Approximately Maximum-Likelihood Trees for Large Alignments, PLoS ONE, vol.5, issue.3, p.9490, 2010.
DOI : 10.1371/journal.pone.0009490.s003

URL : http://doi.org/10.1371/journal.pone.0009490

D. Martin and E. Rybicki, RDP: detection of recombination amongst aligned sequences, Bioinformatics, vol.16, issue.6, pp.562-565, 2000.
DOI : 10.1093/bioinformatics/16.6.562

URL : https://academic.oup.com/bioinformatics/article-pdf/16/6/562/427497/160562.pdf

D. Martin, C. Williamson, and D. Posada, RDP2: recombination detection and analysis from sequence alignments, Bioinformatics, vol.17, issue.10, pp.260-262, 2005.
DOI : 10.1093/oxfordjournals.molbev.a026256

URL : https://academic.oup.com/bioinformatics/article-pdf/21/2/260/458930/bth490.pdf

J. Smith, Analyzing the mosaic structure of genes, Journal of Molecular Evolution, vol.34, issue.2, pp.126-135, 1992.
DOI : 10.1007/BF00182389

M. Gibbs, J. Armstrong, and A. Gibbs, Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences, Bioinformatics, vol.16, issue.7, pp.573-82, 2000.
DOI : 10.1093/bioinformatics/16.7.573

URL : https://academic.oup.com/bioinformatics/article-pdf/16/7/573/614523/160573.pdf

M. Boni, D. Posada, and M. Feldman, An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets, Genetics, vol.176, issue.2, pp.1035-1082, 2007.
DOI : 10.1534/genetics.106.068874

URL : http://www.genetics.org/content/genetics/176/2/1035.full.pdf

D. Martin, B. Murrell, M. Golden, A. Khoosal, and B. Muhire, RDP4: Detection and analysis of recombination patterns in virus genomes, Virus Evolution, vol.454, issue.455, p.3, 2015.
DOI : 10.1016/j.virol.2014.01.029

URL : https://academic.oup.com/ve/article-pdf/1/1/vev003/10241357/vev003.pdf

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

T. Jombart, S. Devillard, A. Dufour, and D. Pontier, Revealing cryptic spatial patterns in genetic variability by a new multivariate method, Heredity, vol.28, issue.1, pp.92-103, 2008.
DOI : 10.1007/BF01031609

URL : https://hal.archives-ouvertes.fr/hal-00428188

R. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing

P. Lachenbruch and M. Goldstein, Discriminant Analysis, Biometrics, vol.35, issue.1, pp.69-85, 1979.
DOI : 10.2307/2529937

A. Drummond, M. Suchard, D. Xie, and A. Rambaut, Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, vol.188, issue.9, pp.1969-73, 2012.
DOI : 10.1080/10635150390238879

URL : https://academic.oup.com/mbe/article-pdf/29/8/1969/13648091/mss075.pdf

G. Baele, P. Lemey, T. Bedford, A. Rambaut, M. Suchard et al., Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty, Molecular Biology and Evolution, vol.391, issue.9, pp.2157-67, 2012.
DOI : 10.1038/35400

URL : https://academic.oup.com/mbe/article-pdf/29/9/2157/13647202/mss084.pdf

P. Lemey, A. Rambaut, A. Drummond, and M. Suchard, Bayesian Phylogeography Finds Its Roots, PLoS Computational Biology, vol.90, issue.9, p.1000520, 2009.
DOI : 10.1371/journal.pcbi.1000520.s002

URL : https://doi.org/10.1371/journal.pcbi.1000520

M. Newton and A. Raftery, Approximate Bayesian Inference with the Weighted Likelihood Bootstrap, J R Stat Soc B, vol.56, pp.3-48, 1994.

C. Firth, A. Kitchen, B. Shapiro, M. Suchard, E. Holmes et al., Using Time-Structured Data to Estimate Evolutionary Rates of Double-Stranded DNA Viruses, Molecular Biology and Evolution, vol.9, issue.2, pp.2038-51, 2010.
DOI : 10.1016/j.micinf.2006.11.008

URL : https://academic.oup.com/mbe/article-pdf/27/9/2038/13642808/msq088.pdf