M. Mackinnon and K. Marsh, The Selection Landscape of Malaria Parasites, Science, vol.328, issue.5980, pp.866-871, 2010.
DOI : 10.1126/science.1185410

L. Van-valen, Molecular evolution as predicted by natural selection, Journal of Molecular Evolution, vol.28, issue.2, pp.89-101, 1974.
DOI : 10.1007/BF01796554

N. Jemmely, M. Niang, and P. Preiser, evasion of immunity, Future Microbiology, vol.5, issue.4, pp.663-682, 2010.
DOI : 10.2217/fmb.10.21

G. Mitta, C. Adema, B. Gourbal, E. Loker, and T. A. , Compatibility polymorphism in snail/schistosome interactions: From field to theory to molecular mechanisms, Developmental & Comparative Immunology, vol.37, issue.1, pp.1-8, 2012.
DOI : 10.1016/j.dci.2011.09.002
URL : https://hal.archives-ouvertes.fr/halsde-00631055

A. Theron and C. Coustau, Are <I>Biomphalaria</I> snails resistant to <I>Schistosoma mansoni</I>?, Journal of Helminthology, vol.79, issue.3, pp.187-191, 2005.
DOI : 10.1079/JOH2005299

J. Morgan, R. Dejong, G. Adeoye, E. Ansa, and C. Barbosa, Origin and diversification of the human parasite Schistosoma mansoni, Molecular Ecology, vol.11, issue.12, pp.3889-3902, 2005.
DOI : 10.1111/j.1365-294X.2005.02709.x
URL : https://hal.archives-ouvertes.fr/hal-01495237

E. Roger, G. Mitta, Y. Mone, A. Bouchut, and A. Rognon, Molecular determinants of compatibility polymorphism in the Biomphalaria glabrata/Schistosoma mansoni model: New candidates identified by a global comparative proteomics approach, Molecular and Biochemical Parasitology, vol.157, issue.2, pp.205-216, 2008.
DOI : 10.1016/j.molbiopara.2007.11.003
URL : https://hal.archives-ouvertes.fr/halsde-00286494

E. Roger, C. Grunau, R. Pierce, H. Hirai, and B. Gourbal, Controlled Chaos of Polymorphic Mucins in a Metazoan Parasite (Schistosoma mansoni) Interacting with Its Invertebrate Host (Biomphalaria glabrata), PLoS Neglected Tropical Diseases, vol.20, issue.23, p.330, 2008.
DOI : 10.1371/journal.pntd.0000330.s002
URL : https://hal.archives-ouvertes.fr/halsde-00344615

Y. Mone, B. Gourbal, D. Duval, D. Pasquier, L. Kieffer-jaquinod et al., A Large Repertoire of Parasite Epitopes Matched by a Large Repertoire of Host Immune Receptors in an Invertebrate Host/Parasite Model, PLoS Neglected Tropical Diseases, vol.462, issue.Pt 3, p.813, 2010.
DOI : 10.1371/journal.pntd.0000813.t004
URL : https://hal.archives-ouvertes.fr/halsde-00515823

C. Adema, L. Hertel, R. Miller, and E. Loker, A family of fibrinogen-related proteins that precipitates parasite-derived molecules is produced by an invertebrate after infection, Proceedings of the National Academy of Sciences, vol.94, issue.16, pp.8691-8696, 1997.
DOI : 10.1073/pnas.94.16.8691

P. Hanington, M. Forys, J. Dragoo, S. Zhang, and C. Adema, Role for a somatically diversified lectin in resistance of an invertebrate to parasite infection, Proceedings of the National Academy of Sciences, vol.107, issue.49, pp.21087-21092, 2010.
DOI : 10.1073/pnas.1011242107

S. Zhang, Y. Zeng, and E. Loker, Expression profiling and binding properties of fibrinogen-related proteins (FREPs), plasma proteins from the schistosome snail host Biomphalaria glabrata, Innate Immunity, vol.14, issue.3, pp.175-189, 2008.
DOI : 10.1177/1753425908093800

C. Cosseau, H. Azzi, A. Rognon, J. Boissier, and S. Gourbière, Epigenetic and phenotypic variability in populations of Schistosoma mansoni- a possible kick-off for adaptive host/parasite evolution, Oikos, vol.17, issue.4, pp.669-678, 2010.
DOI : 10.1111/j.1600-0706.2009.18040.x

D. Umlauf, P. Fraser, and T. Nagano, The role of long non-coding RNAs in chromatin structure and gene regulation: variations on a theme, Biological Chemistry, vol.389, issue.4, pp.323-331, 2008.
DOI : 10.1515/BC.2008.047

N. Dillon, The Impact of Gene Location in the Nucleus on Transcriptional Regulation, Developmental Cell, vol.15, issue.2, pp.182-186, 2008.
DOI : 10.1016/j.devcel.2008.07.013

J. Lee, E. Smith, and A. Shilatifard, The Language of Histone Crosstalk, Cell, vol.142, issue.5, pp.682-685, 2010.
DOI : 10.1016/j.cell.2010.08.011

C. Pal and I. Miklos, Epigenetic Inheritance, Genetic Assimilation and Speciation, Journal of Theoretical Biology, vol.200, issue.1, pp.19-37, 1999.
DOI : 10.1006/jtbi.1999.0974

A. Cortes, V. Crowley, A. Vaquero, and T. Voss, A View on the Role of Epigenetics in the Biology of Malaria Parasites, PLoS Pathogens, vol.24, issue.12, p.1002943, 2012.
DOI : 10.1371/journal.ppat.1002943.g002

M. Salminen, J. Carr, D. Burke, and F. Mccutchan, Identification of Breakpoints in Intergenotypic Recombinants of HIV Type 1 by Bootscanning, AIDS Research and Human Retroviruses, vol.11, issue.11, pp.1423-1425, 1995.
DOI : 10.1089/aid.1995.11.1423

D. Martin, P. Lemey, M. Lott, V. Moulton, and D. Posada, RDP3: a flexible and fast computer program for analyzing recombination, Bioinformatics, vol.26, issue.19, pp.2462-2463, 2010.
DOI : 10.1093/bioinformatics/btq467

J. Smith, Analyzing the mosaic structure of genes, Journal of Molecular Evolution, vol.34, issue.2, pp.126-129, 1992.
DOI : 10.1007/BF00182389

D. Posada and K. Crandall, Evaluation of methods for detecting recombination from DNA sequences: Computer simulations, Proceedings of the National Academy of Sciences, vol.98, issue.24, pp.13757-13762, 2001.
DOI : 10.1073/pnas.241370698

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.573-582, 2000.
DOI : 10.1093/bioinformatics/16.7.573

D. Mendonca, R. Bouton, D. Bertin, B. Escriva, H. Noel et al., A functionally conserved member of the FTZ-F1 nuclear receptor family from Schistosoma mansoni, European Journal of Biochemistry, vol.14, issue.22, pp.5700-5711, 2002.
DOI : 10.1046/j.1432-1033.2002.03287.x

N. Bech, S. Beltran, J. Portela, A. Rognon, and J. Allienne, Follow-up of the genetic diversity and snail infectivity of a Schistosoma mansoni strain from field to laboratory, Infection, Genetics and Evolution, vol.10, issue.7, pp.1039-1045, 2010.
DOI : 10.1016/j.meegid.2010.06.012
URL : https://hal.archives-ouvertes.fr/halsde-00514796

F. Dubois, S. Caby, F. Oger, C. Cosseau, and M. Capron, Histone deacetylase inhibitors induce apoptosis, histone hyperacetylation and up-regulation of gene transcription in Schistosoma mansoni, Molecular and Biochemical Parasitology, vol.168, issue.1, pp.7-15, 2009.
DOI : 10.1016/j.molbiopara.2009.06.001
URL : https://hal.archives-ouvertes.fr/halsde-00459184

A. Azzi, C. Cosseau, and C. Grunau, Schistosoma mansoni: Developmental arrest of miracidia treated with histone deacetylase inhibitors, Experimental Parasitology, vol.121, issue.3, pp.288-291, 2009.
DOI : 10.1016/j.exppara.2008.11.010
URL : https://hal.archives-ouvertes.fr/halsde-00371695

K. Geyer, R. Lopez, C. Chalmers, I. Munshi, S. Truscott et al., Cytosine methylation regulates oviposition in the pathogenic blood fluke Schistosoma mansoni, Nature Communications, vol.142, p.424, 2011.
DOI : 10.1590/S0074-02761998000700060

G. Raddatz, P. Guzzardo, N. Olova, M. Fantappie, and M. Rampp, Dnmt2-dependent methylomes lack defined DNA methylation patterns, Proceedings of the National Academy of Sciences, vol.110, issue.21, pp.8627-8631, 2013.
DOI : 10.1073/pnas.1306723110

E. Jablonka and M. Lamb, Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life, 2005.

O. Bossdorf, C. Richards, and M. Pigliucci, Epigenetics for ecologists, Ecology Letters, vol.5, issue.0, pp.106-115, 2008.
DOI : 10.1038/ng1929

E. Danchin, A. Charmantier, F. Champagne, A. Mesoudi, and B. Pujol, Beyond DNA: integrating inclusive inheritance into an extended theory of evolution, Nature Reviews Genetics, vol.439, issue.7, pp.475-486, 2011.
DOI : 10.1038/nrg3028

E. Jablonka, M. Lamb, and E. Avital, ???Lamarckian??? mechanisms in darwinian evolution, Trends in Ecology & Evolution, vol.13, issue.5, pp.206-210, 1998.
DOI : 10.1016/S0169-5347(98)01344-5

M. Pigliucci, C. Murren, and C. Schlichting, Phenotypic plasticity and evolution by genetic assimilation, Journal of Experimental Biology, vol.209, issue.12, pp.2362-2367, 2006.
DOI : 10.1242/jeb.02070

M. Luijsterburg, M. White, R. Van-driel, and R. Dame, The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes, Critical Reviews in Biochemistry and Molecular Biology, vol.178, issue.10, pp.393-418, 2008.
DOI : 10.1126/science.1063127

R. Rapp and J. Wendel, Epigenetics and plant evolution, New Phytologist, vol.78, issue.1, pp.81-91, 2005.
DOI : 10.1111/j.1469-8137.2005.01491.x

R. Grant-downton and H. Dickinson, Epigenetics and its Implications for Plant Biology 2. The 'Epigenetic Epiphany': Epigenetics, Evolution and Beyond, Annals of Botany, vol.97, issue.1, pp.11-27, 2006.
DOI : 10.1093/aob/mcj001

E. Richards, Inherited epigenetic variation ??? revisiting soft inheritance, Nature Reviews Genetics, vol.17, issue.5, pp.395-401, 2006.
DOI : 10.1038/nrg1834

O. Bossdorf and Y. Zhang, A truly ecological epigenetics study, Molecular Ecology, vol.87, issue.8, pp.1572-1574, 2011.
DOI : 10.1111/j.1365-294X.2011.05044.x

A. Boyko and I. Kovalchuk, Epigenetic control of plant stress response, Environmental and Molecular Mutagenesis, vol.15, issue.1, pp.61-72, 2008.
DOI : 10.1002/em.20347

E. Jablonka and G. Raz, Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution, The Quarterly Review of Biology, vol.84, issue.2, pp.131-176, 2009.
DOI : 10.1086/598822

E. Gomez-diaz, M. Jorda, M. Peinado, and A. Rivero, Epigenetics of Host???Pathogen Interactions: The Road Ahead and the Road Behind, PLoS Pathogens, vol.5, issue.1666, p.1003007, 2012.
DOI : 10.1371/journal.ppat.1003007.s003

K. Verhoeven, V. Dijk, P. Biere, and A. , Changes in genomic methylation patterns during the formation of triploid asexual dandelion lineages, Molecular Ecology, vol.39, issue.2, pp.315-324, 2010.
DOI : 10.1111/j.1365-294X.2009.04460.x

S. Uchida, K. Hara, A. Kobayashi, K. Otsuki, and H. Yamagata, Epigenetic Status of Gdnf in the Ventral Striatum Determines Susceptibility and Adaptation to Daily Stressful Events, Neuron, vol.69, issue.2, pp.359-372, 2011.
DOI : 10.1016/j.neuron.2010.12.023

V. Crowley, N. Rovira-graells, R. De-pouplana, L. Cortes, and A. , Heterochromatin formation in bistable chromatin domains controls the epigenetic repression of clonally variant Plasmodium falciparum genes linked to erythrocyte invasion, Molecular Microbiology, vol.439, issue.2, pp.391-406, 2011.
DOI : 10.1111/j.1365-2958.2011.07574.x

L. Kulakova, S. Singer, J. Conrad, and T. Nash, Epigenetic mechanisms are involved in the control of Giardia lamblia antigenic variation, Molecular Microbiology, vol.22, issue.6, pp.1533-1542, 2006.
DOI : 10.1074/jbc.275.15.11432

C. Prucca, I. Slavin, R. Quiroga, E. Elias, and F. Rivero, Antigenic variation in Giardia lamblia is regulated by RNA interference, Nature, vol.92, issue.7223, pp.750-754, 2008.
DOI : 10.1038/nature07585

G. Rudenko, African trypanosomes: the genome and adaptations for immune evasion, Essays In Biochemistry, vol.51, pp.47-62, 2011.
DOI : 10.1042/bse0510047

O. Osipovich and E. Oltz, Regulation of antigen receptor gene assembly by genetic???epigenetic crosstalk, Seminars in Immunology, vol.22, issue.6, pp.313-322, 2010.
DOI : 10.1016/j.smim.2010.07.001

Y. Bergman and H. Cedar, Epigenetic control of recombination in the immune system, Seminars in Immunology, vol.22, issue.6, pp.323-329, 2010.
DOI : 10.1016/j.smim.2010.07.003

S. Ohno, U. Wolf, and N. Atkin, EVOLUTION FROM FISH TO MAMMALS BY GENE DUPLICATION, Hereditas, vol.21, issue.Suppl. 1, pp.169-187, 1968.
DOI : 10.1111/j.1601-5223.1968.tb02169.x

S. Rodin, D. Parkhomchuk, and A. Riggs, Epigenetic Changes and Repositioning Determine the Evolutionary Fate of Duplicated Genes, Biochemistry (Moscow), vol.15, issue.5, pp.559-567, 2005.
DOI : 10.1007/s10541-005-0149-5

A. Theron, J. Pages, and A. Rognon, Schistosoma mansoni:Distribution Patterns of Miracidia amongBiomphalaria glabrataSnail as Related to Host Susceptibility and Sporocyst Regulatory Processes, Experimental Parasitology, vol.85, issue.1, pp.1-9, 1997.
DOI : 10.1006/expr.1996.4106

J. Portela, C. Grunau, C. Cosseau, S. Beltran, and C. Dantec, Whole-genome in-silico subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni, BMC Genomics, vol.11, issue.1, p.387, 2010.
DOI : 10.1111/j.1365-294X.2008.03888.x
URL : https://hal.archives-ouvertes.fr/halsde-00495369

E. Roger, B. Gourbal, C. Grunau, R. Pierce, and R. Galinier, Expression analysis of highly polymorphic mucin proteins (Sm PoMuc) from the parasite Schistosoma mansoni, Molecular and Biochemical Parasitology, vol.157, issue.2, pp.217-227, 2008.
DOI : 10.1016/j.molbiopara.2007.11.015
URL : https://hal.archives-ouvertes.fr/halsde-00286479

M. Reese, Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome, Computers & Chemistry, vol.26, issue.1, pp.51-56, 2001.
DOI : 10.1016/S0097-8485(01)00099-7

O. Kohany, A. Gentles, L. Hankus, and J. Jurka, Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor, BMC Bioinformatics, vol.7, issue.1, p.474, 2006.
DOI : 10.1186/1471-2105-7-474

J. Rozas, J. Sanchez-delbarrio, X. Messeguer, and R. Rozas, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, vol.19, issue.18, pp.2496-2497, 2003.
DOI : 10.1093/bioinformatics/btg359

F. Ronquist, M. Teslenko, P. Van-der-mark, D. Ayres, and A. Darling, MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, vol.61, issue.3, pp.539-542, 2012.
DOI : 10.1093/sysbio/sys029

J. Huelsenbeck, B. Larget, and M. Alfaro, Bayesian Phylogenetic Model Selection Using Reversible Jump Markov Chain Monte Carlo, Molecular Biology and Evolution, vol.21, issue.6, pp.1123-1133, 2004.
DOI : 10.1093/molbev/msh123

. Nei, Molecular Evolutionary Genetics, 1987.

C. Cockerham and B. Weir, Covariances of Relatives Stemming from a Population Undergoing Mixed Self and Random Mating, Biometrics, vol.40, issue.1, pp.157-164, 1984.
DOI : 10.2307/2530754

K. Belkhir, K. Dawson, and F. Bonhomme, A Comparison of Rarefaction and Bayesian Methods for Predicting the Allelic Richness of Future Samples on the Basis of Currently Available Samples, Journal of Heredity, vol.97, issue.5, pp.483-492, 2006.
DOI : 10.1093/jhered/esl030
URL : https://hal.archives-ouvertes.fr/halsde-00339548

F. Rousset, Equilibrium values of measures of population subdivision for stepwise mutation processes, Genetics, vol.142, issue.4, pp.1357-1362, 1996.

M. Slatkin, A measure of population subdivision based on microsatellite allele frequencies, Genetics, vol.139, issue.1, pp.457-462, 1995.

C. Cosseau, A. Azzi, K. Smith, M. Freitag, and G. Mitta, Native chromatin immunoprecipitation (N-ChIP) and ChIP-Seq of Schistosoma mansoni: Critical experimental parameters, Molecular and Biochemical Parasitology, vol.166, issue.1, pp.70-76, 2009.
DOI : 10.1016/j.molbiopara.2009.02.015
URL : https://hal.archives-ouvertes.fr/halsde-00459175

C. Grunau, S. Clark, and A. Rosenthal, Bisulfite genomic sequencing: systematic investigation of critical experimental parameters, Nucleic Acids Research, vol.29, issue.13, pp.65-65, 2001.
DOI : 10.1093/nar/29.13.e65