Publications produced by Clonix partners during the project

1.    Barres, B., C. Dutech, A. Andrieux, F. Halkett, and P. Frey (2012) Exploring the role of asexual multiplication in poplar rust epidemics: impact on diversity and genetic structure. Mol Ecol. 21(20): p. 4996-5008.
2.    Masucci, A., S. Arnaud-Haond, V. Eguíluz, E. Hernández-García, and E. Serrão (2012) Genetic flow directionality and geographical segregation in a Cymodocea nodosa genetic diversity network. EPJ Data Science. 1(1): p. 1-11.
3.    Xhaard, C., B. Barres, A. Andrieux, L. Bousset, F. Halkett, and P. Frey (2012) Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Mol Ecol. 21(10): p. 2383-98.
4.    Massa, S.I., C.M. Paulino, E.A. Serrao, C.M. Duarte, and S. Arnaud-Haond (2013) Entangled effects of allelic and clonal (genotypic) richness in the resistance and resilience of experimental populations of the seagrass Zostera noltii to diatom invasion. Bmc Ecology. 13.

5.    Murat, C., A. Rubini, C. Riccioni, H. De la Varga, E. Akroume, B. Belfiori, . . . F. Paolocci (2013) Fine-scale spatial genetic structure of the black truffle (Tuber melanosporum) investigated with neutral microsatellites and functional mating type genes. New Phytol. 199(1): p. 176-87.
6.    Arnaud-Haond, S., Y. Moalic, C. Barnabé, F.J. Ayala, and M. Tibayrenc (2014) Discriminating Micropathogen Lineages and Their Reticulate Evolution through Graph Theory-Based Network Analysis: The Case of <italic>Trypanosoma cruzi</italic>, the Agent of Chagas Disease. PLoS ONE. 9(8): p. e103213.

7.    Arnaud-Haond, S., Y. Moalic, E. Hernandez-Garcia, V.M. Eguiluz, F. Alberto, E.A. Serrao, and C.M. Duarte (2014) Disentangling the Influence of Mutation and Migration in Clonal Seagrasses Using the Genetic Diversity Spectrum for Microsatellites. Journal of Heredity. 105(4): p. 532-541.
8.    Becheler, R., E. Benkara, Y. Moalic, C. Hily, and S. Arnaud-Haond (2014) Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring. Heredity. 112(2): p. 114-121.
9.    Dia, A., L. Guillou, S. Mauger, E. Bigeard, D. Marie, M. Valero, and C. Destombe (2014) Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum. Molecular Ecology. 23(3): p. 549-560.
10.    Stoeckel, S. and J.P. Masson (2014) The exact distributions of F(IS) under partial asexuality in small finite populations with mutation. PLoS One. 9(1): p. e85228.

11.Sere, M., J. Kabore, V. Jamonneau, A. M. G. Belem, F. J. Ayala, and T. De Meeus. 2014. Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes. Parasite Vector 7.

12. Ament-Velasquez, S. L., E. Figuet, M. Ballenghien, E. E. Zattara, J. L. Norenburg, F. A. Fernandez-Alvarez, J. Bierne, N. Bierne, and N. Galtier. 2016. Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect. Mol Ecol 25:3356-3369.
13. Bailleul, D., S. Stoeckel, and S. Arnaud-Haond. 2016. RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r. Methods in Ecology and Evolution 7:966-970.

14. Couceiro, L., M. Le Gac, H. M. Hunsperger, S. Mauger, C. Destombe, J. M. Cock, S. Ahmed, S. M. Coelho, M. Valero, and A. F. Peters. 2015. Evolution and maintenance of haploid-diploid life cycles in natural populations: The case of the marine brown alga Ectocarpus. Evolution 69:1808-1822.

15. De Meeus, T. 2015. Genetic identities and local inbreeding in pure diploid clones with homoplasic markers: SNPs may be misleading. Infect Genet Evol 33:227-232.

16. Gilabert, A., C. A. Dedryver, S. Stoeckel, M. Plantegenest, and J. C. Simon. 2015. Longitudinal clines in the frequency distribution of 'super-clones' in an aphid crop pest. Bull Entomol Res 105:694-703.

17. Kivela, M., S. Arnaud-Haond, and J. Saramaki. 2015. EDENetworks: a user-friendly software to build and analyse networks in biogeography, ecology and population genetics. Mol Ecol Resour 15:117-122.

18. Reichel, K., V. Bahier, C. Midoux, N. Parisey, J. P. Masson, and S. Stoeckel. 2015. Interpretation and approximation tools for big, dense Markov chain transition matrices in population genetics. Algorithms Mol Biol 10:31.

19. Reichel, K., J. P. Masson, F. Malrieu, S. Arnaud-Haond, and S. Stoeckel. 2016. Rare sex or out of reach equilibrium? The dynamics of F IS in partially clonal organisms. BMC Genet 17:76.

20. Rouger, R., K. Reichel, F. Malrieu, J. P. Masson, and S. Stoeckel. 2016. Effects of complex life cycles on genetic diversity: cyclical parthenogenesis. Heredity 117:336-347.

21. Becheler, R., J. P. Masson, S. Arnaud-Haond, F. Halkett, S. Mariette, M. L. Guillemin, M. Valero, C. Destombe, and S. Stoeckel. 2017. ClonEstiMate, a Bayesian method for quantifying rates of clonality of populations genotyped at two-time steps. Mol Ecol Resour 17:e251-e267.