E. Koonin, A. Mushegian, and P. Bork, Non-orthologous gene displacement Trends in genetics : TIG 1996, pp.334-336

J. Foster, P. Davis, S. Raverdy, M. Sibley, E. Raleigh et al., Evolution of Bacterial Phosphoglycerate Mutases: Non-Homologous Isofunctional Enzymes Undergoing Gene Losses, Gains and Lateral Transfers, PLoS ONE, vol.5, issue.10, 2010.
DOI : 10.1371/journal.pone.0013576.s006

P. Karp and M. Riley, Representations of metabolic knowledge, Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, pp.207-215, 1993.

E. Koonin, Comparative genomics, minimal gene-sets and the last universal common ancestor, Nature Reviews Microbiology, vol.176, issue.2, pp.127-136, 2003.
DOI : 10.1038/nature01278

L. Akman, A. Yamashita, H. Watanabe, K. Oshima, T. Shiba et al., Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia, Nature Genetics, vol.69, issue.3, pp.402-407, 2002.
DOI : 10.1038/ng986

E. Zientz, T. Dandekar, and R. Gross, Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiology and molecular biology reviews : MMBR, pp.745-770, 2004.

J. Foster, M. Ganatra, I. Kamal, J. Ware, K. Makarova et al., The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode, PLoS Biology, vol.15, issue.1450, 2005.
DOI : 10.1371/journal.pbio.0030121.t003

J. Mccutcheon and N. Moran, Parallel genomic evolution and metabolic interdependence in an ancient symbiosis, Proceedings of the National Academy of Sciences, vol.104, issue.49, pp.19392-19397, 2007.
DOI : 10.1073/pnas.0708855104

P. Baumann, L. Baumann, C. Lai, D. Rouhbakhsh, N. Moran et al., Genetics, physiology, and evolutionary relationships of the genus Buchnera: intracellular symbionts of aphids. Annual review of microbiology, pp.55-94, 1995.

S. Shigenobu, H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa, Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp, Nature, vol.407, issue.6800, pp.81-86, 2000.

R. Gil, F. Silva, E. Zientz, F. Delmotte, F. González-candelas et al., The genome sequence of Blochmannia floridanus: Comparative analysis of reduced genomes, Proceedings of the National Academy of Sciences of the United States of America, pp.1009388-9393, 2003.
DOI : 10.1073/pnas.1533499100

P. Degnan, A. Lazarus, and J. Wernegreen, Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects, Genome Research, vol.15, issue.8, pp.1023-1033, 2005.
DOI : 10.1101/gr.3771305

M. López-sánchez, A. Neef, J. Peretó, P. Navarrete, R. Pignatelli et al., Evolutionary Convergence and Nitrogen Metabolism in Blattabacterium strain Bge, Primary Endosymbiont of the Cockroach Blattella germanica, PLoS Genetics, vol.15, issue.11, p.1000721, 2009.
DOI : 10.1371/journal.pgen.1000721.s005

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

S. Dray and A. Dufour, The ade4 package: implementing the duality diagram for ecologists, Journal of Statistical Software, vol.22, issue.4, pp.1-20, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00434575