B. Batut, C. Knibbe, G. Marais, and V. Daubin, Reductive genome evolution at both ends of the bacterial population size spectrum, Nature Reviews Microbiology, vol.73, issue.12, pp.841-850, 2014.
DOI : 10.1128/MMBR.00035-08

B. Batut, G. Beslon, and C. Knibbe, Unexpected genome inflation and streamlining in variable environments, Proceedings of Jobim 2016, pp.320-322, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01375653

B. Batut, G. Beslon, and C. Knibbe, Genome inflation under variable environments, 2016.

E. Colizzi and P. Hogeweg, Evolution of Functional Diversification within Quasispecies, Genome Biology and Evolution, vol.6, issue.8, 2014.
DOI : 10.1093/gbe/evu150

F. De-boer and P. Hogeweg, Co-evolution and ecosystem based problem solving, Ecological Informatics, vol.9, pp.47-58, 2012.
DOI : 10.1016/j.ecoinf.2012.03.002

V. Cooper, M. Schneider, R. Blot, and . Lenski, Mechanisms Causing Rapid and Parallel Losses of Ribose Catabolism in Evolving Populations of Escherichia coli B, Journal of Bacteriology, vol.183, issue.9, pp.2834-2841, 2001.
DOI : 10.1128/JB.183.9.2834-2841.2001

A. Crombach and P. Hogeweg, Chromosome Rearrangements and the Evolution of Genome Structuring and Adaptability, Molecular Biology and Evolution, vol.24, issue.5, pp.1130-1139, 2007.
DOI : 10.1093/molbev/msm033

T. Cuypers and P. Hogeweg, Virtual Genomes in Flux: An Interplay of Neutrality and Adaptability Explains Genome Expansion and Streamlining, Genome Biology and Evolution, vol.4, issue.3, pp.212-229, 2012.
DOI : 10.1093/gbe/evr141

F. Fet, Proactive EVLIT program Variability: mechanisms and consequences Project reference: 610427 Version 1

T. Cuypers and P. Hogeweg, A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation, PLoS Computational Biology, vol.1, issue.4, 2014.
DOI : 10.1371/journal.pcbi.1003547.s007

URL : http://doi.org/10.1371/journal.pcbi.1003547

. Td-cuypers, P. Jp-rutten, and . Hogeweg, Mutate or Regulate: evolutionary strategies along a continuum of ecological time scales, 2015.

B. Van, D. , and P. Hogeweg, Multi-level evolution, differential gene mobility, and the persistence of population diversity, Proceedings of the European Conference on Artificial Life 2015, pp.9-11, 2015.

B. Van-dijk and P. Hogeweg, In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility, Genome Biology and Evolution, vol.8, issue.1, pp.176-188, 2016.
DOI : 10.1093/gbe/evv255

S. Fischer, G. Bernard, C. Beslon, and . Knibbe, A Model for Genome Size Evolution, Bulletin of Mathematical Biology, vol.104, issue.41, pp.2249-2291, 2014.
DOI : 10.1073/pnas.0705366104

URL : https://hal.archives-ouvertes.fr/hal-01090984

S. Hickinbotham and P. Hogeweg, Evolution towards extinction in replicase models: inevitable unless... 2 nd EvoEvo Workshop, 2016.

C. Knibbe and D. Parsons, What happened to my genes? Insights on gene family dynamics from digital genetics experiments, Proceedings of ALIFE 14, pp.33-40, 2014.
DOI : 10.7551/978-0-262-32621-6-ch006

URL : https://hal.archives-ouvertes.fr/hal-01093110

C. Knibbe, D. Schneider, and G. Beslon, evolution without (point) mutations, 2016.

J. Plucain, L. Hindré, . Gac, . Tenaillon, C. Cruveiller et al., Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli, Science, vol.6, issue.6, pp.3431366-1369, 2014.
DOI : 10.1186/1471-2105-6-209

URL : https://hal.archives-ouvertes.fr/hal-00961496

P. Puigbo, . Lobkovsky, Y. Dm-kristensen, E. Wolf, and . Koonin, Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes, BMC Biology, vol.9, issue.1, p.66, 2014.
DOI : 10.1080/106351501753328839

. Vp-richards, . Palmer, . Pd-pavinski-bitar, . Qin, . Weinstock et al., Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus, Genome Biology and Evolution, vol.6, issue.4, pp.741-753, 2014.
DOI : 10.1093/gbe/evu048

C. Raeside, . Gaffé, . De-deatherage, . Tenaillon, . Briska et al., Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli, mBio, vol.5, issue.5, pp.1377-1391, 2014.
DOI : 10.1128/mBio.01377-14

URL : http://doi.org/10.1128/mbio.01377-14

C. Rocabert, C. Knibbe, and G. Beslon, Towards an Integrated Evolutionary Model to Study Evolution of Evolution, First EvoEvo Workshop, vol.15, 2015.

C. Rocabert, C. Knibbe, D. Consuegra, G. Schneider, and . Beslon, Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification, PLOS Computational Biology, vol.69, issue.2, 2016.
DOI : 10.1371/journal.pcbi.1005459.s006

URL : https://hal.archives-ouvertes.fr/hal-01508751

F. Fet, Proactive EVLIT program Variability: mechanisms and consequences Project reference: 610427 Version 1

P. Jp-rutten, G. Hogeweg, and . Beslon, Evolution of mutator populations in constant environments. 2 nd EvoEvo Workshop, 2016.

P. Jp-rutten, G. Hogeweg, and . Beslon, Adapting the engine to the fuel: hypermutator populations can escape the mutational burden by reorganizing their genome structure, 2016.

R. Sanjuan, S. Moya, and . Elena, The distribution of fitness effects caused by singlenucleotide substitutions in an RNA virus, pp.8396-8401, 2004.

N. Takeuchi and P. Hogeweg, Evolution of complexity in RNA-like replicator systems, Biology Direct, vol.3, issue.1, p.11, 2008.
DOI : 10.1186/1745-6150-3-11

Y. Vadée-le-brun, J. Rouzaud-cornabas, and G. Beslon, Epigenetic inheritance speeds up evolution of artificial organisms, Proceedings of the European Conference on Artificial Life 2015, pp.439-446, 2015.

Y. Vadée-le-brun, J. Rouzaud-cornabas, and G. Beslon, In Silico Experimental Evolution suggests a complex intertwining of selection, robustness and drift in the evolution of genetic networks complexity, Proceedings of the Artificial Life Conference 2016, pp.180-187, 2016.

D. Wloch, R. Szafraniec, R. Borts, and . Korona, Direct estimate of the mutation rate and the distribution of fitness effects in the yeast Saccharomyces cerevisiae, Genetics, vol.159, issue.2, pp.441-452, 2001.