What is complexity?, BioEssays, vol.407, issue.12, p.10851094, 2002. ,
DOI : 10.1002/bies.10192
Genome instability: a mechanistic view of its causes and consequences, Nature Reviews Genetics, vol.16, issue.3, p.204217, 2008. ,
DOI : 10.1038/nrg2268
Evolution of Genetic Potential, PLoS Computational Biology, vol.21, issue.3, p.32, 2005. ,
DOI : 0226-1776(1998)021[0047:PFLNA]2.0.CO;2
Evidence that gene amplication underlies adaptive mutability of the bacterial lac operon, Science, issue.5391, p.28211331135, 1998. ,
Quasispecies dynamics with network constraints, Journal of Theoretical Biology, vol.312, p.114119, 2012. ,
DOI : 10.1016/j.jtbi.2012.07.032
A branching-process model for the evolution of transposable elements incorporating selection, Journal of Mathematical Biology, vol.27, issue.8, p.29743761, 1991. ,
DOI : 10.1007/BF00160190
In silico experimental evolution: a tool to test evolutionary scenarios, BMC Bioinformatics, vol.14, issue.Suppl 15, 2013. ,
DOI : 10.1016/j.jtbi.2006.09.005
URL : https://hal.archives-ouvertes.fr/hal-00873232
Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonad genomes, Proceedings of the Royal Society B: Biological Sciences, vol.266, issue.1433, p.26620532059, 1433. ,
DOI : 10.1098/rspb.1999.0886
Nuclear DNA Content and Minimum Generation Time in Herbaceous Plants, Proceedings of the Royal Society B: Biological Sciences, vol.181, issue.1063, pp.109135-4403285, 1063. ,
DOI : 10.1098/rspb.1972.0042
Do plants have a one-way ticket to genomic obesity ?, Plant Cell, vol.9, issue.9, pp.15091514-12237393, 1997. ,
Mutational Dynamics of Microsatellites, Molecular Biotechnology, vol.179, issue.103, p.250266, 2009. ,
DOI : 10.1007/s12033-009-9230-4
Shift in the velocity of a front due to a cuto, Phys Rev E, vol.56, issue.3, p.25972604, 1997. ,
Nuclear volume control by nucleoskeletal DNA, selection for cell volume and cell growth rate, and the solution of the DNA c value paradox, J Cell Sci, vol.34, issue.1, p.247278, 1978. ,
The Evolution of genome size, 1985. ,
The Skeletal Function of Non-Genic Nuclear DNA: New Evidence from Ancient Cell Chimaeras, Genetica, vol.106, issue.12, p.313, 1999. ,
DOI : 10.1007/978-94-011-4631-9_1
Unifying evolutionary dynamics: From individual stochastic processes to macroscopic models, Theoretical Population Biology, vol.69, issue.3, p.297321, 2006. ,
DOI : 10.1016/j.tpb.2005.10.004
URL : https://hal.archives-ouvertes.fr/inria-00164784
Evolution of discrete populations and the canonical diusion of adaptive dynamics, Ann Appl Probab, vol.17, issue.1, p.102155, 2007. ,
Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation, Nature Reviews Genetics, vol.418, issue.3, p.195205, 2009. ,
DOI : 10.1038/nrg2526
The evolutionary dynamics of repetitive DNA in eukaryotes, Nature, vol.371, issue.6494, p.371215220, 1994. ,
DOI : 10.1038/371215a0
Genomic Rearrangements: Mutational Mechanisms, Encyclopedia of Life Sciences, 2011. ,
DOI : 10.1002/9780470015902.a0022926
Maize HapMap2 identies extant variation from a genome in ux, 2012. ,
Mechanisms Causing Rapid and Parallel Losses of Ribose Catabolism in Evolving Populations of Escherichia coli B, Journal of Bacteriology, vol.183, issue.9, p.28342841, 2001. ,
DOI : 10.1128/JB.183.9.2834-2841.2001
Evolution of Evolvability in Gene Regulatory Networks, PLoS Computational Biology, vol.10, issue.7, p.1000112, 2008. ,
DOI : 10.1371/journal.pcbi.1000112.s005
Dynamics of Genome Rearrangement in Bacterial Populations, PLoS Genetics, vol.3, issue.6, p.1000128, 2008. ,
DOI : 10.1371/journal.pgen.1000128.s009
Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in Arabidopsis, Genome Research, vol.12, issue.7, 2002. ,
DOI : 10.1101/gr.132102
The dynamical theory of coevolution: a derivation from stochastic ecological processes, Journal of Mathematical Biology, vol.39, issue.5-6, pp.5-6579612, 1996. ,
DOI : 10.1007/BF02409751
The dynamics of adaptation: An illuminating example and a Hamilton???Jacobi approach, Theoretical Population Biology, vol.67, issue.4, p.257271, 2005. ,
DOI : 10.1016/j.tpb.2004.12.003
Selsh genes, the phenotype paradigm and genome evolution, Nature, issue.5757, p.284601603, 1980. ,
Mutational robustness can facilitate adaptation, Nature, vol.99, issue.7279, p.463353355, 2010. ,
DOI : 10.1038/nature08694
A constant rate of spontaneous mutation in DNA-based microbes., Proceedings of the National Academy of Sciences, vol.88, issue.16, 1991. ,
DOI : 10.1073/pnas.88.16.7160
Selforganization of matter and the evolution of biological macromolecules, Die Naturwissenschaften, vol.164, issue.10, p.58465523, 1971. ,
DOI : 10.1007/BF00623322
Molecular quasi-species, The Journal of Physical Chemistry, vol.92, issue.24, p.9268816891, 1988. ,
DOI : 10.1021/j100335a010
The hypercycle, a principle of natural selforganization, 1979. ,
Size-Dependent Mutability and Microsatellite Constraints, Molecular Biology and Evolution, vol.16, issue.7, 1999. ,
DOI : 10.1093/oxfordjournals.molbev.a026185
Some measure-valued markov processes in populationgenetics theory, Indiana U Math J, vol.28, issue.5, p.817843, 1979. ,
Insertion Sequence-Driven Evolution of Escherichia coli in Chemostats, Journal of Molecular Evolution, vol.164, issue.10, 2011. ,
DOI : 10.1007/s00239-011-9439-2
Evolutionarily singular strategies and the adaptive growth and branching of the evolutionary tree, Evolutionary Ecology, vol.34, issue.1, 1998. ,
DOI : 10.1023/A:1006554906681
Is small indel bias a determinant of genome size?, Trends in Genetics, vol.19, issue.9, p.485488, 2003. ,
DOI : 10.1016/S0168-9525(03)00192-6
Insertiondeletion biases and the evolution of genome size, Gene, vol.324, p.1534, 2004. ,
Coincidence, coevolution, or causation? DNA content, cellsize, and the C-value enigma, Biological Reviews, vol.3, issue.Supplement 4, p.65101, 2001. ,
DOI : 10.1111/j.1469-185X.2000.tb00059.x
Mechanisms for human genomic rearrangements, PathoGenetics, vol.1, issue.1, p.4, 2008. ,
DOI : 10.1186/1755-8417-1-4
The g-value paradox, Evolution and Development, vol.282, issue.2, p.7375, 2002. ,
DOI : 10.1126/science.1058040
???Changing by doubling???, the impact of Whole Genome Duplications in the evolution of eukaryotes, Comptes Rendus Biologies, vol.332, issue.2-3, p.241253, 2009. ,
DOI : 10.1016/j.crvi.2008.07.007
Diusion models in population genetics, J Appl Probab, vol.1, issue.2, p.177232, 1964. ,
Evolutionary Rate at the Molecular Level, Nature, vol.16, issue.5129, p.624626, 1968. ,
DOI : 10.1038/217624a0
The neutral theory of molecular evolution, 1983. ,
Species-specic double-strand break repair and genome evolution in plants, EMBO J, issue.20, p.1955625566, 2000. ,
Structuration des génomes par sélection indirecte de la variabilité mutationnelle : une approche de modélisation et de simulation, Thèse de doctorat, 2006. ,
A Long-Term Evolutionary Pressure on the Amount of Noncoding DNA, Molecular Biology and Evolution, vol.24, issue.10, pp.242344-2353, 2007. ,
DOI : 10.1093/molbev/msm165
URL : https://hal.archives-ouvertes.fr/hal-00391447
Population genetics of unequal crossing over, Journal of Molecular Evolution, vol.7, issue.3, p.201247, 1975. ,
DOI : 10.1007/BF01732983
The consequences of genetic drift for bacterial genome complexity, Genome Research, vol.19, issue.8, p.1914501454, 2009. ,
DOI : 10.1101/gr.091785.109
Deletional Bias across the Three Domains of Life, Genome Biology and Evolution, vol.1, issue.0, 2009. ,
DOI : 10.1093/gbe/evp016
The branching process with logistic growth, The Annals of Applied Probability, vol.15, issue.2, p.15061535, 2005. ,
DOI : 10.1214/105051605000000098
Probability of xation under weak selection : A branching process unifying approach, Theor Popul Biol, vol.69, issue.4, p.419441, 2006. ,
On the role of unequal exchange in the containment of transposable element copy number, Genetical Research, vol.44, issue.03, p.223235, 1988. ,
DOI : 10.1073/pnas.84.1.174
Individual histories and selection in heterogeneous populations, Proceedings of the National Academy of Sciences, vol.107, issue.29, p.1318313188, 2010. ,
DOI : 10.1073/pnas.0912538107
Strong Mutational Bias Toward Deletions in the Drosophila melanogaster Genome Is Compensated by Selection, Genome Biology and Evolution, vol.5, issue.3, 2013. ,
DOI : 10.1093/gbe/evt021
Epigenetic Regulation of Transposable Elements in Plants, Annual Review of Plant Biology, vol.60, issue.1, p.4366, 2009. ,
DOI : 10.1146/annurev.arplant.59.032607.092744
Genomic rearrangements and sporadic disease, Nature Genetics, vol.15, issue.7s, pp.43-47, 2007. ,
DOI : 10.1038/ng2084
Streamlining and simplication of microbial genome architecture, Ann Rev Microbiol, vol.60, issue.1, p.327349, 2006. ,
Evolution of the mutation rate The origins of genome complexity, Trends Genet Science, vol.26, issue.85649, p.30214011404, 2003. ,
Deletional bias and the evolution of bacterial genomes, Trends in Genetics, vol.17, issue.10, p.17589596, 2001. ,
DOI : 10.1016/S0168-9525(01)02447-7
A branching process model for the evolution of transposable elements, Journal of Mathematical Biology, vol.110, issue.3, p.347357, 1988. ,
DOI : 10.1007/BF00277395
Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp, J Bacteriol, issue.17, p.18043254331, 1998. ,
From The Cover: Bacterial genome size reduction by experimental evolution, Proceedings of the National Academy of Sciences, vol.102, issue.34, 2005. ,
DOI : 10.1073/pnas.0503654102
Error thresholds of replication in nite populations mutation frequencies and the onset of muller's ratchet, J Theor Biol, vol.137, issue.4, p.375395, 1989. ,
What is a quasispecies?, Trends in Ecology & Evolution, vol.7, issue.4, p.118121, 1992. ,
DOI : 10.1016/0169-5347(92)90145-2
The Nature and Dynamics of Bacterial Genomes, Science, vol.311, issue.5768, p.31117301733, 2006. ,
DOI : 10.1126/science.1119966
Genes Lost and Genes Found: Evolution of Bacterial Pathogenesis and Symbiosis, Science, vol.292, issue.5519, p.29210961099, 2001. ,
DOI : 10.1126/science.1058543
Evolution by gene duplication, 1970. ,
DOI : 10.1007/978-3-642-86659-3
So much "junk" DNA in our genome, Brookhaven Sym Biol, vol.23, p.5065367, 1972. ,
Some calculations on the amount of selsh DNA, P Natl Acad Sci, vol.78, issue.2, p.11291132, 1981. ,
Dierences in the processing of DNA ends in Arabidopsis thaliana and tobacco : possible implications for genome evolution, Plant Mol Biol, vol.51, issue.4, p.523531, 2003. ,
Selsh DNA, Nature, issue.5792, p.288645646, 1980. ,
Selsh DNA : the ultimate parasite, Nature, issue.5757, p.284604607, 1980. ,
Evidence for DNA Loss as a Determinant of Genome Size, Science, vol.287, issue.5455, p.28710601062, 2000. ,
DOI : 10.1126/science.287.5455.1060
Evolution of genome size: new approaches to an old problem, Trends in Genetics, vol.17, issue.1, p.2328, 2001. ,
DOI : 10.1016/S0168-9525(00)02157-0
Mutational Equilibrium Model of Genome Size Evolution, Theoretical Population Biology, vol.61, issue.4, p.531544, 2002. ,
DOI : 10.1006/tpbi.2002.1605
High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups, Molecular Biology and Evolution, vol.15, issue.3, p.293302, 1998. ,
DOI : 10.1093/oxfordjournals.molbev.a025926
High intrinsic rate of DNA loss in Drosophila, Nature, vol.384, issue.6607, p.384346349, 1996. ,
DOI : 10.1038/384346a0
Prokaryote and eukaryote evolvability, Biosystems, vol.69, issue.2-3, p.69163185, 2003. ,
DOI : 10.1016/S0303-2647(02)00131-4
DNA amplication and rearrangements in archival Salmonella enterica serovar typhimurium LT2 cultures, J Bacteriol, vol.186, issue.6, p.16781682, 2004. ,
The evolution of gene number : are heritable and non-heritable errors equally important ? Heredity, p.393400, 2000. ,
Are Obese Plant Genomes on a Diet?, Genome Research, vol.10, issue.7, pp.893-894, 2000. ,
DOI : 10.1101/gr.10.7.893
Recombination and genome size, Theoretical and Applied Genetics, vol.73, issue.1, p.7276, 1986. ,
DOI : 10.1007/BF00273721
Genome size and recombination in angiosperms: a second look, Journal of Evolutionary Biology, vol.162, issue.2, 2007. ,
DOI : 10.1007/BF00989326
Models of the population genetics of transposable elements, Genetical Research, vol.85, issue.03, p.171, 2005. ,
DOI : 10.1017/S0016672305007585
URL : https://hal.archives-ouvertes.fr/hal-00121626
The Distribution of Inversion Lengths in Bacteria, Lagergren, J., éditeur : Comparative Genomics, numéro 3388 de Lecture Notes in Computer Science, p.97108, 2005. ,
DOI : 10.1007/978-3-540-32290-0_8
The relationship between proteome size, structural disorder and organism complexity, Genome Biology, vol.12, issue.12, p.12113, 2011. ,
DOI : 10.1093/nar/gkq973
Rapid evolution of enormous, multichromosomal genomes in owering plant mitochondria with exceptionally high mutation rates, 2012. ,
Evolution of repeated DNA sequences by unequal crossover, Science, vol.191, issue.4227, p.191528535, 1976. ,
DOI : 10.1126/science.1251186
Quantitative variation and chromosomal location of satellite DNAs, Genetical Research, vol.113, issue.01, p.4152, 1987. ,
DOI : 10.1016/0022-2836(67)90019-8
An Introduction to Markov Processes, 2005. ,
DOI : 10.1007/978-3-642-40523-5
Quantifying Organismal Complexity using a Population Genetic Approach, PLoS ONE, vol.441, issue.2, p.217, 2007. ,
DOI : 10.1371/journal.pone.0000217.g003
The Genetic Organization of Chromosomes, Annual Review of Genetics, vol.5, issue.1, p.237256, 1971. ,
DOI : 10.1146/annurev.ge.05.120171.001321
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths, PLoS Genetics, vol.68, issue.1, p.1000344, 2009. ,
DOI : 10.1371/journal.pgen.1000344.s016
URL : https://hal.archives-ouvertes.fr/hal-00390293
Causes of Insertion Sequences Abundance in Prokaryotic Genomes, Molecular Biology and Evolution, vol.24, issue.4, p.969981, 2007. ,
DOI : 10.1093/molbev/msm014
DNA motifs that sculpt the bacterial chromosome, Nature Reviews Microbiology, vol.15, issue.1, p.1526, 2011. ,
DOI : 10.1038/nrmicro2477
URL : https://hal.archives-ouvertes.fr/hal-01019344
RNA virus evolution via a tness-space model, Phys Rev L, issue.23, p.7644404443, 1996. ,
Neutral evolution of mutational robustness, Proceedings of the National Academy of Sciences, vol.96, issue.17, p.9697169720, 1999. ,
DOI : 10.1073/pnas.96.17.9716
Retrotransposon BARE-1 and Its Role in Genome Evolution in the Genus Hordeum, THE PLANT CELL ONLINE, vol.11, issue.9, p.17691784, 1999. ,
DOI : 10.1105/tpc.11.9.1769
Robustness and evolvability: a paradox resolved, Proceedings of the Royal Society B: Biological Sciences, vol.46, issue.17, p.27591100, 1630. ,
DOI : 10.1073/pnas.96.17.9716
Persistence of tandem arrays : Implications for satellite and simplesequence DNAs, Genetics, vol.115, issue.3, p.553567, 1987. ,
Feast and famine in plant genomes, Genetica, vol.115, issue.1, p.3747, 2002. ,
Did Genetic Drift Drive Increases in Genome Complexity?, PLoS Genetics, vol.41, issue.8, p.1001080, 2010. ,
DOI : 10.1371/journal.pgen.1001080.t001
Probability of xation of an advantageous mutant in a viral quasispecies, Genetics, vol.163, issue.2, p.467474, 2003. ,
Denumerable Markov Chains : Generating Functions, Boundary Theory , Random Walks on Trees, 2009. ,
DOI : 10.4171/071
Protein stability imposes limits on organism complexity and speed of molecular evolution, Proceedings of the National Academy of Sciences, vol.104, issue.41, p.1041615216157, 2007. ,
DOI : 10.1073/pnas.0705366104