SPECIES, Evolution, vol.7, issue.10, pp.3302-3310 ,
DOI : 10.1111/j.1558-5646.2012.01674.x
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
Genome size correlates with reproductive fitness in seed beetles, Proceedings of the Royal Society B: Biological Sciences, vol.47, issue.1815, p.20151421, 2015. ,
DOI : 10.1086/595754
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4614751
Comparison of Sequencing Utility Programs, The Open Bioinformatics Journal, vol.7, issue.1, pp.1-8, 2013. ,
DOI : 10.2174/1875036201307010001
Analysis of Drosophila Species Genome Size and Satellite DNA Content Reveals Significant Differences Among Strains as Well as Between Species, Genetics, vol.177, issue.3, pp.1277-1290, 2007. ,
DOI : 10.1534/genetics.107.075069
Preventing the pollution of mitochondrial datasets with nuclear mitochondrial paralogs (numts), Mitochondrion, vol.11, issue.2, 2011. ,
DOI : 10.1016/j.mito.2010.10.004
URL : https://hal.archives-ouvertes.fr/halsde-00815371
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000. ,
DOI : 10.1093/oxfordjournals.molbev.a026334
Skeletal DNA and the Evolution of Genome Size, Annual Review of Biophysics and Bioengineering, vol.11, issue.1, pp.273-302, 1982. ,
DOI : 10.1146/annurev.bb.11.060182.001421
Genome Size: Does Bigger Mean Worse?, Current Biology, vol.14, issue.6, pp.233-235, 2004. ,
DOI : 10.1016/j.cub.2004.02.054
URL : http://doi.org/10.1016/j.cub.2004.02.054
Selfish genes, the phenotype paradigm and genome evolution, Nature, vol.284, issue.5757, pp.601-603, 1980. ,
DOI : 10.1038/284601a0
Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs, BMC Evolutionary Biology, vol.8, issue.1, p.255, 2008. ,
DOI : 10.1186/1471-2148-8-255
URL : https://hal.archives-ouvertes.fr/hal-00428202
Eyes underground: Regression of visual protein networks in subterranean mammals, Molecular Phylogenetics and Evolution, vol.78, pp.260-270, 2014. ,
DOI : 10.1016/j.ympev.2014.05.016
Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax, Nature Communications, vol.19, pp.10-1038, 2014. ,
DOI : 10.1038/ncomms4966
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes, PLOS Genetics, vol.9, issue.s1, p.1005323, 2015. ,
DOI : 10.1371/journal.pgen.1005323.s017
The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples, Genetics, vol.186, issue.1, pp.207-218, 2010. ,
DOI : 10.1534/genetics.110.114397
Rapid Flow Cytometric Analysis of the Cell Cycle in Intact Plant Tissues, Science, vol.220, issue.4601, pp.1049-1051, 1983. ,
DOI : 10.1126/science.220.4601.1049
Adaptive protein evolution in animals and the effective population size hypothesis, PLoS Genet, vol.12, pp.1-23, 2016. ,
Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate???Invertebrate Gap, PLoS Genetics, vol.335, issue.4, p.1003457, 2013. ,
DOI : 10.1371/journal.pgen.1003457.s008
URL : https://hal.archives-ouvertes.fr/hal-00866204
Bioconductor: open software development for computational biology and bioinformatics, 2004. ,
Large-scale detection of in vivo transcription errors, Proceedings of the National Academy of Sciences, vol.4, issue.4, pp.18584-18589, 2013. ,
DOI : 10.1093/gbe/evs028
Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nature Biotechnology, vol.30, issue.7, pp.644-652, 2011. ,
DOI : 10.1101/GR.229202. ARTICLE PUBLISHED ONLINE BEFORE MARCH 2002
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3571712
Coincidence, coevolution, or causation? DNA content, cellsize, and the C-value enigma, Biological Reviews, vol.3, issue.Supplement 4, pp.65-101, 2001. ,
DOI : 10.1111/j.1469-185X.2000.tb00059.x
Animal genome size database, 2005. ,
The evolution of the genome, 2005. ,
Population size and genome size in fishes: a closer look, Genome, vol.51, pp.309-313, 2008. ,
Variation in genome size???an ecological interpretation, Nature, vol.46, issue.5879, pp.151-153, 1982. ,
DOI : 10.1038/299151a0
Effects of organic matter availability on the life history and production of a top vertebrate predator (Plethodontidae: Gyrinophilus palleucus) in two cave streams, Freshwater Biology, vol.42, issue.Suppl, pp.1746-1760, 2011. ,
DOI : 10.1111/j.1365-2427.2011.02609.x
The rate of adaptive evolution in animal mitochondria, Molecular Ecology, vol.24, issue.103, pp.67-78, 2016. ,
DOI : 10.1111/mec.13475
URL : https://hal.archives-ouvertes.fr/hal-01246333
The genomic basis of adaptive evolution in threespine sticklebacks, Nature, vol.279, issue.7392, pp.55-61, 2012. ,
DOI : 10.1038/nature10944
Improved tests for the equality of normal coefficients of variation, Computational Statistics, vol.36, issue.1-2, pp.215-232, 2014. ,
DOI : 10.1007/s00180-013-0445-2
The consequences of genetic drift for bacterial genome complexity, Genome Research, vol.19, issue.8, pp.1450-1454, 2009. ,
DOI : 10.1101/gr.091785.109
Regressive evolution of an eye pigment gene in independently evolved eyeless subterranean diving beetles, Biology Letters, vol.13, issue.5479, pp.496-499, 2005. ,
DOI : 10.1126/science.289.5479.631
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009. ,
DOI : 10.1093/bioinformatics/btp324
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009. ,
DOI : 10.1093/bioinformatics/btp352
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2723002
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis, Science, vol.319, issue.5862, pp.1632-1635, 2008. ,
DOI : 10.1126/science.1151532
The origins of genome architecture, 2007. ,
Statistical Inference on the Mechanisms of Genome Evolution, PLoS Genetics, vol.27, issue.Suppl, p.1001389, 2011. ,
DOI : 10.1371/journal.pgen.1001389
The Repatterning of Eukaryotic Genomes by Random Genetic Drift, Annual Review of Genomics and Human Genetics, vol.12, issue.1, pp.347-366, 2011. ,
DOI : 10.1146/annurev-genom-082410-101412
The Origins of Genome Complexity, Science, vol.302, issue.5649, pp.1401-1404, 2003. ,
DOI : 10.1126/science.1089370
Phylogenies and the Comparative Method: A General Approach to Incorporating Phylogenetic Information into the Analysis of Interspecific Data, The American Naturalist, vol.149, issue.4, pp.646-667, 1997. ,
DOI : 10.1086/286013
Adaptive protein evolution at the Adh locus in Drosophila, Nature, vol.351, issue.6328, pp.652-654, 1991. ,
DOI : 10.1038/351652a0
Frequent adaptation and the McDonald-Kreitman test, Proceedings of the National Academy of Sciences, vol.24, issue.23, pp.8615-8620, 2013. ,
DOI : 10.1093/bioinformatics/btn522
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3666677
Illumina Sequencing Library Preparation for Highly Multiplexed Target Capture and Sequencing, Cold Spring Harbor Protocols, vol.2010, issue.6, 2010. ,
DOI : 10.1101/pdb.prot5448
Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, issue.1, p.116, 2011. ,
DOI : 10.1186/1471-2105-8-396
URL : https://hal.archives-ouvertes.fr/hal-00698365
Genetic drift and mutational hazard in the evolution of salamander genomic gigantism, Evolution, vol.13, issue.D1, pp.2865-2878, 2016. ,
DOI : 10.1111/evo.13084
Timetree of Aselloidea Reveals Species Diversification Dynamics in Groundwater, Systematic Biology, vol.62, issue.4, pp.512-522, 2013. ,
DOI : 10.1093/sysbio/syt015
URL : https://hal.archives-ouvertes.fr/halsde-00837844
The curvHDR method for gating flow cytometry samples, BMC Bioinformatics, vol.11, issue.1, p.44, 2010. ,
DOI : 10.1186/1471-2105-11-44
URL : http://doi.org/10.1186/1471-2105-11-44
Estimating the Distribution of Selection Coefficients from Phylogenetic Data with Applications to Mitochondrial and Viral DNA, Molecular Biology and Evolution, vol.20, issue.8, pp.1231-1239, 2003. ,
DOI : 10.1093/molbev/msg147
EVIDENCE FOR REPEATED LOSS OF SELECTIVE CONSTRAINT IN RHODOPSIN OF AMBLYOPSID CAVEFISHES (TELEOSTEI: AMBLYOPSIDAE), Evolution, vol.4, issue.3, pp.732-748, 2013. ,
DOI : 10.1111/j.1558-5646.2012.01822.x
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data, BMC Bioinformatics, vol.11, issue.1, p.378, 2010. ,
DOI : 10.1186/1471-2105-11-378
RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads, Bioinformatics, vol.29, issue.6, pp.792-793, 2013. ,
DOI : 10.1093/bioinformatics/btt054
The Nearly Neutral Theory of Molecular Evolution, Annual Review of Ecology and Systematics, vol.23, issue.1, pp.263-286, 1992. ,
DOI : 10.1146/annurev.es.23.110192.001403
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse, Nature, vol.43, issue.7456, pp.74-78, 2013. ,
DOI : 10.1093/sysbio/syq010
The Evolutionary Consequences of Polyploidy, Cell, vol.131, issue.3, pp.452-462, 2007. ,
DOI : 10.1016/j.cell.2007.10.022
APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004. ,
DOI : 10.1093/bioinformatics/btg412
Evolution of genome size: new approaches to an old problem, Trends in Genetics, vol.17, issue.1, pp.23-28, 2001. ,
DOI : 10.1016/S0168-9525(00)02157-0
nlme: Linear and Nonlinear Mixed Effects Models. R package version 3, pp.1-117, 2014. ,
Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism, Nature Genetics, vol.101, issue.1, pp.107-111, 2005. ,
DOI : 10.1038/ng1700
Truth or Consequences: Effects of Phylogenetic Accuracy on Two Comparative Methods, Journal of Theoretical Biology, vol.167, issue.3, pp.293-300, 1994. ,
DOI : 10.1006/jtbi.1994.1071
R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2013. ,
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons, PLoS ONE, vol.27, issue.9, p.22594, 2011. ,
DOI : 10.1371/journal.pone.0022594.s001
URL : https://hal.archives-ouvertes.fr/hal-00830089
Surface spreading of synaptonemal complexes in three isopod crustacean species, Genetica, vol.18, issue.2, pp.125-132, 1988. ,
DOI : 10.1007/BF00058844
Ligation Bias in Illumina Next-Generation DNA Libraries: Implications for Sequencing Ancient Genomes, PLoS ONE, vol.108, issue.10, p.78575, 2013. ,
DOI : 10.1371/journal.pone.0078575.s010
Measurement of protein using bicinchoninic acid, Analytical Biochemistry, vol.150, issue.1, pp.76-85, 1985. ,
DOI : 10.1016/0003-2697(85)90442-7
Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation, Science, vol.64, issue.4, pp.738-742, 2014. ,
DOI : 10.1111/j.1755-0998.2010.02873.x
Estimation of the Neutrality Index, Molecular Biology and Evolution, vol.28, issue.1, pp.63-70, 2011. ,
DOI : 10.1093/molbev/msq249
Statistical method for testing the neutral mutation hypothesis by dna polymorphism, Genetics, vol.123, pp.585-595, 1989. ,
Characterization of the Long-Wavelength Opsin from Mecoptera and Siphonaptera: Does a Flea See?, Molecular Biology and Evolution, vol.22, issue.5, pp.1165-1174, 2005. ,
DOI : 10.1093/molbev/msi110
The Genetic Organization of Chromosomes, Annual Review of Genetics, vol.5, issue.1, pp.237-256, 1971. ,
DOI : 10.1146/annurev.ge.05.120171.001321
Quantitative food web analysis supports the energy-limitation hypothesis in cave stream ecosystems, Oecologia, vol.155, issue.3, pp.859-869, 2014. ,
DOI : 10.1007/s00442-014-3042-3
Evolution of Genome Size in Drosophila. Is the
Invader's Genome Being Invaded by Transposable
Elements?, Molecular Biology and Evolution, vol.19, issue.7, pp.1154-1161, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004173
URL : https://hal.archives-ouvertes.fr/hal-00427308
Nucleotypic Effect in Homeotherms: Body-Mass-Corrected Basal Metabolic Rate of Mammals is Related to Genome Size, Evolution, vol.49, issue.6, pp.1249-1259, 1995. ,
DOI : 10.2307/2410449
A ROLE FOR NONADAPTIVE PROCESSES IN PLANT GENOME SIZE EVOLUTION?, Evolution, vol.7, issue.152, pp.2097-2109, 2010. ,
DOI : 10.1111/j.1558-5646.2010.00967.x
Drift and Genome Complexity Revisited, PLoS Genetics, vol.26, issue.6, p.1002092, 2011. ,
DOI : 10.1371/journal.pgen.1002092.t002
URL : https://hal.archives-ouvertes.fr/hal-00698327
Did Genetic Drift Drive Increases in Genome Complexity?, PLoS Genetics, vol.41, issue.8, p.1001080, 2010. ,
DOI : 10.1371/journal.pgen.1001080.t001
URL : http://doi.org/10.1371/journal.pgen.1001080
Effect of temperature and dietary elemental composition on RNA/protein ratio in a rotifer, Functional Ecology, vol.17, issue.5, pp.1154-1160, 2011. ,
DOI : 10.1111/j.1365-2435.2011.01864.x
Lowly Expressed Genes in Arabidopsis thaliana Bear the Signature of Possible Pseudogenization by Promoter Degradation, Molecular Biology and Evolution, vol.28, issue.3, pp.1193-1203, 2011. ,
DOI : 10.1093/molbev/msq298
PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007. ,
DOI : 10.1093/molbev/msm088
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.322.1650
Codon-substitution models for heterogeneous selection pressure at amino acid sites, Genetics, vol.155, pp.431-449, 2000. ,