F. Abascal, R. Zardoya, and D. Posada, ProtTest: selection of best-fit models of protein evolution, Bioinformatics, vol.21, issue.9, pp.2104-2105, 2005.
DOI : 10.1093/bioinformatics/bti263

N. Agier, O. Romano, F. Touzain, M. Lagomarsino, and G. Fischer, The Spatiotemporal Program of Replication in the Genome of Lachancea kluyveri, Genome Biology and Evolution, vol.5, issue.2, pp.370-388, 2013.
DOI : 10.1093/gbe/evt014

M. Alekseyev and P. Pevzner, Breakpoint graphs and ancestral genome reconstructions, Genome Research, vol.19, issue.5, pp.943-957, 2009.
DOI : 10.1101/gr.082784.108

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

A. Avelar, L. Perfeito, I. Gordo, and M. Ferreira, Genome architecture is a selectable trait that can be maintained by antagonistic pleiotropy, Nat Commun, vol.4, p.2235, 2013.

T. Bailey and C. Elkan, Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proc Int Conf Intell Syst Mol Biol, vol.2, pp.28-36, 1994.

C. Berthelot, M. Muffato, and J. Abecassis, The 3D Organization of Chromatin Explains Evolutionary Fragile Genomic Regions, Cell Reports, vol.10, issue.11, pp.1913-1924
DOI : 10.1016/j.celrep.2015.02.046

A. Bhutkar, S. Schaeffer, S. Russo, M. Xu, T. Smith et al., Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes, Genetics, vol.179, issue.3, pp.1657-1680, 2008.
DOI : 10.1534/genetics.107.086108

G. Bourque, E. Zdobnov, P. Bork, P. Pevzner, and G. Tesler, Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages, Genome Research, vol.15, issue.1, pp.98-110, 2005.
DOI : 10.1101/gr.3002305

G. Butler, M. Rasmussen, M. Lin, M. Santos, S. Sakthikumar et al., Evolution of pathogenicity and sexual reproduction in eight Candida genomes, Nature, vol.440, issue.7247, pp.657-662, 2009.
DOI : 10.1038/nature08064

A. Carbone, A. Zinovyev, and F. Kepes, Codon adaptation index as a measure of dominating codon bias, Bioinformatics, vol.19, issue.16, pp.2005-2015, 2003.
DOI : 10.1093/bioinformatics/btg272

M. Csuros and I. Miklos, Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model, Molecular Biology and Evolution, vol.26, issue.9, pp.2087-2095, 2009.
DOI : 10.1093/molbev/msp123

D. Rienzi, S. Lindstrom, K. Lancaster, R. Rolczynski, L. Raghuraman et al., Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii, Yeast, vol.14, issue.2, pp.137-151, 2011.
DOI : 10.1002/yea.1826

F. Dietrich, S. Voegeli, S. Brachat, A. Lerch, K. Gates et al., The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome, Science, vol.304, issue.5668, pp.304-307, 2004.
DOI : 10.1126/science.1095781

G. Drillon and G. Fischer, Comparative study on synteny between yeasts and vertebrates, Comptes Rendus Biologies, vol.334, issue.8-9, pp.629-638, 2011.
DOI : 10.1016/j.crvi.2011.05.011
URL : https://hal.archives-ouvertes.fr/hal-00626818

G. Drillon, A. Carbone, and G. Fischer, SynChro: A Fast and Easy Tool to Reconstruct and Visualize Synteny Blocks along Eukaryotic Chromosomes, PLoS ONE, vol.334, issue.3, p.92621, 2014.
DOI : 10.1371/journal.pone.0092621.t002
URL : https://hal.archives-ouvertes.fr/hal-01358096

B. Dujon, D. Sherman, G. Fischer, P. Durrens, S. Casaregola et al., Genome evolution in yeasts, Nature, vol.316, issue.6995, pp.35-44, 2004.
DOI : 10.1093/nar/gkg056
URL : https://hal.archives-ouvertes.fr/hal-00104411

A. Enright, V. Kunin, and C. Ouzounis, Protein families and TRIBES in genome sequence space, Nucleic Acids Research, vol.31, issue.15, pp.4632-4638, 2003.
DOI : 10.1093/nar/gkg495

T. Faraut, Addressing chromosome evolution in the whole-genome sequence era, Chromosome Research, vol.298, issue.1, pp.5-16, 2008.
DOI : 10.1007/s10577-007-1208-0

J. Fell, A. Statzell-tallman, and C. Kurtzman, Lachancea meyersii sp. nov., an ascosporogenous yeast from mangrove regions in the Bahama Islands, Stud Mycol, vol.50, pp.359-363, 2004.

J. Felsentein, Phylogenetic inference package (PHYLIP), version 3.5, 1995.

G. Fischer, C. Neuveglise, P. Durrens, C. Gaillardin, and B. Dujon, Evolution of Gene Order in the Genomes of Two Related Yeast Species, Genome Research, vol.11, issue.12, pp.2009-2019, 2001.
DOI : 10.1101/gr.212701
URL : https://hal.archives-ouvertes.fr/hal-00306595

G. Fischer, E. Rocha, F. Brunet, M. Vergassola, and B. Dujon, Highly variable rates of genome rearrangements between Hemiascomycetous yeast lineages, PLoS Genetics, vol.preprint, issue.2006, p.32, 2006.
DOI : 10.1371/journal.pgen.0020032.eor

K. Freel, G. Charron, J. Leducq, C. Landry, and J. Schacherer, Lachancea quebecensis sp. nov., a yeast species consistently isolated from tree bark in the Canadian province of Qu??bec, International Journal of Systematic and Evolutionary Microbiology, vol.65, issue.10, pp.3392-3399, 2015.
DOI : 10.1099/ijsem.0.000426

K. Freel, A. Friedrich, and J. Schacherer, Mitochondrial genome evolution in yeasts: an all-encompassing view, FEMS Yeast Research, vol.15, issue.4, p.23, 2015.
DOI : 10.1093/femsyr/fov023

A. Friedrich, P. Jung, C. Reisser, G. Fischer, and J. Schacherer, Population Genomics Reveals Chromosome-Scale Heterogeneous Evolution in a Protoploid Yeast, Molecular Biology and Evolution, vol.32, issue.1, pp.184-192, 2015.
DOI : 10.1093/molbev/msu295
URL : https://hal.archives-ouvertes.fr/hal-01087685

A. Fruhmesser, J. Blake, E. Haberlandt, B. Baying, B. Raeder et al., Disruption of EXOC6B in a patient with developmental delay, epilepsy, and a de novo balanced t(2;8) translocation, European Journal of Human Genetics, vol.15, issue.10, pp.1177-1180, 2013.
DOI : 10.1016/j.ajhg.2011.09.015

T. Gabaldon, T. Martin, M. Marcet-houben, P. Durrens, M. Bolotin-fukuhara et al., Comparative genomics of emerging pathogens in the Candida glabrata clade, BMC Genomics, vol.14, issue.1, p.623, 2013.
DOI : 10.1016/0097-8485(93)85006-X
URL : https://hal.archives-ouvertes.fr/inserm-00871184

S. Gadagkar and S. Kumar, Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates Are Heterotachous, Molecular Biology and Evolution, vol.22, issue.11, pp.2139-2141, 2005.
DOI : 10.1093/molbev/msi212

Y. Gagnon, M. Blanchette, and N. El-mabrouk, A flexible ancestral genome reconstruction method based on gapped adjacencies, BMC Bioinformatics, vol.13, p.4, 2012.

V. Galeote, M. Novo, M. Salema-oom, C. Brion, E. Valerio et al., FSY1, a horizontally transferred gene in the Saccharomyces cerevisiae EC1118 wine yeast strain, encodes a high-affinity fructose/H+ symporter, Microbiology, vol.156, issue.12, pp.3754-3761, 2010.
DOI : 10.1099/mic.0.041673-0

S. Gonzalez, J. Alcoba-florez, and F. Laich, Lachancea lanzarotensis sp. nov., an ascomycetous yeast isolated from grapes and wine fermentation in Lanzarote, Canary Islands, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.63, issue.Pt 1, pp.358-363, 2013.
DOI : 10.1099/ijs.0.046029-0

J. Gordon, K. Byrne, and K. Wolfe, Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome, PLoS Genetics, vol.55, issue.5, p.1000485, 2009.
DOI : 10.1371/journal.pgen.1000485.s003

J. Gordon, K. Byrne, and K. Wolfe, Mechanisms of Chromosome Number Evolution in Yeast, PLoS Genetics, vol.55, issue.4, p.1002190, 2011.
DOI : 10.1371/journal.pgen.1002190.s010

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

C. Hittinger, A. Rokas, F. Bai, T. Boekhout, P. Goncalves et al., Genomics and the making of yeast biodiversity, Current Opinion in Genetics & Development, vol.35, pp.100-109, 2015.
DOI : 10.1016/j.gde.2015.10.008

B. Jones, A. Rajaraman, E. Tannier, and C. Chauve, ANGES: reconstructing ANcestral GEnomeS maps, Bioinformatics, vol.28, issue.18, pp.2388-2390, 2012.
DOI : 10.1093/bioinformatics/bts457
URL : https://hal.archives-ouvertes.fr/hal-00733180

K. Katoh and H. Toh, Recent developments in the MAFFT multiple sequence alignment program, Briefings in Bioinformatics, vol.9, issue.4, pp.286-298, 2008.
DOI : 10.1093/bib/bbn013

Y. Kelkar and H. Ochman, Causes and Consequences of Genome Expansion in Fungi, Genome Biology and Evolution, vol.4, issue.1, pp.13-23, 2012.
DOI : 10.1093/gbe/evr124

M. Kellis, B. Birren, and E. Lander, Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae, Nature, vol.428, issue.6983, pp.617-624, 2004.
DOI : 10.1038/nature02424

K. Khalturin, G. Hemmrich, S. Fraune, A. R. Bosch, and T. , More than just orphans: are taxonomically-restricted genes important in evolution?, Trends in Genetics, vol.25, issue.9, pp.404-413, 2009.
DOI : 10.1016/j.tig.2009.07.006

C. Kurtzman, Phylogenetic circumscription of , and other members of the Saccharomycetaceae, and the proposal of the new genera , , , and, FEMS Yeast Research, vol.4, issue.3, pp.233-245, 2003.
DOI : 10.1016/S1567-1356(03)00175-2

I. Lafontaine and B. Dujon, Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis, BMC Genomics, vol.11, issue.1, p.260, 2010.
DOI : 10.1186/1471-2164-11-260

I. Lafontaine, G. Fischer, E. Talla, and B. Dujon, Gene relics in the genome of the yeast Saccharomyces cerevisiae, Gene, vol.335, pp.1-17, 2004.
DOI : 10.1016/j.gene.2004.03.028

C. Lee, C. Yao, Y. Liu, C. Hsieh, and S. Young, Lachancea dasiensis sp. nov., an ascosporogenous yeast isolated from soil and leaves in Taiwan, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.59, issue.7, pp.1818-1822, 2009.
DOI : 10.1099/ijs.0.008789-0

P. Librado, F. Vieira, and J. Rozas, BadiRate: estimating family turnover rates by likelihood-based methods, Bioinformatics, vol.28, issue.2, pp.279-281, 2012.
DOI : 10.1093/bioinformatics/btr623

V. Louis, L. Despons, A. Friedrich, T. Martin, P. Durrens et al., , an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization, G3 (Bethesda), pp.299-311, 2012.
DOI : 10.1534/g3.111.000745

T. Lowe and S. Eddy, tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence, Nucleic Acids Research, vol.25, issue.5, pp.955-964, 1997.
DOI : 10.1093/nar/25.5.0955

J. Ma, L. Zhang, B. Suh, B. Raney, R. Burhans et al., Reconstructing contiguous regions of an ancestral genome, Genome Research, vol.16, issue.12, pp.1557-1565, 2006.
DOI : 10.1101/gr.5383506

M. Marcet-houben and T. Gabaldon, Acquisition of prokaryotic genes by fungal genomes, Trends in Genetics, vol.26, issue.1, pp.5-8, 2010.
DOI : 10.1016/j.tig.2009.11.007

M. Marcet-houben and T. Gabaldon, Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage, PLOS Biology, vol.18, issue.8, p.1002220, 2015.
DOI : 10.1371/journal.pbio.1002220.s024

S. Marsit, A. Mena, F. Bigey, F. Sauvage, A. Couloux et al., Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts, Molecular Biology and Evolution, vol.32, issue.7, pp.1695-1707, 2015.
DOI : 10.1093/molbev/msv057

A. Mclysaght and D. Guerzoni, New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.159, issue.1678, p.20140332, 2015.
DOI : 10.1146/annurev-biochem-070611-102400

M. Mestre, J. Ulloa, C. Rosa, M. Lachance, and S. Fontenla, Lachancea nothofagi sp. nov., a yeast associated with Nothofagus species in Patagonia, Argentina, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.60, issue.9, pp.2247-2250, 2010.
DOI : 10.1099/ijs.0.018929-0

A. Mighell, N. Smith, P. Robinson, and A. Markham, Vertebrate pseudogenes, FEBS Letters, vol.206, issue.2-3, pp.109-114, 2000.
DOI : 10.1016/S0014-5793(00)01199-6

J. Mistry, R. Finn, S. Eddy, A. Bateman, and M. Punta, Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions, Nucleic Acids Research, vol.41, issue.12, p.121, 2013.
DOI : 10.1093/nar/gkt263

L. Morales and B. Dujon, Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts, Microbiology and Molecular Biology Reviews, vol.76, issue.4, pp.721-739, 2012.
DOI : 10.1128/MMBR.00022-12

G. Morel, L. Sterck, D. Swennen, M. Marcet-houben, D. Onesime et al., Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts, Scientific Reports, vol.26, p.11571, 2015.
DOI : 10.1038/srep11571
URL : https://hal.archives-ouvertes.fr/hal-01201920

M. Moyses-oliveira, R. Guilherme, V. Meloni, D. Battista, A. De-mello et al., X-linked intellectual disability related genes disrupted by balanced X-autosome translocations, American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, vol.24, issue.2, pp.669-677, 2015.
DOI : 10.1002/ajmg.b.32355

M. Muffato, R. Crollius, and H. , Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time, BioEssays, vol.270, issue.2, pp.122-134, 2008.
DOI : 10.1002/bies.20707

P. Munz, An analysis of interference in the fission yeast Schizosaccharomyces pombe, Genetics, vol.137, pp.701-707, 1994.

E. Myers, G. Sutton, A. Delcher, I. Dew, D. Fasulo et al., A Whole-Genome Assembly of Drosophila, Science, vol.287, issue.5461, pp.2196-2204, 2000.
DOI : 10.1126/science.287.5461.2196

S. Ohno, A. Ouangraoua, E. Tannier, and C. Chauve, Evolution by gene duplication Reconstructing the architecture of the ancestral amniote genome, Bioinformatics, vol.27, pp.2664-2671, 1970.

C. Payen, R. Koszul, B. Dujon, and G. Fischer, Segmental Duplications Arise from Pol32-Dependent Repair of Broken Forks through Two Alternative Replication-Based Mechanisms, PLoS Genetics, vol.294, issue.9, p.1000175, 2008.
DOI : 10.1371/journal.pgen.1000175.s001

C. Payen, G. Fischer, C. Marck, C. Proux, D. Sherman et al., Unusual composition of a yeast chromosome arm is associated with its delayed replication, Genome Research, vol.19, issue.10, pp.1710-1721, 2009.
DOI : 10.1101/gr.090605.108
URL : https://hal.archives-ouvertes.fr/inria-00407518

Q. Peng, P. Pevzner, and G. Tesler, The Fragile Breakage versus Random Breakage Models of Chromosome Evolution, PLoS Computational Biology, vol.65, issue.2, p.14, 2006.
DOI : 10.1371/journal.pcbi.0020014.sg002

L. Pereira, C. Costa, . Jr, B. Brasileiro, M. De-morais et al., Lachancea mirantina sp. nov., an ascomycetous yeast isolated from the cachaca fermentation process, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.61, issue.4, pp.989-992, 2011.
DOI : 10.1099/ijs.0.020008-0

J. Perez-ortin, A. Querol, S. Puig, and E. Barrio, Molecular Characterization of a Chromosomal Rearrangement Involved in the Adaptive Evolution of Yeast Strains, Genome Research, vol.12, issue.10, pp.1533-1539, 2002.
DOI : 10.1101/gr.436602

J. Poyatos and L. Hurst, The determinants of gene order conservation in yeasts, Genome Biology, vol.8, issue.11, p.233, 2007.
DOI : 10.1186/gb-2007-8-11-r233

P. Puigbo, A. Lobkovsky, D. Kristensen, Y. Wolf, and E. Koonin, Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes, BMC Biology, vol.9, issue.1, p.66, 2014.
DOI : 10.1186/s12915-014-0066-4

F. Quintero-rivera, Q. Xi, K. Keppler-noreuil, J. Lee, A. Higgins et al., MATR3 disruption in human and mouse associated with bicuspid aortic valve, aortic coarctation and patent ductus arteriosus, Human Molecular Genetics, vol.24, issue.8, pp.2375-2389, 2015.
DOI : 10.1093/hmg/ddv004

G. Richard, A. Kerrest, I. Lafontaine, and B. Dujon, Comparative Genomics of Hemiascomycete Yeasts: Genes Involved in DNA Replication, Repair, and Recombination, Molecular Biology and Evolution, vol.22, issue.4, pp.1011-1023, 2005.
DOI : 10.1093/molbev/msi083

T. Rolland and B. Dujon, Yeasty clocks: Dating genomic changes in yeasts, Comptes Rendus Biologies, vol.334, issue.8-9, pp.620-628, 2011.
DOI : 10.1016/j.crvi.2011.05.010

T. Rolland, C. Neuveglise, C. Sacerdot, and B. Dujon, Insertion of Horizontally Transferred Genes within Conserved Syntenic Regions of Yeast Genomes, PLoS ONE, vol.13, issue.3, p.6515, 2009.
DOI : 10.1371/journal.pone.0006515.s008

J. Rowley, THE CRITICAL ROLE OF CHROMOSOME TRANSLOCATIONS IN HUMAN LEUKEMIAS, Annual Review of Genetics, vol.32, issue.1, pp.495-519, 1998.
DOI : 10.1146/annurev.genet.32.1.495

L. Salichos and A. Rokas, Inferring ancient divergences requires genes with strong phylogenetic signals, Nature, vol.27, issue.7449, pp.327-331, 2013.
DOI : 10.1038/nature12130

L. Salichos, A. Stamatakis, and A. Rokas, Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees, Molecular Biology and Evolution, vol.31, issue.5, pp.1261-1271, 2014.
DOI : 10.1093/molbev/msu061

V. Sarilar, C. Bleykasten-grosshans, and C. Neuveglise, Evolutionary Dynamics of hAT DNA Transposon Families in Saccharomycetaceae, Genome Biology and Evolution, vol.7, issue.1, 2014.
DOI : 10.1093/gbe/evu273
URL : https://hal.archives-ouvertes.fr/hal-01204467

V. Sarilar, H. Devillers, K. Freel, J. Schacherer, and C. Neuveglise, Draft genome sequence of Lachancea lanzarotensis CBS 12615 T , an ascomycetous yeast isolated from grapes, Genome Announc, vol.3, pp.292-307, 2015.

D. Scannell, A. Frank, G. Conant, K. Byrne, M. Woolfit et al., Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication, Proceedings of the National Academy of Sciences, vol.104, issue.20, pp.8397-8402, 2007.
DOI : 10.1073/pnas.0608218104

D. Scannell, O. Zill, A. Rokas, C. Payen, M. Dunham et al., Genus, G3: Genes|Genomes|Genetics, vol.1, issue.1, pp.11-25, 2011.
DOI : 10.1534/g3.111.000273

C. Schluth-bolard, A. Labalme, M. Cordier, M. Till, G. Nadeau et al., Breakpoint mapping by next generation sequencing reveals causative gene disruption in patients carrying apparently balanced chromosome rearrangements with intellectual deficiency and/or congenital malformations, Journal of Medical Genetics, vol.50, issue.3, pp.144-150, 2013.
DOI : 10.1136/jmedgenet-2012-101351

A. Schneider, J. Puechberty, B. Ng, C. Coubes, V. Gatinois et al., genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder, American Journal of Medical Genetics Part A, vol.25, issue.12, pp.3031-3037, 2015.
DOI : 10.1002/ajmg.a.37350

M. Semon and K. Wolfe, Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor, Trends in Genetics, vol.23, issue.3, pp.108-112, 2007.
DOI : 10.1016/j.tig.2007.01.003

B. Snel, P. Bork, and M. Huynen, Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content, Genome Research, vol.12, issue.1, pp.17-25, 2002.
DOI : 10.1101/gr.176501

J. Souciet, B. Dujon, C. Gaillardin, M. Johnston, P. Baret et al., Comparative genomics of protoploid Saccharomycetaceae, Genome Res, vol.19, pp.1696-1709, 2009.
URL : https://hal.archives-ouvertes.fr/inria-00407511

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014.
DOI : 10.1093/bioinformatics/btu033

I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev, Natural history and evolutionary principles of gene duplication in fungi, Nature, vol.32, issue.7158, pp.54-61, 2007.
DOI : 10.1038/nature06107

M. Weng, J. Blazier, M. Govindu, and R. Jansen, Reconstruction of the Ancestral Plastid Genome in Geraniaceae Reveals a Correlation between Genome Rearrangements, Repeats, and Nucleotide Substitution Rates, Molecular Biology and Evolution, vol.31, issue.3, pp.645-659, 2014.
DOI : 10.1093/molbev/mst257

J. Wisecaver, J. Slot, and A. Rokas, The Evolution of Fungal Metabolic Pathways, PLoS Genetics, vol.39, issue.12, p.1004816, 2014.
DOI : 10.1371/journal.pgen.1004816.s014

K. Wolfe and D. Shields, Molecular evidence for an ancient duplication of the entire yeast genome, Nature, vol.387, issue.6634, pp.708-713, 1997.
DOI : 10.1038/42711

H. Wong, H. Marie-nelly, S. Herbert, P. Carrivain, H. Blanc et al., A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus, Current Biology, vol.22, issue.20, pp.1881-1890, 2012.
DOI : 10.1016/j.cub.2012.07.069
URL : https://hal.archives-ouvertes.fr/pasteur-01420017

Z. Yang, PAML: a program package for phylogenetic analysis by maximum likelihood, Bioinformatics, vol.13, issue.5, pp.555-556, 1997.
DOI : 10.1093/bioinformatics/13.5.555

E. Zuckerkandl and L. Pauling, Molecular disease, evolution, and genetic heterogeneity, Horizons in biochemistry, pp.189-225, 1962.