P. Almeida, C. Gonçalves, S. Teixeira, D. Libkind, and M. Bontrager, A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum, Nature Communications, vol.22, p.4044, 2014.
DOI : 10.1038/ncomms5044
URL : https://hal.archives-ouvertes.fr/hal-01002466

E. Andersen, J. Gerke, J. Shapiro, J. Crissman, and R. Ghosh, Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity, Nature Genetics, vol.77, issue.3, pp.285-90, 2012.
DOI : 10.1038/nature02697
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365839

E. Baack and L. Rieseberg, A genomic view of introgression and hybrid speciation, Current Opinion in Genetics & Development, vol.17, issue.6, pp.513-518, 2007.
DOI : 10.1016/j.gde.2007.09.001

E. Boyle, S. Weng, J. Gollub, H. Jin, and D. Botstein, GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes, Bioinformatics, vol.20, issue.18, pp.3710-3715, 2004.
DOI : 10.1093/bioinformatics/bth456

J. Cao, K. Schneeberger, S. Ossowski, T. Günther, and S. Bender, Whole-genome sequencing of multiple Arabidopsis thaliana populations, Nature Genetics, vol.155, issue.10, pp.956-63, 2011.
DOI : 10.1016/j.ajhg.2009.01.005

J. Castresana, 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

J. Cherry, C. Ball, S. Weng, G. Juvik, and R. Schmidt, Genetic and physical maps of Saccharomyces cerevisiae, Nature, vol.387, pp.67-73, 1997.

G. Cromie, K. Hyma, C. Ludlow, C. Garmendia-torres, and T. Gilbert, Assessed by RAD-seq, G3: Genes|Genomes|Genetics, vol.3, issue.12, pp.2163-2171, 2013.
DOI : 10.1534/g3.113.007492

D. Da, G. Taboada, R. Doallo, and D. Posada, jModelTest 2: more models, new heuristics and parallel computing, Nat Methods, vol.9, p.772, 2012.

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, Yeast evolutionary genomics, Nature Reviews Genetics, vol.104, issue.7, pp.512-524, 2010.
DOI : 10.1038/nrg2811

L. Duret and N. Galtier, Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes, Annual Review of Genomics and Human Genetics, vol.10, issue.1, pp.285-311, 2009.
DOI : 10.1146/annurev-genom-082908-150001
URL : https://hal.archives-ouvertes.fr/hal-00428399

R. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

J. Fay and J. Benavides, Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae, PLoS Genetics, vol.130, issue.1, p.5, 2005.
DOI : 0016-6731(1992)130[0285:EOTYRU]2.0.CO;2

P. Fearnhead, SequenceLDhot: detecting recombination hotspots, Bioinformatics, vol.22, issue.24, pp.3061-3066, 2006.
DOI : 10.1093/bioinformatics/btl540

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, P. Gonçalves, J. Sampaio, J. Dover, M. Johnston et al., Remarkably ancient balanced polymorphisms in a multi-locus gene network, Nature, vol.5, issue.7285, pp.54-58, 2010.
DOI : 10.1038/nature08791

D. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006.
DOI : 10.1093/molbev/msj030

S. Hutter, A. Vilella, and J. Rozas, Genome-wide DNA polymorphism analyses using VariScan, BMC Bioinformatics, vol.7, issue.1, p.409, 2006.
DOI : 10.1186/1471-2105-7-409

P. Jung, A. Fridedrich, C. Reisser, J. Hou, and J. Schacherer, Mitochondrial Genome Evolution in a Single Protoploid Yeast Species, G3: Genes|Genomes|Genetics, vol.2, issue.9, pp.1113-1127, 2012.
DOI : 10.1534/g3.112.003152

Y. Lesecque, D. Mouchiroud, and L. Duret, GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance, Molecular Biology and Evolution, vol.30, issue.6, pp.1409-1428, 2013.
DOI : 10.1093/molbev/mst056

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009.
DOI : 10.1093/bioinformatics/btp324

H. Li, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.
DOI : 10.1093/bioinformatics/btp352

G. Liti, D. Carter, A. Moses, J. Warringer, and L. Parts, Population genomics of domestic and wild yeasts, Nature, vol.26, issue.7236, pp.337-341, 2009.
DOI : 10.1038/nature07743

G. Liti and J. Schacherer, The rise of yeast population genomics, Comptes Rendus Biologies, vol.334, issue.8-9, pp.612-619, 2011.
DOI : 10.1016/j.crvi.2011.05.009

M. Lynch, W. Sung, K. Morris, N. Coffey, and C. Landry, A genome-wide view of the spectrum of spontaneous mutations in yeast, Proceedings of the National Academy of Sciences, vol.105, issue.27, pp.9272-9277, 2008.
DOI : 10.1073/pnas.0803466105

M. Lynch, The Origins of Genome Architecture, 2007.

J. Mccullough and I. Herskowitz, Mating pheromones of Saccharomyces kluyveri: pheromone interactions between Saccharomyces kluyveri and Saccharomyces cerevisiae, J Bacteriol, vol.138, pp.146-154, 1979.

G. Mcvean, S. Myers, S. Hunt, P. Deloukas, and D. Bentley, The Fine-Scale Structure of Recombination Rate Variation in the Human Genome, Science, vol.304, issue.5670, pp.581-584, 2004.
DOI : 10.1126/science.1092500

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.721-760, 2012.
DOI : 10.1128/MMBR.00022-12

C. Payen, G. Fischer, C. Marck, C. Proux, and D. Sherman, 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

J. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, pp.945-959, 2000.

S. Purcell, N. B. Todd-brown, K. Thomas, L. Ferreira, and M. , PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses, The American Journal of Human Genetics, vol.81, issue.3, pp.559-575, 2007.
DOI : 10.1086/519795

D. Ruderfer, S. Pratt, H. Seidel, and L. Kruglyak, Population genomic analysis of outcrossing and recombination in yeast, Nature Genetics, vol.132, issue.9, pp.1077-1081, 2006.
DOI : 10.1093/bioinformatics/18.2.337

J. Schacherer, J. Shapiro, D. Ruderfer, and L. Kruglyak, Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae, Nature, vol.13, issue.7236, pp.342-345, 2009.
DOI : 10.1038/nature07670
URL : https://hal.archives-ouvertes.fr/hal-00370158

D. Skelly, G. Merrihew, M. Riffle, C. Connelly, and E. Kerr, Integrative phenomics reveals insight into the structure of phenotypic diversity in budding yeast, Genome Research, vol.23, issue.9, pp.1496-504, 2013.
DOI : 10.1101/gr.155762.113

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

N. Sueoka, Intrastrand parity rules of DNA base composition and usage biases of synonymous codons, Journal of Molecular Evolution, vol.171, issue.3, pp.318-325, 1995.
DOI : 10.1007/BF00163236

F. Tajima, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989.

I. Tsai, D. Bensasson, A. Burt, and V. Koufopanou, Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle, Proceedings of the National Academy of Sciences, vol.105, issue.12, pp.4957-4962, 2008.
DOI : 10.1073/pnas.0707314105

Q. Wang, W. Liu, G. Liti, S. Wang, and F. Bai, in natural environments remote from human activity, Molecular Ecology, vol.16, issue.Botany, pp.5404-5417, 2012.
DOI : 10.1111/j.1365-294X.2012.05732.x

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

Z. Yang, PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007.
DOI : 10.1093/molbev/msm088