S. Aeschbacher, M. A. Beaumont, and A. Futschik, A novel approach for choosing summary statistics in approximate Bayesian computation, Genetics, vol.192, issue.3, 2012.

S. Aeschbacher, J. P. Selby, J. H. Willis, and G. Coop, Population-genomic inference of the strength and timing of selection against gene flow, Proceedings of the National Academy of Sciences of the United States of America, vol.114, 2017.

N. Alcala, J. D. Jensen, A. Telenti, and S. Vuilleumier, The genomic signature of population reconnection following isolation: from theory to HIV, Bethesda), vol.3, issue.1, 2016.

P. Andolfatto, Adaptive evolution of non-coding DNA in Drosophila, Nature, vol.437, issue.7062, 2005.

N. Barton and B. O. Bengtsson, The barrier to genetic exchange between hybridising populations, Heredity, vol.57, issue.3, 1986.

N. Fagundes, N. Ray, M. Beaumont, S. Neuenschwander, F. M. Salzano et al., Statistical evaluation of alternative models of human evolution, Proceedings of the National Academy of Sciences of the United States of America, vol.104, issue.45, 2007.

C. Fraïsse, K. Belkhir, J. J. Welch, and N. Bierne, Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels, Molecular Ecology, vol.25, issue.1, pp.269-286, 2016.

C. Fraïsse, C. Roux, J. J. Welch, and N. Bierne, Gene-flow in a mosaic hybrid zone: is local introgression adaptive?, Genetics, vol.197, issue.3, 2014.

P. Gayral, J. Melo-ferreira, S. Glémin, N. Bierne, M. Carneiro et al., Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap, PLOS Genetics, vol.9, issue.4, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00866204

R. N. Gutenkunst, R. D. Hernandez, S. H. Williamson, and C. D. Bustamante, Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data, PLOS Genetics, vol.5, issue.10, 2009.

E. Han, J. S. Sinsheimer, and J. Novembre, Characterizing bias in population genetic inferences from low-coverage sequencing data, Molecular Biology and Evolution, vol.31, issue.3, 2013.

G. Hewitt, The genetic legacy of the quaternary ice ages, Nature, vol.405, issue.6789, 2000.

J. Hey and R. Nielsen, Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics, Proceedings of the National Academy of Sciences of the United States of America, vol.104, issue.8, 2007.

R. R. Hudson, Generating samples under a Wright-Fisher neutral model of genetic variation, Bioinformatics, vol.18, issue.2, 2002.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, 2009.

S. Li and M. Jakobsson, Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation, BMC Genetics, vol.13, issue.1, 2012.

X. Li, Y. Jian, C. Xie, J. Wu, Y. Xu et al., Fast diffusion of domesticated maize to temperate zones, Scientific Reports, vol.7, issue.1, 2017.
DOI : 10.1038/s41598-017-02125-0
URL : https://doi.org/10.1038/s41598-017-02125-0

S. Lukic and J. Hey, Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion, Genetics, vol.192, issue.2, pp.619-639, 2012.

I. Marino, A. Benazzo, C. Agostini, M. Mezzavilla, S. M. Hoban et al., Evidence for past and present hybridization in three Antarctic icefish species provides new perspectives on an evolutionary radiation, Molecular Ecology, vol.22, 1920.
DOI : 10.1111/mec.12458

R. C. Mccoy, N. R. Garud, J. L. Kelley, C. L. Boggs, and D. A. Petrov, Genomic inference accurately predicts the timing and severity of a recent bottleneck in a nonmodel insect population, Molecular Ecology, vol.23, issue.1, 2014.

L. Naduvilezhath, L. E. Rose, and D. Metzler, Jaatha: a fast composite-likelihood approach to estimate demographic parameters, Molecular Ecology, vol.20, issue.13, 2011.

. Fraïsse, PeerJ, 2018.

R. Nielsen, T. Korneliussen, A. Albrechtsen, Y. Li, and J. Wang, SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data, PLOS ONE, vol.7, issue.7, 2012.

R. Nielsen and J. Wakeley, Distinguishing migration from isolation: a Markov chain Monte Carlo approach, Genetics, vol.158, issue.2, pp.885-896, 2001.

M. A. Nunes and D. J. Balding, On optimal selection of summary statistics for approximate Bayesian computation, Statistical Applications in Genetics and Molecular Biology, vol.9, issue.1, 2010.

X. Qi, H. An, A. P. Ragsdale, T. E. Hall, R. N. Gutenkunst et al., Genomic inferences of domestication events are corroborated by written records in Brassica rapa, Molecular Ecology, vol.26, issue.13, 2017.

S. E. Ramos-onsins, B. E. Stranger, T. Mitchell-olds, and M. Aguadé, Multilocus analysis of variation and speciation in the closely related species Arabidopsis halleri and A. lyrata, Genetics, vol.166, issue.1, 2004.

J. D. Robinson, L. Bunnefeld, J. Hearn, G. N. Stone, and M. J. Hickerson, ABC inference of multi-population divergence with admixture from unphased population genomic data, Molecular Ecology, vol.23, issue.18, 2014.

J. Romiguier, P. Gayral, M. Ballenghien, A. Bernard, V. Cahais et al., Comparative population genomics in animals uncovers the determinants of genetic diversity, Nature, vol.515, issue.7526, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01313724

J. Ross-ibarra, S. I. Wright, J. P. Foxe, A. Kawabe, L. Derose-wilson et al., Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata, PLOS ONE, vol.3, issue.6, 2008.

C. Rougeux, L. Bernatchez, and P. Gagnaire, Modeling the multiple facets of speciation-withgene-flow toward inferring the divergence history of lake Whitefish species pairs (Coregonus clupeaformis), Genome Biology and Evolution, vol.9, issue.8, pp.2057-2074, 2017.

C. Roux, V. Castric, M. Pauwels, S. I. Wright, P. Saumitou-laprade et al., Does speciation between Arabidopsis halleri and Arabidopsis lyrata coincide with major changes in a molecular target of adaptation?, PLOS ONE, vol.6, issue.11, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00644381

C. Roux, C. Fraïsse, V. Castric, X. Vekemans, G. H. Pogson et al., Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone, Journal of Evolutionary Biology, vol.27, issue.8, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01110882

C. Roux, C. Fraïsse, J. Romiguier, Y. Anciaux, N. Galtier et al., Shedding light on the grey zone of speciation along a continuum of genomic divergence, PLOS Biology, vol.14, issue.12, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01899028

C. Roux, G. Tsagkogeorga, N. Bierne, and N. Galtier, Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species, Molecular Biology and Evolution, vol.30, issue.7, 2013.

A. Shafer, L. M. Gattepaille, R. Stewart, and J. Wolf, Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus, Molecular Ecology, vol.24, issue.2, 2015.

. Fraïsse, PeerJ, 2018.

A. Simon, N. Bierne, and J. J. Welch, Coadapted genomes and selection on hybrids: Fisher's geometric model explains a variety of empirical patterns, 2017.

A. Simon and M. Duranton, Digest: Demographic inferences accounting for selection at linked sites, Evolution, vol.72, issue.6, pp.1330-1332, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01865718

D. Skibinski, J. A. Beardmore, and T. F. Cross, Aspects of the population genetics of Mytilus (Mytilidae; Mollusca) in the British Isles, Biological Journal of the Linnean Society, vol.19, issue.2, 1983.

M. L. Smith, M. Ruffley, A. Espíndola, D. C. Tank, J. Sullivan et al., Demographic model selection using random forests and the site frequency spectrum, Molecular Ecology, vol.26, issue.17, 2017.

V. C. Sousa, M. Carneiro, N. Ferrand, and J. Hey, Identifying loci under selection against gene flow in isolation-with-migration models, Genetics, vol.194, issue.1, pp.211-233, 2013.

V. Sousa and J. Hey, Understanding the origin of species with genome-scale data: modelling gene flow, Nature Reviews Genetics, vol.14, issue.6, 2013.

F. Tajima, Evolutionary relationship of DNA sequences in finite populations, Genetics, vol.105, issue.2, pp.437-460, 1983.

F. Tajima, DNA polymorphism in a subdivided population: the expected number of segregating sites in the two-subpopulation model, Genetics, vol.123, issue.1, pp.229-240, 1989.

F. Tajima, The effect of change in population size on DNA polymorphism, Genetics, vol.123, issue.3, pp.597-601, 1989.

A. Tellier, P. Pfaffelhuber, B. Haubold, L. Naduvilezhath, L. E. Rose et al., Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum, PLOS ONE, vol.6, issue.5, 2011.

M. Tine, H. Kuhl, P. Gagnaire, B. Louro, E. Desmarais et al., European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation, Nature Communications, vol.5, issue.1, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01922671

G. Tsagkogeorga, V. Cahais, and N. Galtier, The population genomics of a fast evolver: high levels of diversity, functional constraint, and molecular adaptation in the tunicate Ciona intestinalis, 2012.

, Genome Biology and Evolution, vol.4, issue.8

J. Wakeley and J. Hey, Estimating ancestral population parameters, Genetics, vol.145, issue.3, pp.847-855, 1997.

Y. Wang and J. Hey, Estimating divergence parameters with small samples from a large number of loci, Genetics, vol.184, issue.2, pp.363-379, 2010.

G. A. Watterson, On the number of segregating sites in genetical models without recombination, Theoretical Population Biology, vol.7, issue.2, pp.256-276, 1975.

D. Wegmann, C. Leuenberger, and L. Excoffier, Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood, Genetics, vol.182, issue.4, 2009.

C. Wu, The genic view of the process of speciation, Journal of Evolutionary Biology, vol.14, issue.6, 2001.

A. T. Xue and M. J. Hickerson, The aggregate site frequency spectrum for comparative population genomic inference, Molecular Ecology, vol.24, issue.24, 2015.