C. Aimé and F. Austerlitz, Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans, Eur. J. Hum. Genet, vol.25, pp.360-365, 2017.

C. Aime, G. Laval, P. E. Verdu, P. Segurel, L. Chaix et al., Human Genetic Data Reveal Contrasting Demographic Patterns between Sedentary and Nomadic Populations That Predate the Emergence of Farming, Mol. Biol. Evol, vol.30, pp.2629-2644, 2013.

C. Aimé, P. Verdu, L. Ségurel, B. Martinez-­cruz, T. Hegay et al., Microsatellite data show recent demographic expansions in sedentary but not in nomadic human populations in Africa and Eurasia, Eur. J. Hum. Genet, vol.22, pp.1201-1207, 2014.

C. Batini, J. Lopes, D. M. Behar, F. Calafell, L. B. Jorde et al., Insights into the Demographic History of African Pygmies from Complete Mitochondrial Genomes, Mol. Biol. Evol, vol.28, pp.1099-1110, 2011.

M. A. Beaumont, Joint determination of topology, divergence time, and immigration in population trees, Genetics, and Human Prehistory, pp.135-154, 2008.

M. A. Beaumont, W. Zhang, and D. J. Balding, Approximate Bayesian Computation in Population, Genetics, vol.162, pp.2025-2035, 2002.

A. C. Beichman, T. N. Phung, and K. E. Lohmueller, Comparison of Single Genome and Allele Frequency Data Reveals Discordant Demographic Histories, G3, vol.7, pp.3605-3620, 2017.

A. Bhaskar and Y. S. Song, Descartes' rule of signs and the identifiability of population demographic models from genomic variation data, Ann. Stat, vol.42, pp.2469-2493, 2014.

A. Bhaskar, Y. Wang, and Y. S. Song, Efficient inference of population size histories and locus-­specific mutation rates from large-­sample genomic variation data, Genome Res, vol.25, pp.268-279, 2015.

M. Blum, Approximate Bayesian computation: a nonparametric perspective, J. Am. Stat. Assoc.? ?, vol.105, pp.1178-1187, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00373301

M. Blum and O. François, Non-­linear regression models for Approximate Bayesian Computation, Stat. Comput, vol.20, pp.63-73, 2010.

M. Blum, M. A. Nunes, D. Prangle, and S. A. Sisson, A Comparative Review of Dimension Reduction Methods in Approximate Bayesian Computation, Stat. Sci, vol.28, pp.189-208, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00861839

S. Boitard, W. Rodríguez, F. Jay, S. Mona, and F. Austerlitz, Inferring Population Size History from Large Samples of Genome-­Wide Molecular Data-­ An Approximate Bayesian Computation Approach, PLoS Genet, vol.12, p.1005877, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01605807

S. R. Browning and B. L. Browning, 09/2015. Accurate Non-­parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent, Am. J. Hum. Genet, vol.97, pp.404-418

S. Carmi, K. Y. Hui, E. Kochav, X. Liu, J. Xue et al., Sequencing an Ashkenazi reference panel supports population-­targeted personal genomics and illuminates Jewish and European origins, Nat. Commun, vol.5, p.4835, 2014.

L. Chikhi, W. Rodríguez, S. Grusea, P. Santos, S. Boitard et al., The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice, Heredity, vol.120, pp.13-24, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01633154

, A global reference for human genetic variation, Nature, vol.526, pp.68-74, 2015.

J. Cornuet, F. Santos, M. A. Beaumont, C. P. Robert, J. Marin et al., Inferring population history with DIY ABC: a user-­friendly approach to approximate Bayesian computation, Bioinformatics, vol.24, p.2713, 2008.

M. P. Cox, D. A. Morales, A. E. Woerner, J. Sozanski, J. D. Wall et al., Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-­Saharan African Foraging and Farming Populations, PLoS One, vol.4, p.6366, 2009.

K. Csilléry, M. Blum, O. E. Gaggiotti, and O. François, Approximate Bayesian computation (ABC) in practice, Trends Ecol. Evol, vol.25, pp.410-418, 2010.

K. Csilléry, O. François, and M. Blum, 06/2012. abc: an R package for approximate Bayesian computation (ABC): ? R package: abc?, Methods Ecol. Evol, vol.3, pp.475-479

O. Delaneau and J. Marchini, Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel, Nat. Commun. ?, vol.5, p.3934, 2014.

O. Delaneau, J. Zagury, and J. Marchini, Improved whole-­chromosome phasing for disease and population genetic studies, Nat. Methods, vol.10, pp.5-6, 2013.

M. A. Depristo, E. Banks, R. Poplin, K. V. Garimella, J. R. Maguire et al., A framework for variation discovery and genotyping using next-­generation DNA sequencing data, Nat. Genet, vol.43, pp.491-498, 2011.

R. Drmanac, A. B. Sparks, M. J. Callow, A. L. Halpern, N. L. Burns et al., Human Genome Sequencing Using Unchained Base Reads on Self-­Assembling DNA Nanoarrays, Science, vol.327, pp.78-81, 2010.

L. Excoffier, I. Dupanloup, E. Huerta-­sanchez, V. C. Sousa, and M. Foll, Robust Demographic Inference from Genomic and SNP Data, PLoS Genet, vol.9, p.1003905, 2013.

L. Excoffier, A. Estoup, and J. Cornuet, Bayesian Analysis of an Admixture Model With Mutations and Arbitrarily Linked Markers, Genetics, vol.169, pp.1727-1738, 2005.

L. Excoffier and S. Schneider, Why hunter-­gatherer populations do not show signs of Pleistocene demographic expansions, Proc. Natl. Acad. Sci. U. S. A, vol.96, pp.10597-10602, 1999.

M. C. Fontaine, A. Snirc, A. Frantzis, E. Koutrakis, B. Öztürk et al., History of expansion and anthropogenic collapse in a top marine predator of the Black Sea estimated from genetic data, Proc. Natl. Acad. Sci. U. S. A, vol.109, pp.2569-2576, 2012.

K. A. Frazer, D. G. Ballinger, D. R. Cox, D. A. Hinds, L. L. Stuve et al., A second generation human haplotype map of over 3.1 million SNPs, Nature, vol.449, pp.851-861, 2007.

L. M. Gattepaille, M. Jakobsson, and M. Blum, Inferring population size changes with sequence and SNP data: lessons from human bottlenecks, Heredity, vol.110, pp.409-419, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00809457

E. Gazave, L. Ma, D. Chang, A. Coventry, F. Gao et al., Neutral genomic regions refine models of recent rapid human population growth, Proceedings of the National Academy of Sciences, vol.111, pp.757-762, 2014.

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 Genet, vol.5, p.1000695, 2009.

K. Harris and R. Nielsen, Inferring demographic history from a spectrum of shared haplotype lengths, PLoS Genet, vol.9, p.1003521, 2013.

A. G. Hinch, A. Tandon, N. Patterson, Y. Song, N. Rohland et al., The landscape of recombination in African Americans, Nature, vol.476, pp.170-175, 2011.

A. Keinan, J. C. Mullikin, N. Patterson, and D. Reich, Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans, Nat. Genet, vol.10, pp.1251-1255, 2007.

A. Kong, D. F. Gudbjartsson, J. Sainz, G. M. Jonsdottir, S. A. Gudjonsson et al., A high-­resolution recombination map of the human genome, Nat. Genet, vol.31, pp.241-247, 2002.

M. Lapierre, A. Lambert, and G. Achaz, Accuracy of demographic inferences from the site frequency spectrum: the case of the Yoruba population, Genetics, vol.206, pp.439-449, 2017.

P. Liao, G. A. Satten, and Y. Hu, PhredEM: a phred-score-informed genotype-calling approach for next-generation sequencing studies, Genet. Epidemiol, vol.41, pp.375-387, 2017.

H. Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, vol.27, pp.2987-2993, 2011.

H. Li and R. Durbin, Inference of human population history from individual whole-­genome sequences, Nature, vol.475, pp.493-496, 2011.

S. Li and M. Jakobsson, Estimating demographic parameters from large-­scale population genomic data using Approximate Bayesian Computation, BMC Genet, vol.13, p.22, 2012.

X. Liu and Y. Fu, Exploring population size changes using SNP frequency spectra, Nat. Genet, vol.47, pp.555-559, 2015.
DOI : 10.1038/ng.3254

URL : http://europepmc.org/articles/pmc4414822?pdf=render

I. M. Macleod, D. M. Larkin, H. A. Lewin, B. J. Hayes, and M. E. Goddard, Inferring Demography from Runs of Homozygosity in Whole-­Genome Sequence, with Correction for Sequence Errors, Mol. Biol. Evol, vol.30, pp.2209-2223, 2013.

P. Marjoram and J. D. Wall, Fast" coalescent" simulation, BMC Genet, vol.7, p.1, 2006.

E. R. Martin, D. D. Kinnamon, M. A. Schmidt, E. H. Powell, S. Zuchner et al., SeqEM: an adaptive genotype-­calling approach for next-­generation sequencing studies, Bioinformatics, vol.26, pp.2803-2810, 2010.

O. Mazet, W. Rodriguez, S. Grusea, S. Boitard, and L. Chikhi, On the importance of being structured: instantaneous coalescence rates and human evolution-lessons for ancestral population size inference, Heredity, vol.116, pp.362-371, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01633153

G. Mcvean and N. J. Cardin, Approximating the coalescent with recombination, Philos. Trans. R. Soc. Lond. B Biol. Sci, vol.360, pp.1387-1393, 2005.

P. F. Palamara, T. Lencz, A. Darvasi, and &. I. Pe, Length Distributions of Identity by Descent Reveal Fine-­Scale Demographic History, Am. J. Hum. Genet, vol.91, pp.809-822, 2012.

F. P. Palstra, E. Heyer, and F. Austerlitz, Statistical Inference on Genetic Data Reveals the Complex Demographic History of Human Populations in Central Asia, Mol. Biol. Evol, vol.32, pp.1411-1424, 2015.

E. Patin, G. Laval, L. B. Barreiro, A. Salas, O. Semino et al., Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a Multilocus Resequencing Data Set, PLoS Genet, vol.5, p.1000448, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00397240

E. Patin, K. J. Siddle, G. Laval, H. Quach, C. Harmant et al., The impact of agricultural emergence on the genetic history of African rainforest hunter-­gatherers and agriculturalists, Nat. Commun. ?, vol.5, p.3163, 2014.
URL : https://hal.archives-ouvertes.fr/halshs-01178754

P. Pudlo, J. Marin, A. Estoup, J. Cornuet, M. Gautier et al., Reliable ABC model choice via random forests, Bioinformatics, vol.32, pp.859-866, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01067925

M. D. Rasmussen, M. J. Hubisz, I. Gronau, and A. Siepel, Genome-­wide inference of ancestral recombination graphs, PLoS Genet, vol.10, p.1004342, 2014.

A. Scally and R. Durbin, Revising the human mutation rate: implications for understanding human evolution, Nat. Rev. Genet, vol.13, pp.745-753, 2012.

S. F. Schaffner, C. Foo, S. Gabriel, D. Reich, M. J. Daly et al., Calibrating a coalescent simulation of human genome sequence variation, Genome Res, vol.15, p.1576, 2005.

S. Schiffels and R. Durbin, Inferring human population size and separation history from multiple genome sequences, Nat. Genet, vol.46, pp.919-925, 2014.
DOI : 10.1101/005348

URL : https://www.biorxiv.org/content/biorxiv/early/2014/05/23/005348.full.pdf

C. M. Schlebusch and M. Jakobsson, Tales of Human Migration, Admixture, and Selection in Africa, Annu. Rev. Genomics Hum. Genet, vol.19, pp.405-428, 2018.

J. G. Schraiber and J. M. Akey, Methods and models for unravelling human evolutionary history, Nat. Rev. Genet. ?, vol.16, p.727, 2015.

L. Ségurel, M. J. Wyman, and M. Przeworski, Determinants of Mutation Rate Variation in the Human Germline, Annu. Rev. Genomics Hum. Genet, vol.15, pp.47-70, 2014.

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, Mol. Ecol. ?, vol.24, pp.328-345, 2014.

S. Sheehan, K. Harris, and Y. S. Song, Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach, Genetics, vol.194, pp.647-662, 2013.

S. Sheehan and Y. S. Song, Deep learning for population genetic inference, PLoS Comput. Biol, vol.12, p.1004845, 2016.
DOI : 10.1371/journal.pcbi.1004845

URL : https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004845&type=printable

P. Sjödin, A. E. Sjöstrand, M. Jakobsson, and M. Blum, Resequencing Data Provide No Evidence for a Human Bottleneck in Africa during the Penultimate Glacial Period, Mol. Biol. Evol.?, vol.29, pp.1851-1860, 2012.

P. Soares, F. Alshamali, J. B. Pereira, V. Fernandes, N. M. Silva et al., The Expansion of mtDNA Haplogroup L3 within and out of Africa, Mol. Biol. Evol, vol.29, pp.915-927, 2012.

M. Sunnåker, A. G. Busetto, E. Numminen, J. Corander, M. Foll et al., Approximate Bayesian Computation, PLoS Comput. Biol, vol.9, p.1002803, 2013.

J. A. Tennessen, A. W. Bigham, O. Connor, T. D. Fu, W. Kenny et al., Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes, Science, vol.337, pp.64-69, 2012.

J. Terhorst, J. A. Kamm, and Y. S. Song, Robust and scalable inference of population history from hundreds of unphased whole genomes, Nat. Genet, vol.49, pp.303-309, 2017.

C. Theunert, K. Tang, M. Lachmann, S. Hu, and M. Stoneking, Inferring the History of Population Size Change from Genome-­Wide SNP Data, Mol. Biol. Evol, vol.29, pp.3653-3667, 2012.

K. R. Veeramah and M. F. Hammer, The impact of whole-­genome sequencing on the reconstruction of human population history, Nat. Rev. Genet, vol.15, pp.149-162, 2014.

J. D. Wall, L. F. Tang, B. Zerbe, M. N. Kvale, P. Kwok et al., Estimating genotype error rates from high-­coverage next-­generation sequence data, Genome Res, vol.11, pp.1734-1739, 2014.

, Group Proba Ncurrent Ninterm Nbot Nancient TExp2