S. Aflitos, E. Schijlen, H. Jong, D. De-ridder, and S. Smit, Exploring 690 genetic variation in the tomato (Solanum section Lycopersicon) clade by 691 whole-genome sequencing, Plant Journal, vol.80, pp.136-148, 2014.

J. A. Agren, W. Wang, D. Koenig, B. Neuffer, and D. Weigel, Mating system 693 shifts and transposable element evolution in the plant genus Capsella, 2014.

, Bmc Genomics, vol.15

C. Alonso-blanco, J. Andrade, C. Becker, F. Bemm, and J. Bergelson, 135 696 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis 697 thaliana, Cell, vol.166, pp.481-491, 20161.

N. H. Barton, Linkage and the Limits to Natural-Selection, Genetics, vol.140, pp.699-821, 1995.

Y. Brandvain and S. I. Wright, The limits of natural selection in a 701 nonequilibrium world, Trends in Genetics, vol.32, pp.201-210, 2016.

J. L. Campos-parada and B. Charlesworth, The effects on neutral variability 703 of recurrent selective sweeps and background selection, p.358309, 2019.

A. R. Carson, E. N. Smith, H. Matsui, S. K. Braekkan, and K. Jepsen, Effective 705 filtering strategies to improve data quality from population-based whole 706 exome sequencing studies, Bmc Bioinformatics, vol.15, 2014.

D. Castellano, J. James, and A. Eyre-walker, Nearly Neutral Evolution Across 708 the Drosophila melanogaster Genome, Molecular Biology and Evolution, pp.709-164, 2018.

B. Charlesworth, M. T. Morgan, and D. Charlesworth, The Effect, vol.711, 1993.

, Deleterious Mutations on Neutral Molecular Variation, Genetics, vol.134, pp.712-1289

J. Chen, S. Glemin, and M. Lascoux, Genetic Diversity and the Efficacy of 714 Purifying Selection across Plant and Animal Species, Molecular Biology 715 and Evolution, vol.34, pp.1417-1428, 2017.

J. M. Chia, C. Song, P. J. Bradbury, D. Costich, and N. De-leon, Maize 717 HapMap2 identifies extant variation from a genome in flux, Genetics, vol.718, pp.803-238, 2012.

J. M. Comeron, Background selection as null hypothesis in population 720 genomics: insights and challenges from Drosophila studies, Phil. Trans. R, 2017.

, Soc. B, vol.372, p.20160471

G. Coop, Does linked selection explain the narrow range of genetic diversity 723 across species? bioRxiv doi, 2016.

R. B. Corbett-detig, D. L. Hartl, and T. B. Sackton, Natural Selection 725 Constrains Neutral Diversity across A Wide Range of Species, Plos Biology, vol.726, p.13, 2015.

I. Cvijovic, B. H. Good, and M. M. Desai, The effect of strong purifying 728 selection on genetic diversity, Genetics, vol.209, pp.1235-1278, 2018.

R. Do, D. Balick, H. Li, I. Adzhubei, S. Sunyaev et al., No evidence that 730 selection has been less effective at removing deleterious mutations in 731 Europeans than in Africans, Nature genetics, vol.47, p.126, 2015.

H. Ellegren and N. Galtier, Determinants of genetic diversity, Nature 733 Reviews Genetics, vol.17, pp.422-433, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01900639

L. M. Evans, G. T. Slavov, E. Rodgers-melnick, J. Martin, and P. Ranjan, 735 Population genomics of Populus trichocarpa identifies signatures of 736 selection and adaptive trait associations, Nature Genetics, vol.46, pp.1089-1096, 2014.

A. Eyre-walker, The genomic rate of adaptive evolution, Trends in Ecology, vol.738, pp.569-575, 2006.

A. Eyre-walker and P. D. Keightley, The distribution of fitness effects of 740 new mutations, Nature Reviews Genetics, vol.8, pp.610-618, 2007.

A. Eyre-walker and P. D. Keightley, Estimating the Rate of Adaptive 742, 2009.

, Molecular Evolution in the Presence of Slightly Deleterious Mutations and 743 Population Size Change, Molecular Biology and Evolution, vol.26, pp.2097-2108

P. Faivre-rampant, G. Zaina, V. Jorge, S. Giacomello, and V. Segura, New 745 resources for genetic studies in Populus nigra: genome-wide SNP 746 discovery and development of a 12k Infinium array, Molecular Ecology, vol.747, pp.1023-1036, 2016.

J. C. Fay and C. I. Wu, Hitchhiking under positive Darwinian selection, Genetics, vol.749, pp.1405-1413, 2000.

N. Galtier, Adaptive Protein Evolution in Animals and the Effective 751 Population Size Hypothesis, Plos Genetics, vol.12, 2016.

J. H. Gillespie, The role of population size in molecular evolution, 753 Theoretical Population Biology, vol.55, pp.145-156, 1999.

J. H. Gillespie, Genetic drift in an infinite population: The 755 pseudohitchhiking model, Genetics, vol.155, pp.909-919, 2000.

J. H. Gillespie, Is the population size of a species relevant to its evolution?, Evolution, vol.55, pp.2161-2169, 2001.

J. H. Gillespie, Population genetics : a concise guide, 2004.

I. Gordo and F. Dionisio, Nonequilibrium model for estimating parameters of 761 deleterious mutations, Physical Review. E, Statistical, Nonlinear, and Soft 762 Matter Physics, vol.71, p.31907, 2005.

T. I. Gossmann, M. Woolfit, and A. Eyre-walker, Quantifying the variation in the 764 effective population size within a genome, Genetics, vol.189, pp.1389-1402, 2011.

B. C. Haller and P. W. Messer, SLiM 3: Forward Genetic Simulations 766 Beyond the Wright-Fisher Model, Molecular Biology and Evolution, vol.36, pp.767-632, 2019.

W. Huang, A. Massouras, Y. Inoue, J. Peiffer, and M. Ramia, Natural 769 variation in genome architecture among 205 Drosophila melanogaster 770 Genetic Reference Panel lines, Genome Research, vol.24, pp.1193-1208, 2014.

J. James, D. Castellano, and A. Eyre-walker, DNA sequence diversity and the 772 efficiency of natural selection in animal mitochondrial DNA, Heredity, vol.118, pp.773-88, 2017.

J. D. Jensen, Y. Kim, V. B. Dumont, C. F. Aquadro, and C. D. Bustamante, 775 Distinguishing between selective sweeps and demography using DNA 776 polymorphism data, Genetics, vol.170, pp.1401-1410, 2005.

J. D. Jensen, B. A. Payseur, W. Stephan, C. F. Aquadro, and M. Lynch, The 778 importance of the Neutral Theory in 1968 and 50 years on: A response to 779 Kern and Hahn, Evolution, vol.73, pp.111-114, 2018.

A. D. Kern and M. W. Hahn, The Neutral Theory in Light of Natural 781 Selection, Molecular Biology and Evolution, vol.35, pp.1366-1371, 2018.

M. Kimura, Model of Effectively Neutral Mutations in Which Selective 783 Constraint Is Incorporated, Proceedings of the National Academy of 784 Sciences of the United States of America, vol.76, pp.3440-3444, 1979.

M. Kimura, The Neutral Theory of Molecular Evolution, 1983.

M. Kimura and T. Ohta, Protein Polymorphism as a Phase of Molecular 788 Evolution, Nature, vol.229, p.467, 1971.

D. Koenig, J. Hagmann, R. Li, F. Bemm, and T. Slotte, Long-term balancing 790 selection drives evolution of immunity genes in Capsella, 2018.

M. Kreitman, The neutral theory is dead. Long live the neutral theory, Bioessays, vol.792, pp.678-683, 1996.

H. Li and R. Durbin, Fast and accurate long-read alignment with Burrows-794 Wheeler transform, Bioinformatics, vol.26, pp.589-595, 2010.

E. S. Mace, S. S. Tai, E. K. Gilding, Y. H. Li, and P. J. Prentis, Whole-genome 796 sequencing reveals untapped genetic potential in Africa's indigenous 797 cereal crop sorghum, Nature Communications, vol.4, 2013.

S. H. Martin, K. K. Dasmahapatra, N. J. Nadeau, C. Salazar, and J. R. Walters, 799 Genome-wide evidence for speciation with gene flow in Heliconius 800 butterflies, Genome Research, vol.23, pp.1817-1828, 2013.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, and K. Cibulskis, The, vol.802, 2010.

, Genome Analysis Toolkit: A MapReduce framework for analyzing next-803 generation DNA sequencing data, Genome Research, vol.20, pp.1297-1303

G. G. Murray, A. E. Soares, B. J. Novak, N. K. Schaefer, J. A. Cahill et al.,

R. Demboski, A. Doll, R. R. Da-fonseca, T. L. Fulton, M. T. Gilbert et al., , p.806

B. Heintzman, G. Letts, B. L. Mcintosh, M. O'connell, M. Peck et al.,

K. M. Rice, A. G. Santos, S. H. Sohrweide, R. B. Vohr, R. E. Corbett-detig et al., Natural selection shaped the rise and fall of 809 passenger pigeon genomic diversity, Science, vol.358, issue.6365, pp.951-954, 2017.

M. Nei, Y. Suzuki, and M. Nozawa, The Neutral Theory of Molecular 811 Evolution in the Genomic Era, Annual Review of Genomics and Human 812 Genetics, vol.11, pp.265-289, 2010.

P. Y. Novikova, N. Hohmann, V. Nizhynska, T. Tsuchimatsu, and J. Ali, 814 Sequencing of the genus Arabidopsis identifies a complex history of 815 nonbifurcating speciation and abundant trans-specific polymorphism, 2016.