S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biol, vol.11, pp.1344-1349, 2010.

S. G. Atienza, R. De-la-rosa, L. Le-on, A. Mart-in, and A. Belaj, Identification of QTL for agronomic traits of importance for olive breeding, Mol. Breed, vol.34, pp.725-737, 2014.

E. Barghini, L. Natali, R. M. Cossu, T. Giordani, M. Pindo et al., The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome, Genome Biol. Evol, vol.6, pp.776-791, 2014.

G. Bartolini, G. Prevost, C. Messeri, and G. Carignani, Olive germplasm: cultivars and world-wide collections, vol.459, p.pp, 1998.

A. J. Bass, J. D. Storey, A. Dabney, and D. Robinson, qvalue: Q-value estimation for false discovery rate control, 2015.

A. Belaj, M. Dominguez-garc-ia, C. Atienza, and S. G. , Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits, Tree Genet. Genomes, vol.8, pp.365-378, 2012.

E. Bellucci, E. Bitocchi, and A. Ferrarini, Decreased nucleotide and expression diversity and modified coexpression patterns characterize domestication in the common bean, Plant Cell, vol.26, pp.1901-1912, 2014.

I. Ben-sadok, J. Celton, L. Essalouh, A. Z. El-aabidine, G. Garcia et al., QTL mapping of flowering and fruiting traits in olive, PLoS ONE, vol.8, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01209909

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B, vol.57, pp.289-300, 1995.

G. Besnard and R. Rubio-de-casas, Single vs multiple independent olive domestications: the jury is (still) out, New Phytol, vol.209, pp.466-470, 2016.

G. Besnard, P. Baradat, and A. Bervill-e, Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars, Theor. Appl. Genet, vol.102, pp.251-258, 2001.

G. Besnard, P. Baradat, C. Breton, B. Khadari, and A. Bervill-e, Olive domestication from structure of oleasters and cultivars using nuclear RAPDs and mitochondrial RFLPs, Genet. Sel. Evol, vol.33, pp.251-268, 2001.

G. Besnard, A. El-bakkali, H. Haouane, D. Baali-cherif, A. Moukhli et al., Population genetics of Mediterranean and Saharan olives: geographic patterns of differentiation and evidence for early generations of admixture, Ann. Bot, vol.112, pp.1293-1302, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268461

G. Besnard, P. Hern-andez, B. Khadari, G. Dorado, and V. Savolainen, Genomic profiling of plastid DNA variation in the Mediterranean olive tree, BMC Plant Biol, vol.11, 2011.

G. Besnard, B. Khadari, and M. Navascu-es, The complex history of the olive tree: from Late Quaternary diversification of Mediterranean lineages to primary domestication in the northern Levant, Proc. R. Soc. Ser. B, vol.280, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00801271

G. Besnard, J. Terral, and A. Cornille, On the origins and domestication of the olive: a review and perspectives, Ann. Bot, vol.121, pp.385-403, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01827090

C. Breton, M. Tersac, and A. Bervill-e, Genetic diversity and gene flow between the wild olive (oleaster, Olea europaea L.) and the olive: several Plio-Pleistocene refuge zones in the Mediterranean basin suggested by simple sequence repeats analysis, J. Biogeogr, vol.33, pp.1916-1928, 2006.

C. Breton, J. F. Terral, C. Pinatel, F. Bonhomme, F. Bervill-e et al., The origins of the domestication of the olive tree, C. R. Biol, vol.332, pp.1059-1064, 2009.

R. Carmona, A. Zafra, and P. Seoane, ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome. Front, Plant Sci, vol.6, 2015.

Y. Carri-on, M. Ntinou, and E. Badal, Olea europaea L. in the north Mediterranean Basin during the Pleniglacial and the Early-Middle Holocene, Quat. Sci. Rev, vol.29, pp.952-968, 2010.

M. A. Chapman, C. H. Pashley, J. Wenzler, J. Hvala, S. Tang et al., A genomic scan for selection reveals candidates for genes involved in the evolution of cultivated sunflower (Helianthus annuus), Plant Cell, vol.20, pp.2931-2945, 2008.

K. Chen and N. Rajewsky, The evolution of gene regulation by transcription factors and microRNAs, Nat. Rev. Genet, vol.8, pp.93-103, 2007.

M. R. Christie, M. L. Marine, S. E. Fox, R. A. French, and M. S. Blouin, A single generation of domestication heritably alters the expression of hundreds of genes, Nat. Commun, vol.7, 2016.

Y. Cl-ement, S. Gautier, and Y. Holtz, Evolutionary forces affecting synonymous variations in plant genomes, PLoS Genet, vol.13, 2017.

A. Conesa, P. Madrigal, and S. Tarazona, A survey of best practices for RNA-seq data analysis, Genome Biol, vol.17, 2016.

C. Team and R. , R: a language and environment for statistical computing, R Foundation for Statistical Computing, 2015.

A. Cornille, P. Gladieux, and M. J. Smulders, New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties, PLoS Genet, vol.8, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01209929

F. Cruz, I. Julca, and J. Garrido, Genome sequence of the olive tree Olea europaea. GigaScience, 5, 29, 2016.

P. Danecek, A. Auton, and G. Abecasis, Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves, Bioinformatics, vol.27, pp.1-11, 2011.

C. M. D-iez and B. S. Gaut, The jury may be out, but it is important that it deliberates: a response to Besnard and Rubio de Casas about olive domestication, New Phytol, vol.209, pp.471-473, 2016.

C. M. D-iez, A. Imperato, L. Rallo, D. Barranco, and I. Trujillo, Worldwide core collection of olive cultivars based on simple sequence repeat and morphological markers, Crop Sci, vol.52, pp.211-221, 2012.

C. M. D-iez, I. Trujillo, N. Martinez-urdiroz, D. Barranco, L. Rallo et al., Olive domestication and diversification in the Mediterranean Basin, New Phytol, vol.206, pp.436-447, 2015.

J. Doebley, A. Stec, and C. Gustus, ) teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance, Genetics, vol.141, pp.333-346, 1995.

J. F. Doebley, B. S. Gaut, and B. D. Smith, The molecular genetics of crop domestication, Cell, vol.127, pp.1309-1321, 2006.

N. Duan, Y. Bai, and H. Sun, Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement, Nat. Commun, vol.8, p.249, 2017.

N. Duforet-frebourg, E. Bazin, and M. G. Blum, Genome scans for detecting footprints of local adaptation using a Bayesian factor model, Mol. Biol. Evol, vol.31, pp.2483-2495, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01053023

N. Duforet-frebourg, K. Luu, G. Laval, E. Bazin, and M. G. Blum, Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 Genomes data, Mol. Biol. Evol, vol.33, pp.1082-1093, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01280469

A. El-bakkali, H. Haouane, A. Moukhli, E. Costes, P. Van-damme et al., Construction of core collections suitable for association mapping to optimize use of Mediterranean olive (Olea europaea L.) genetic resources, PLoS ONE, vol.8, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01268004

. Fao, Food Agric, 2018.

J. M. Flowers, K. M. Hazzouri, and M. Gros-balthazard, Cross-species hybridization and the origin of North African date palms, Proc. Natl Acad. Sci. USA, vol.116, pp.1651-1658, 2019.

M. Foll and O. Gaggiotti, A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective, Genetics, vol.180, pp.977-993, 2008.
URL : https://hal.archives-ouvertes.fr/halsde-00377961

E. Galili, D. J. Stanley, J. Sharvit, and M. Weinstein-evron, Evidence for earliest olive-oil production in submerged settlements of the Carmel Coast, Israel. J. Archaeol. Sci, vol.24, pp.1141-1150, 1997.

P. Gallusci, C. Hodgman, E. Teyssier, and G. B. Seymour, DNA methylation and chromatin regulation during fleshy fruit development and ripening, Front. Plant Sci, vol.7, 2016.

B. S. Gaut, C. M. Iez, and P. L. Morrell, Genomics and the contrasting dynamics of annual and perennial domestication, Trends Genet, vol.31, pp.709-719, 2015.

P. Gepts, Plant domestication as a long-term selection experiment, Plant Breed. Rev, vol.24, pp.1-44, 2004.

P. Gepts, The contribution of genetic and genomic approaches to plant domestication studies, Curr. Opin. Plant Biol, vol.18, pp.51-59, 2014.

M. Gros-balthazard, M. Galimberti, and A. Kousathanas, The discovery of wild date palms in Oman reveals a complex domestication history involving centers in the middle East and Africa, Curr. Biol, vol.27, pp.2211-2218, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608053

H. Hannachi, C. Breton, M. Msallem, S. Ben-el-hadj, M. El-gazzah et al., Are olive cultivars distinguishable from oleaster trees based on morphology of drupes and pits, oil composition and microsatellite polymorphisms, Acta Bot. Gallica, vol.155, pp.531-545, 2008.

H. Haouane, A. El-bakkali, A. Moukhli, C. Tollon, S. Santoni et al., Genetic structure and core collection of the World Olive Germplasm Bank of Marrakech: towards the optimised management and use of Mediterranean olive genetic resources, Genetica, vol.139, pp.1083-1094, 2011.

M. B. Hufford, X. Xu, and J. Van-heerwaarden, Comparative population genomics of maize domestication and improvement, Nat. Genet, vol.44, pp.808-811, 2012.

D. Iaria, A. Chiappetta, and I. Muzzalupo, De novo transcriptome sequencing of Olea europaea L. to identify genes involved in the development of the pollen tube, Sci. World J, vol.2016, pp.1-7, 2016.

C. M. Kalua, M. S. Allen, D. R. Bedgood, A. G. Bishop, P. D. Prenzler et al., Olive oil volatile compounds, flavour development and quality: a critical review, Food Chem, vol.100, pp.273-286, 2007.

D. Kaniewski, E. Van-campo, T. Boiy, J. Terral, B. Khadari et al., Primary domestication and early uses of the emblematic olive tree: palaeobotanical, historical and molecular evidence from the Middle East, Biol. Rev, vol.87, pp.885-899, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00959519

P. D. Keightley, D. L. Halligan, and M. Kirkpatrick, Inference of mutation parameters and selective constraint in mammalian coding sequences by Approximate Bayesian Computation, Genetics, vol.187, pp.1153-1161, 2011.

B. Khadari and A. Bakkali, Primary selection and secondary diversification: two key processes in the history of olive domestication, Int. J. Agron, p.5607903, 2018.

M. E. Kislev, D. Nadel, and I. Carmi, Epipalaeolithic (19,000 BP) cereal and fruit diet at Ohalo II, Sea of Galilee, Israel. Rev. Palaeobot. Palynol, vol.73, pp.161-166, 1992.

D. Koenig, J. M. Jim-enez-g-omez, and S. Kimura, Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato, Proc. Natl Acad. Sci. USA, vol.110, pp.2655-2662, 2013.

M. Konczal, W. Babik, J. Radwan, E. T. Sadowska, and P. Koteja, Initial molecular-level response to artificial selection for increased aerobic metabolism occurs primarily through changes in gene expression, Mol. Biol. Evol, vol.32, pp.1461-1473, 2015.

T. S. Korneliussen, A. Albrechtsen, and R. Nielsen, ANGSD: analysis of next generation sequencing data, BMC Bioinform, vol.15, 2014.

Z. H. Lemmon, R. Bukowski, Q. Sun, and J. F. Doebley, The role of cis regulatory evolution in maize domestication, PLoS Genet, vol.10, 2014.

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

H. Li, B. Handsaker, and A. Wysoker, The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

N. Liphschitz, R. Gophna, M. Hartman, and G. Biger, The beginning of olive (Olea europaea) cultivation in the Old World: a reassessment, J. Archaeol. Sci, vol.18, pp.441-453, 1991.

F. Liu, Y. Xia, and L. Wu, Enhanced seed oil content by overexpressing genes related to triacylglyceride synthesis, Gene, vol.557, pp.163-71, 2015.

W. Liu, L. Chen, and S. Zhang, Decrease of gene expression diversity during domestication of animals and plants, BMC Evol. Biol, vol.19, 2019.

K. E. Lotterhos and M. C. Whitlock, Evaluation of demographic history and neutral parameterization on the performance of F ST outlier tests, Mol. Ecol, vol.23, pp.2178-2192, 2014.

A. Loumou and C. Giourga, Olive groves: "The life and identity of the Mediterranean, Agric. Human Values, vol.20, pp.87-95, 2003.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, 2014.

R. Lumaret, N. Ouazzani, H. Michaud, G. Vivier, M. Deguilloux et al., Allozyme variation of oleaster populations (wild olive tree) (Olea europaea L.) in the Mediterranean Basin, Heredity, vol.92, pp.343-351, 2004.
URL : https://hal.archives-ouvertes.fr/halshs-00458933

K. Luu, E. Bazin, and M. G. Blum, PCAdapt: an R package to perform genome scans for selection based on principal component analysis, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01430346

, La domestication des plantes: une affaire de super-h eros et de masterminds, Mol. Ecol. Resour, vol.17, pp.268-273, 2016.

A. Mckenna, M. Hanna, and E. Banks, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010.

R. S. Meyer and M. D. Purugganan, Evolution of crop species: genetics of domestication and diversification, Nat. Rev. Genet, vol.14, pp.840-852, 2013.

A. J. Miller and B. L. Gross, From forest to field: perennial fruit crop domestication, Am. J. Bot, vol.98, pp.1389-1414, 2011.

A. Morgulis, G. Coulouris, Y. Raytselis, T. L. Madden, R. Agarwala et al., Database indexing for production MegaBLAST searches, Bioinformatics, vol.24, pp.1757-1764, 2008.

S. Mousavi, L. Regni, and M. Bocchini, Physiological, epigenetic and genetic regulation in some olive cultivars under salt stress, Sci. Rep, vol.9, 2019.

A. Muñoz-m-erida, J. J. Gonz-alez-plaza, and A. Cañada, De novo assembly and functional annotation of the olive (Olea europaea) transcriptome, DNA Res, vol.20, pp.93-108, 2013.

S. Myles, A. R. Boyko, and C. L. Owens, Genetic structure and domestication history of the grape, Proc. Natl Acad. Sci. USA, vol.108, pp.3530-3535, 2011.

B. Nabholz, G. Sarah, F. Sabot, M. Ruiz, H. Adam et al., Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (O. glaberrima), Mol. Ecol, vol.23, pp.2210-2227, 2014.

S. R. Narum and J. E. Hess, Comparison of F ST outlier tests for SNP loci under selection, Mol. Ecol. Resour, vol.11, pp.184-194, 2011.

K. M. Olsen and M. D. Purugganan, Molecular evidence on the origin and evolution of glutinous rice, Genetics, vol.162, pp.941-950, 2002.

K. M. Olsen and J. F. Wendel, A bountiful harvest: genomic insights into crop domestication phenotypes, Annu. Rev. Plant Biol, vol.64, pp.47-70, 2013.

R. Parra, M. A. Paredes, and I. M. Sanchez-calle, Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation, BMC Genom, vol.14, 2013.

J. K. Pickrell and J. K. Pritchard, Inference of population splits and mixtures from genome-wide allele frequency data, PLoS Genet, vol.8, 2012.

D. R. Piperno, Assessing elements of an extended evolutionary synthesis for plant domestication and agricultural origin research, Proc. Natl Acad. Sci. USA, vol.114, pp.6429-6437, 2017.

M. P. Przeworski, G. Coop, and J. D. Wall, The signature of positive selection on standing genetic variation, Evolution, vol.59, pp.2312-2323, 2005.

A. Ray, M. K. Pal, M. Ghosh, and D. Sanyal, Psychodermatological disorders: an assessment of psychiatric morbidity, Int. Med. J, vol.18, pp.300-304, 2011.

B. Rhon-e, C. Mariac, M. Couderc, C. Berthouly-salazar, I. S. Ousseini et al., No excess of CIS-regulatory variation associated with intraspecific selection in wild pearl millet, 2017.

, Genome Biol. Evol, vol.9, pp.388-397

E. J. Richards, Natural epigenetic variation in plant species: a view from the field, Curr. Opin. Plant Biol, vol.14, pp.204-209, 2011.

J. Romiguier, P. Gayral, and M. Ballenghien, Comparative population genomics in animals uncovers the determinants of genetic diversity, Nature, vol.515, pp.261-263, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01313724

E. Rugini, L. Baldoni, R. Muleo, and L. Sebastiani, The Olive Tree Genome. Compendium of Plant Genomes, 2016.

G. Sarah, F. Homa, and S. Pointet, A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives, Mol. Ecol. Resour, vol.17, pp.565-580, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01930391

C. Sauvage, A. Rau, C. Aichholz, J. Chadoeuf, G. Sarah et al., Domestication rewired gene expression and nucleotide diversity patterns in tomato, Plant J, vol.91, pp.631-645, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01594937

L. Skotte, T. S. Korneliussen, and A. Albrechtsen, Estimating individual admixture proportions from next generation sequencing data, Genetics, vol.195, pp.693-702, 2013.

W. Stephan, Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation, Mol. Ecol, vol.25, pp.79-88, 2016.

D. L. Stern and V. Orgogozo, The loci of evolution: how predictable is genetic evolution? Evolution, vol.62, pp.2155-2177, 2008.

M. G. Stetter, D. J. Gates, W. Mei, and J. Ross-ibarra, How to make a domesticate, Curr. Biol, vol.17, 2017.

J. D. Storey, A direct approach to false discovery rates, J. R. Stat. Soc. Ser. B, vol.64, pp.479-498, 2002.

A. Studer, Q. Zhao, J. Ross-ibarra, J. Doebley, F. Supek et al., Identification of a functional transposon insertion in the maize domestication gene tb1, Nat. Genet, vol.43, pp.1160-1163, 2011.

R. Swanson-wagner, R. Briskine, R. Schaefer, M. B. Hufford, J. Ross-ibarra et al., Reshaping of the maize transcriptome by domestication, Proc. Natl Acad. Sci. USA, vol.109, pp.11878-11883, 2012.

G. Swinnen, A. Goossens, and L. Pauwels, Lessons from domestication: targeting cis-regulatory elements for crop improvement, Trends Plant Sci, vol.21, pp.506-515, 2016.

D. Szkiba, M. Kapun, A. Von-haeseler, and M. Gallach, SNP2GO: functional analysis of genome-wide association studies, Genetics, vol.197, pp.285-289, 2014.

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

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

J. F. Terral, N. Alonso, and R. B. Capdevila, Historical biogeography of olive domestication (Olea europaea L.) as revealed by geometrical morphometry applied to biological and archaeological material, J. Biogeogr, vol.31, pp.63-77, 2004.

T. Unver, Z. Wu, and L. Sterck, Genome of wild olive and the evolution of oil biosynthesis, Proc. Natl Acad. Sci. USA, vol.114, pp.9413-9422, 2017.

A. I. Vatsiou, E. Bazin, and O. E. Gaggiotti, Detection of selective sweeps in structured populations: a comparison of recent methods, Mol. Ecol, vol.25, pp.89-103, 2016.

M. Wang, L. Tu, and M. Lin, Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication, Nat. Genet, vol.49, pp.579-587, 2017.

G. A. Watterson, On the number of segregating sites in genetical models without recombination, Theor. Popul. Biol, vol.7, pp.256-276, 1975.

B. S. Weir and C. C. Cockerham, Estimating F-statistics for the analysis of population-structure, Evolution, vol.38, pp.1358-1370, 1984.

M. D. Young, M. J. Wakefield, G. K. Smyth, and A. Oshlack, Gene ontology analysis for RNA-seq: accounting for selection bias, Genome Biol, vol.11, 2010.

Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, A greedy algorithm for aligning DNA sequences, J. Comput. Biol, vol.7, pp.203-214, 2000.

Y. Zhou, M. Massonnet, J. S. Sanjak, D. Cantu, and B. S. Gaut, Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication, 2017.

, Proc. Natl Acad. Sci. USA, vol.114, pp.11715-11720