Differential expression analysis for sequence count data, Genome Biol, vol.11, pp.1344-1349, 2010. ,
Identification of QTL for agronomic traits of importance for olive breeding, Mol. Breed, vol.34, pp.725-737, 2014. ,
The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome, Genome Biol. Evol, vol.6, pp.776-791, 2014. ,
Olive germplasm: cultivars and world-wide collections, vol.459, p.pp, 1998. ,
qvalue: Q-value estimation for false discovery rate control, 2015. ,
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. ,
Decreased nucleotide and expression diversity and modified coexpression patterns characterize domestication in the common bean, Plant Cell, vol.26, pp.1901-1912, 2014. ,
QTL mapping of flowering and fruiting traits in olive, PLoS ONE, vol.8, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01209909
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. ,
Single vs multiple independent olive domestications: the jury is (still) out, New Phytol, vol.209, pp.466-470, 2016. ,
Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars, Theor. Appl. Genet, vol.102, pp.251-258, 2001. ,
Olive domestication from structure of oleasters and cultivars using nuclear RAPDs and mitochondrial RFLPs, Genet. Sel. Evol, vol.33, pp.251-268, 2001. ,
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
Genomic profiling of plastid DNA variation in the Mediterranean olive tree, BMC Plant Biol, vol.11, 2011. ,
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
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
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. ,
The origins of the domestication of the olive tree, C. R. Biol, vol.332, pp.1059-1064, 2009. ,
ReprOlive: a database with linked data for the olive tree (Olea europaea L.) reproductive transcriptome. Front, Plant Sci, vol.6, 2015. ,
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. ,
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. ,
The evolution of gene regulation by transcription factors and microRNAs, Nat. Rev. Genet, vol.8, pp.93-103, 2007. ,
A single generation of domestication heritably alters the expression of hundreds of genes, Nat. Commun, vol.7, 2016. ,
Evolutionary forces affecting synonymous variations in plant genomes, PLoS Genet, vol.13, 2017. ,
A survey of best practices for RNA-seq data analysis, Genome Biol, vol.17, 2016. ,
R: a language and environment for statistical computing, R Foundation for Statistical Computing, 2015. ,
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
Genome sequence of the olive tree Olea europaea. GigaScience, 5, 29, 2016. ,
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. ,
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. ,
Worldwide core collection of olive cultivars based on simple sequence repeat and morphological markers, Crop Sci, vol.52, pp.211-221, 2012. ,
Olive domestication and diversification in the Mediterranean Basin, New Phytol, vol.206, pp.436-447, 2015. ,
) teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance, Genetics, vol.141, pp.333-346, 1995. ,
The molecular genetics of crop domestication, Cell, vol.127, pp.1309-1321, 2006. ,
Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement, Nat. Commun, vol.8, p.249, 2017. ,
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
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
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
, Food Agric, 2018.
Cross-species hybridization and the origin of North African date palms, Proc. Natl Acad. Sci. USA, vol.116, pp.1651-1658, 2019. ,
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
Evidence for earliest olive-oil production in submerged settlements of the Carmel Coast, Israel. J. Archaeol. Sci, vol.24, pp.1141-1150, 1997. ,
DNA methylation and chromatin regulation during fleshy fruit development and ripening, Front. Plant Sci, vol.7, 2016. ,
Genomics and the contrasting dynamics of annual and perennial domestication, Trends Genet, vol.31, pp.709-719, 2015. ,
Plant domestication as a long-term selection experiment, Plant Breed. Rev, vol.24, pp.1-44, 2004. ,
The contribution of genetic and genomic approaches to plant domestication studies, Curr. Opin. Plant Biol, vol.18, pp.51-59, 2014. ,
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
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. ,
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. ,
Comparative population genomics of maize domestication and improvement, Nat. Genet, vol.44, pp.808-811, 2012. ,
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. ,
Olive oil volatile compounds, flavour development and quality: a critical review, Food Chem, vol.100, pp.273-286, 2007. ,
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
Inference of mutation parameters and selective constraint in mammalian coding sequences by Approximate Bayesian Computation, Genetics, vol.187, pp.1153-1161, 2011. ,
Primary selection and secondary diversification: two key processes in the history of olive domestication, Int. J. Agron, p.5607903, 2018. ,
Epipalaeolithic (19,000 BP) cereal and fruit diet at Ohalo II, Sea of Galilee, Israel. Rev. Palaeobot. Palynol, vol.73, pp.161-166, 1992. ,
Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato, Proc. Natl Acad. Sci. USA, vol.110, pp.2655-2662, 2013. ,
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. ,
ANGSD: analysis of next generation sequencing data, BMC Bioinform, vol.15, 2014. ,
The role of cis regulatory evolution in maize domestication, PLoS Genet, vol.10, 2014. ,
Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, vol.26, pp.589-595, 2010. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
The beginning of olive (Olea europaea) cultivation in the Old World: a reassessment, J. Archaeol. Sci, vol.18, pp.441-453, 1991. ,
Enhanced seed oil content by overexpressing genes related to triacylglyceride synthesis, Gene, vol.557, pp.163-71, 2015. ,
Decrease of gene expression diversity during domestication of animals and plants, BMC Evol. Biol, vol.19, 2019. ,
Evaluation of demographic history and neutral parameterization on the performance of F ST outlier tests, Mol. Ecol, vol.23, pp.2178-2192, 2014. ,
Olive groves: "The life and identity of the Mediterranean, Agric. Human Values, vol.20, pp.87-95, 2003. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, 2014. ,
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
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.
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010. ,
Evolution of crop species: genetics of domestication and diversification, Nat. Rev. Genet, vol.14, pp.840-852, 2013. ,
From forest to field: perennial fruit crop domestication, Am. J. Bot, vol.98, pp.1389-1414, 2011. ,
Database indexing for production MegaBLAST searches, Bioinformatics, vol.24, pp.1757-1764, 2008. ,
Physiological, epigenetic and genetic regulation in some olive cultivars under salt stress, Sci. Rep, vol.9, 2019. ,
De novo assembly and functional annotation of the olive (Olea europaea) transcriptome, DNA Res, vol.20, pp.93-108, 2013. ,
Genetic structure and domestication history of the grape, Proc. Natl Acad. Sci. USA, vol.108, pp.3530-3535, 2011. ,
Transcriptome population genomics reveals severe bottleneck and domestication cost in the African rice (O. glaberrima), Mol. Ecol, vol.23, pp.2210-2227, 2014. ,
Comparison of F ST outlier tests for SNP loci under selection, Mol. Ecol. Resour, vol.11, pp.184-194, 2011. ,
Molecular evidence on the origin and evolution of glutinous rice, Genetics, vol.162, pp.941-950, 2002. ,
A bountiful harvest: genomic insights into crop domestication phenotypes, Annu. Rev. Plant Biol, vol.64, pp.47-70, 2013. ,
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. ,
Inference of population splits and mixtures from genome-wide allele frequency data, PLoS Genet, vol.8, 2012. ,
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. ,
The signature of positive selection on standing genetic variation, Evolution, vol.59, pp.2312-2323, 2005. ,
Psychodermatological disorders: an assessment of psychiatric morbidity, Int. Med. J, vol.18, pp.300-304, 2011. ,
No excess of CIS-regulatory variation associated with intraspecific selection in wild pearl millet, 2017. ,
, Genome Biol. Evol, vol.9, pp.388-397
Natural epigenetic variation in plant species: a view from the field, Curr. Opin. Plant Biol, vol.14, pp.204-209, 2011. ,
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
The Olive Tree Genome. Compendium of Plant Genomes, 2016. ,
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
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
Estimating individual admixture proportions from next generation sequencing data, Genetics, vol.195, pp.693-702, 2013. ,
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. ,
The loci of evolution: how predictable is genetic evolution? Evolution, vol.62, pp.2155-2177, 2008. ,
How to make a domesticate, Curr. Biol, vol.17, 2017. ,
A direct approach to false discovery rates, J. R. Stat. Soc. Ser. B, vol.64, pp.479-498, 2002. ,
Identification of a functional transposon insertion in the maize domestication gene tb1, Nat. Genet, vol.43, pp.1160-1163, 2011. ,
Reshaping of the maize transcriptome by domestication, Proc. Natl Acad. Sci. USA, vol.109, pp.11878-11883, 2012. ,
Lessons from domestication: targeting cis-regulatory elements for crop improvement, Trends Plant Sci, vol.21, pp.506-515, 2016. ,
SNP2GO: functional analysis of genome-wide association studies, Genetics, vol.197, pp.285-289, 2014. ,
Evolutionary relationship of DNA sequences in finite populations, Genetics, vol.105, pp.437-460, 1983. ,
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989. ,
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. ,
Genome of wild olive and the evolution of oil biosynthesis, Proc. Natl Acad. Sci. USA, vol.114, pp.9413-9422, 2017. ,
Detection of selective sweeps in structured populations: a comparison of recent methods, Mol. Ecol, vol.25, pp.89-103, 2016. ,
Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication, Nat. Genet, vol.49, pp.579-587, 2017. ,
On the number of segregating sites in genetical models without recombination, Theor. Popul. Biol, vol.7, pp.256-276, 1975. ,
Estimating F-statistics for the analysis of population-structure, Evolution, vol.38, pp.1358-1370, 1984. ,
Gene ontology analysis for RNA-seq: accounting for selection bias, Genome Biol, vol.11, 2010. ,
A greedy algorithm for aligning DNA sequences, J. Comput. Biol, vol.7, pp.203-214, 2000. ,
Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication, 2017. ,
, Proc. Natl Acad. Sci. USA, vol.114, pp.11715-11720