2016. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana, Cell, vol.166, pp.481-491 ,
Fast model-based estimation of ancestry in unrelated individuals, Genome Res, vol.19, pp.1655-1664, 2009. ,
The evolution of plant sexual diversity, Nat Rev Genet, vol.3, pp.274-284, 2002. ,
Polyploidy and self-fertilization in flowering plants, Am J Bot, vol.94, pp.1527-1533, 2007. ,
The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr, Mol Biol Evol, vol.23, pp.1741-1750, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00091794
Independent S-locus mutations caused self-fertility in Arabidopsis thaliana, PLoS Genet, vol.5, p.1000426, 2009. ,
Repeated adaptive introgression at a gene under multiallelic balancing selection, PLoS Genet, vol.4, p.1000168, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00305315
Molecular evolution within and between selfincompatibility specificities, Mol Biol Evol, vol.27, pp.11-20, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00431197
Plant self-incompatibility in natural populations: a critical assessment of recent theoretical and empirical advances, Mol Ecol, vol.13, pp.2873-2889, 2004. ,
Evolution under strong balancing selection: how many codons determine specificity at the female selfincompatibility gene SRK in Brassicaceae, BMC Evol Biol, vol.7, p.132, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00170453
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory, BMC Bioinformatics, vol.13, p.238, 2012. ,
Efficient cloning of plant genomes into bacterial artificial chromosome (BAC) libraries with larger and more uniform insert size, Plant Biotechnol J, vol.2, pp.181-188, 2004. ,
Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners, Genome Biol, vol.11, p.125, 2010. ,
Pollen-pistil interactions regulating successful fertilization in the Brassicaceae, J Exp Bot, vol.61, pp.1987-1999, 2010. ,
Diversity and linkage of genes in the self-incompatibility gene family in Arabidopsis lyrata, Genetics, vol.164, pp.1519-1535, 2003. ,
Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids, Proc Natl Acad Sci U S A, vol.95, pp.14891-14896, 1998. ,
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118, Fly, vol.6, pp.80-92, 2012. ,
FISH analysis of meiosis in Arabidopsis allopolyploids, Chromosome Res, vol.11, pp.217-226, 2003. ,
Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids, Plant Cell, vol.12, pp.1551-1568, 2000. ,
Extra views on RNA-dependent DNA methylation and MBD6-dependent heterochromatin formation in nucleolar dominance, Nucleus, vol.1, pp.254-259, 2010. ,
A framework for variation discovery and genotyping using nextgeneration DNA sequencing data, Nat Genet, vol.43, pp.491-498, 2011. ,
Dominance hierarchy arising from the evolution of a complex small RNA regulatory network, Science, vol.346, pp.1200-1205, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01110837
Construction and characterization of two BAC libraries representing a deep-coverage of the genome of chicory (Cichorium intybus L., Asteraceae), BMC Res Notes, vol.3, p.1002495, 2010. ,
Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat, Nature, vol.439, pp.749-752, 2006. ,
Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids, Proc Natl Acad Sci U S A, vol.106, pp.17835-17840, 2009. ,
The BOY NAMED SUE quantitative trait locus confers increased meiotic stability to an adapted natural allopolyploid of Arabidopsis, Plant Cell, vol.26, pp.181-194, 2014. ,
Very high resolution interpolated climate surfaces for global land areas, Int J Climatol, vol.25, pp.1965-1978, 2005. ,
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change, Nat Genet, vol.43, pp.476-481, 2011. ,
Generating samples under a Wright-Fisher neutral model of genetic variation, Bioinformatics, vol.18, pp.337-338, 2002. ,
Allopolyploid origin of Arabidopsis suecica (Fries) Norrlin: evidence from chloroplast and nuclear genome markers, Botanica Acta, vol.108, pp.449-456, 1995. ,
Cardaminopsis suecica (Fr.) Hiit., A northern amphidiploid species, Bull Jard Bot Etat Bruxelles, vol.271, pp.591-604, 1957. ,
A unique recent origin of the allotetraploid species Arabidopsis suecica: evidence from nuclear DNA markers, Mol Biol Evol, vol.23, pp.1217-1231, 2006. ,
Ancestral polyploidy in seed plants and angiosperms, Nature, vol.473, pp.97-100, 2011. ,
MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, pp.772-780, 2013. ,
Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
A cryptic modifier causing transient self-incompatibility in Arabidopsis thaliana, Curr Biol, vol.17, pp.734-740, 2007. ,
Does frequency-dependent selection with complex dominance interactions accurately predict allelic frequencies at the selfincompatibility locus in Arabidopsis halleri, Evolution, vol.62, pp.2545-2557, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00305318
Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden, Nat Genet, vol.45, pp.884-890, 2013. ,
SOAPdenovo2: an empirically improved memoryefficient short-read de novo assembler, vol.1, p.18, 2012. ,
Inheritance and dominance of self-incompatibility alleles in polyploid Arabidopsis lyrata, Heredity, vol.93, pp.476-486, 2004. ,
Estimating the number, frequency, and dominance of S-alleles in a natural population of Arabidopsis lyrata (Brassicaceae) with sporophytic control of selfincompatibility, Heredity, vol.90, pp.422-431, 2003. ,
Polyploidy and its effect on evolutionary success: old questions revisited with new tools, Heredity, vol.110, pp.99-104, 2013. ,
Genomic changes in synthetic Arabidopsis polyploids, Plant J, vol.41, pp.221-230, 2005. ,
Unreduced gametes: meiotic mishap or evolutionary mechanism?, Trends Genet, vol.31, pp.5-10, 2015. ,
The Genome Analysis Toolkit: a MapReduce framework for analyzing nextgeneration DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010. ,
Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5 0 terminal nucleotide, Cell, vol.133, pp.116-127, 2008. ,
Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis, Nat Commun, vol.6, p.7453, 2015. ,
AGO1-miR173 complex initiates phased siRNA formation in plants, Proc Natl Acad Sci U S A, vol.105, 2008. ,
Generation of self-incompatible Arabidopsis thaliana by transfer of two S locus genes from A. lyrata, Science, vol.297, pp.247-249, 2002. ,
A role for CHH methylation in the parent-of-origin effect on altered circadian rhythms and biomass heterosis in Arabidopsis intraspecific hybrids, Plant Cell, vol.26, pp.2430-2440, 2014. ,
High-throughput RNA-seq for allelic or locus-specific expression analysis in Arabidopsis-related species, hybrids, and allotetraploids, Methods Mol Biol, vol.1112, pp.33-48, 2014. ,
On the probability of Neanderthal ancestry, Am J Hum Genet, vol.63, pp.1237-1240, 1998. ,
Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism, Nat Genet, vol.48, pp.1077-1082, 2016. ,
The origins of Arabidopsis suecica (Brassicaceae) as indicated by nuclear rDNA sequences, Syst Bot, vol.21, p.559, 1996. ,
The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana, Science, vol.327, pp.92-94, 2010. ,
Ecological structure of recent and last glacial mammalian faunas in northern Eurasia: the case of Altai-Sayan refugium, PLoS One, vol.9, p.85056, 2014. ,
Construction of plant bacterial artificial chromosome (BAC) libraries: an illustrated guide, J Agric Genom, vol.5, pp.1-3, 2000. ,
Nucleolar dominance and silencing of transcription, Trends Plant Sci, vol.4, pp.478-483, 1999. ,
Postembryonic establishment of megabase-scale gene silencing in nucleolar dominance, PLoS One, vol.2, p.1157, 2007. ,
Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis, Genes Dev, vol.26, pp.945-957, 2012. ,
Systematic relationships of Arabidopsis: a molecular and morphological perspective, pp.7-19, 1994. ,
The complete genome sequence of a Neanderthal from the Altai Mountains, Nature, vol.505, pp.43-49, 2014. ,
PLINK: a tool set for whole-genome association and population-based linkage analyses, Am J Hum Genet, vol.81, pp.559-575, 2007. ,
Pathways, mechanisms, and rates of polyploid formation in flowering plants, Annu Rev Ecol Syst, vol.29, pp.467-501, 1998. ,
Genetic history of an archaic hominin group from Denisova Cave in Siberia, Nature, vol.468, pp.1053-1060, 2010. ,
Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica, J Evol Biol, vol.16, pp.1019-1029, 2003. ,
Mode of reproduction in Arabidopsis suecica, Hereditas, vol.141, pp.313-317, 2004. ,
Identification and characterization of a polymorphic receptor kinase gene linked to the self-incompatibility locus of Arabidopsis lyrata, Genetics, vol.158, pp.387-399, 2001. ,
Inferring human population size and separation history from multiple genome sequences, Nat Genet, vol.46, pp.919-925, 2014. ,
S locus genes and the evolution of self-fertility in Arabidopsis thaliana, Plant Cell, vol.19, pp.94-106, 2007. ,
Arabidopsis kamchatica (Fisch. ex DC.) R. Shimizu & Kudoh and A. kamchatica subsp. kawasakiana (Makino) K. Shimizu & Kudoh, new combinations, Acta Phytotaxonomica Et Geobotanica, vol.56, pp.163-172, 2005. ,
Independent origins of self-compatibility in Arabidopsis thaliana, Mol Ecol, vol.17, pp.704-714, 2008. ,
The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri, Mol Ecol, vol.18, pp.4024-4048, 2009. ,
Environmental regulation of heterosis in the allopolyploid Arabidopsis suecica, Plant Physiol, vol.170, pp.2251-2263, 2016. ,
Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons, Biol J Linn Soc, pp.485-501, 2004. ,
Polyploidy and genome evolution in plants, Curr Opin Genet Dev, vol.35, pp.119-125, 2015. ,
Pvclust: an R package for assessing the uncertainty in hierarchical clustering, Bioinformatics, vol.22, pp.1540-1542, 2006. ,
Self-incompatibility in plants, Annu Rev Plant Biol, vol.56, pp.467-489, 2005. ,
The evolution of selfing in Arabidopsis thaliana, Science, vol.317, pp.1070-1072, 2007. ,
Last glacial maximum biomes reconstructed from pollen and plant macrofossil data from northern Eurasia, J Biogeogr, vol.27, pp.609-620, 2000. ,
URL : https://hal.archives-ouvertes.fr/hal-01457720
Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility, Nature, vol.466, pp.983-986, 2010. ,
Genetic and epigenetic changes in a genomic region containing MIR172 in Arabidopsis allopolyploids and their progenitors, Heredity, vol.112, pp.207-214, 2014. ,
Recent loss of self-incompatibility by degradation of the male component in Allotetraploid Arabidopsis kamchatica, PLoS Genet, vol.8, p.1002838, 2012. ,
Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene, Nature, vol.464, pp.1342-1346, 2010. ,
Speciation by genome duplication: repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus, Evolution, vol.69, pp.1487-1500, 2015. ,
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary, Genome Res, vol.24, pp.1334-1347, 2014. ,
Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution, Philos Trans R Soc Lond B Biol Sci, vol.369, 2014. ,
The origins of genomic duplications in Arabidopsis, Science, vol.290, pp.2114-2117, 2000. ,
Genomewide nonadditive gene regulation in Arabidopsis allotetraploids, Genetics, vol.172, pp.507-517, 2006. ,
Jalview Version 2-a multiple sequence alignment editor and analysis workbench, Bioinformatics, vol.25, pp.1189-1191, 2009. ,
Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis, PLoS Genet, vol.6, p.1001141, 2010. ,
Cytological, molecular mechanisms and temperature stress regulating production of diploid male gametes in Dianthus caryophyllus L, Plant Physiol Biochem, vol.97, pp.255-263, 2015. ,