,
Defining the core Arabidopsis thaliana root microbiome, Nature, vol.488, pp.86-90, 2012. ,
The Drosophila melanogaster genetic reference panel, Nature, vol.482, pp.173-178, 2012. ,
On the importance of patch attributes, environmental factors and past human impacts as determinants of perennial plant species richness and diversity in Mediterranean semiarid steppes, Diversity and Distribution, vol.10, pp.21-29, 2004. ,
Genomic resources and their influence on the detection of the signal of positive selection in genome scans, Molecular ecology, vol.25, pp.170-184, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01444669
The pls package: principal component and partial least squares regression in R, Journal of Statistical Software, vol.18, pp.1-23, 2007. ,
Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis, Nature, vol.441, pp.947-952, 2006. ,
, , 2016.
The scale of population structure in Arabidopsis thaliana, PLoS Genetics, vol.6, p.1000843, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00457092
Evolutionary and plastic responses to climate changes in terrestrial plant populations, Evol. Appl, vol.7, pp.123-139, 2014. ,
Predicting responses to contemporary environmental change using evolutionary response architectures, Am. Nat, p.189, 2017. ,
Genomic patterns of pleiotropy and the evolution of complexity, Proc. Natl. Acad. Sci. U.S.A, vol.107, pp.18034-18039, 2010. ,
The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms, Nat. Rev. Genet, vol.12, pp.204-213, 2011. ,
How fast is fast? Eco-evolutionary dynamics and rates of change in populations and phenotypes, Ecol. Evol, vol.6, pp.573-581, 2016. ,
Is rapid evolution common in introduced plant species, J. Ecol, vol.99, pp.214-224, 2011. ,
Rapid evolution of flowering time by an annual plant in response to a climate fluctuation, Proc. Natl. Acad. Sci. U.S.A, vol.104, pp.1278-1282, 2007. ,
The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish, Science, vol.354, pp.1305-1308 ,
, References to Supplementary Information
The scale of population structure in Arabidopsis thaliana, PLoS Genet, vol.6, p.1000843, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00457092
A comprehensive, highresolution database of historical and projected climate surfaces for western, North America. B. Am. Meteorol. Soc, vol.94, p.1307, 2013. ,
Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana, Mol. Ecol, vol.22, pp.4222-4240, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00860399
The ade4 package-I-One-table methods, R News, vol.4, p.5, 2004. ,
URL : https://hal.archives-ouvertes.fr/hal-00427558
Linkage and association mapping of Arabidopsis thaliana flowering time in nature, PLoS Genet, vol.6, p.1000940, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00468455
Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments, Genetics, vol.162, pp.1875-1884, 2002. ,
Natural variation among accessions of Arabidopsis thaliana: beyond the flowering date, what morphological traits are relevant to study adaptation? In Plant adaptation: molecular biology and ecology, pp.135-142, 2004. ,
Density-dependent processes influencing the evolutionary dynamics of dispersal: a functional analysis of seed dispersal in Arabidopsis thaliana (Brassicaceae), Am. J. Bot, vol.92, pp.960-971, 2005. ,
The genetics of intra-and interspecific competitive response and effect in a local population of an annual plant species, Funct. Ecol, vol.29, pp.1361-1370, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01134029
Adaptive value of phenological traits in stressful environments: predictions based on seed production and Laboratory Natural Selection, PLoS One, vol.7, p.32069, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00685041
The dominance of the herbicide resistant cost in several Arabidopsis thaliana mutant lines, Genetics, vol.166, pp.449-460, 2004. ,
Building of an experimental cline with Arabidopsis thaliana to estimate herbicide fitness cost, Genetics, vol.173, pp.1023-1031, 2006. ,
Genome-wide association mapping of fertility reduction upon heat stress reveals developmental stage-specific QTLs in Arabidopsis thaliana, The Plant Cell, vol.27, pp.1857-1874, 2015. ,
Cytonuclear interactions affect adaptive phenotypic traits of the annual plant Arabidopsis thaliana in ecologically realistic conditions, Proc. Natl. Acad. Sci. U.S.A, vol.113, pp.3687-3692, 2016. ,
The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009. ,
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res, vol.22, pp.568-576, 2012. ,
The genetics underlying natural variation in the biotic interactions of Arabidopsis thaliana: the challenges of linking evolutionary genetics and community ecology, Curr. Top. Dev. Biol, vol.119, pp.111-156, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01606774
A R2R3-MYB gene, AtMYB30, acts as a positive regulator of the hypersensitive cell death program in plants in response to pathogen attack, Proc. Natl. Acad. Sci. U.S.A, vol.99, pp.10179-10184, 2002. ,
An atypical kinase under balancing selection confers broadspectrum disease resistance in Arabidopsis, PLoS Genet, vol.9, p.1003766, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01110788
Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines, Nature, vol.465, pp.627-631, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00468440
Variance component model to account for sample structure in genomewide association studies, Nat. Genet, vol.42, pp.348-354, 2010. ,
New strategies and tools in quantitative genetics: How to go from the phenotype to the genotype?, Annual Review of Plant Biology, vol.68, pp.435-455, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01607849
Plant transfers in historical perspective: a review article, Environment and History, vol.10, pp.3-29, 2004. ,
Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana, Nature Reviews Genetics, vol.11, pp.867-879, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00563568
Genotype and maternal environment affect belowground interactions between Arabidopsis thaliana and its competitors, Oikos, vol.118, p.15411551, 2009. ,
Linkage and association mapping of Arabidopsis thaliana flowering time in nature, PLoS Genetics, vol.6, p.1000940, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00468455
Investigation of the geographical scale of adaptive phenological variation and its underlying genetics in Arabidopsis thaliana, Molecular ecology, vol.22, pp.4222-4240, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-00860399
The genetic architecture of Maize flowering time, Science, vol.325, pp.714-718, 2009. ,
Comprehensive list of names of plant pathogenic bacteria, Journal of Plant Pathology, vol.92, pp.551-592, 2010. ,
, List of new names of plant pathogenic bacteria, vol.94, pp.21-27, 2008.
URL : https://hal.archives-ouvertes.fr/hal-01210013
, List of new names of plant pathogenic bacteria, vol.96, pp.223-226, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01210013
A native at home and abroad: the history, politics, ethics and aesthetics of acacias, Diversity and Distributions, vol.17, pp.810-821, 2011. ,
Monitoring adaptive genetic responses to environmental change, Molecular ecology, vol.21, pp.1311-1329, 2012. ,
Habitat type shapes long-term plant biodiversity budgets in two densely populated regions in north-western, Europe. Diversity and Distributions, vol.21, pp.631-642, 2014. ,
Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions, The American naturalist, vol.188, pp.379-397, 2016. ,
A single amino acid mutation contributes to adaptive beach mouse color pattern, Science, vol.313, pp.101-104, 2006. ,
Climate change and evolutionary adaptation, Nature, vol.470, pp.479-485, 2011. ,
Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel, Nature Genetics, vol.44, pp.212-216, 2012. ,
A multiparent advanced generation inter-cross population for genetic analysis in wheat, Plant Biotechnology Journal, vol.10, pp.826-839, 2012. ,
An atypical kinase under balancing selection confers broad-spectrum disease resistance in Arabidopsis, PLoS Genetics, vol.9, p.1003766, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01110788
Balancing biodiversity in a changing environment: extinction debt, immigration credit and species turnover, Trends in Ecology and Evolution, vol.25, pp.153-160, 2010. ,
Pseudomonas viridiflava and P. syringae-natural pathogens of Arabidopsis thaliana, The American Phytopathological Society, vol.15, pp.1195-1203, 2002. ,
Determinants of loss of mammal species during the Late Quaternary 'megafauna' extinctions: life history and ecology, but not body size, Proceedings of the Royal Society B, vol.269, pp.2221-2227, 2002. ,
Variance component model to account for sample structure in genome-wide association studies, Nature Genetics, vol.42, pp.348-354, 2010. ,
The long-term maintenance of a resistance polymorphism through diffuse interactions, Nature, vol.512, pp.436-440, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01110849
Epigenomic diversity in a global collection of Arabidopsis thaliana accessions, Cell, vol.166, pp.492-505, 2016. ,
The multivariate association between genome-wide DNAmethylation and climate across the range of Arabidopsis thaliana, Molecular Ecology, vol.25, pp.1823-1837, 2016. ,
Rapid shifts in plant distribution with recent climate change, Proceedings of the National Academy of Sciences of the United States of America, vol.105, pp.11823-11826, 2008. ,
Naturally occurring genetic variation in Arabidopsis thaliana, Annual Review of Plant Biology, vol.55, pp.141-172, 2004. ,
A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana, PLoS Genetics, vol.5, p.1000551, 2009. ,
Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation, Journal of Evolutionary Biology, vol.22, pp.1435-1446, 2009. ,
Characterizing genomic variation of Arabidopsis thaliana: the roles of geography and climate, Molecular ecology, vol.21, pp.5512-5529, 2012. ,
Genome-environment associations in sorghum landraces predict adaptive traits, Science Advances, vol.1, p.1400218, 2015. ,
Small-mammal diversity in Spain during the late Pleistocene to early Holocene: Climate, landscape, and human impact, Geology, vol.41, pp.267-270, 2013. ,
The relative power of genome scans to detect local adaptation depends on sampling design and statistical method, Molecular ecology, vol.24, pp.1031-1046, 2015. ,
The Drosophila melanogaster genetic reference panel, Nature, vol.482, pp.173-178, 2012. ,
Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina, Molecular ecology, vol.19, pp.3824-3835, 2010. ,
Prehistoric Extinctions on Islands and Continents. MacPhee RDE, Extinctions in Near Time: Causes, Contexts, and Consequences, pp.17-55, 1999. ,
DOI : 10.1007/978-1-4757-5202-1_2
Ecological and evolutionary responses of Mediterranean plants to global change, Environmental and Experimental Botany, vol.103, pp.53-67, 2014. ,
The extent of linkage disequilibrium in Rice, Oryza sativa L.). Genetics, vol.177, pp.2223-2232, 2007. ,
Mean and variance change in climate scenarios: methods, agricultural applications, and measures of uncertainty, Climatic Change, vol.35, pp.367-396, 1997. ,
Arabidopsis thaliana: a model plant for genome analysis, Science, vol.282, pp.662-682, 1998. ,
DOI : 10.1126/science.282.5389.662
The Arabidopsis book, 2002. ,
, Ecosystem an Human Well-being, synthesis, 2005.
Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis, Nature, vol.441, pp.947-952, 2006. ,
The evolutionary maintenance of alternative phenotypes, The American naturalist, vol.139, pp.971-989, 1992. ,
, Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity, vol.115, pp.293-301, 2015.
Demographic fate of Arabidopsis thaliana cohorts of autumn-and springgerminated plants along an altitudinal gradient, Journal of Ecology, vol.100, pp.1009-1018, 2012. ,
The future of biodiversity, Science, vol.269, pp.347-350, 1995. ,
The biodiversity of species and their rates of extinction, distribution, and protection, Science, vol.344, p.1246752, 2014. ,
The scale of population structure in Arabidopsis thaliana, PLoS Genetics, vol.6, p.1000843, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00457092
Genomeenvironment association study suggests local adaptation to climate at the regional scale in Fagus sylvatica, New Phytologist, vol.210, pp.589-601, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01309135
The role of phenotypic plasticity in driving genetic evolution, Proceedings of the royal society B, vol.270, pp.1433-1440, 2003. ,
The Rabbit in Australia. Biogeography and Ecology in Australia, 1959. ,
Natural variation among accessions of Arabidopsis thaliana: beyond the flowering date, what morphological traits are relevant to study adaptation? Plant adaptation: molecular genetics and ecology Ottawa, pp.135-142, 2004. ,
Signatures of local adaptation in candidate genes of oaks (Quercus spp.) with respect to present and future climatic conditions, Molecular ecology, vol.25, pp.5907-5924, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01606846
, The ecology of invasions by animals and plants, vol.31, pp.659-666, 1958.
Microgeographic adaptation and the spatial scale of evolution, Trends in Ecology and Evolution, vol.29, pp.165-176, 2014. ,
Chapter Four-The genetics underlying natural variation in the biotic interactions of Arabidopsis thaliana: the challenges of linking evolutionary genetics and community ecology, Current topics in developmental biology, vol.119, pp.111-156, 2016. ,
How to be early flowering: an evolutionary perspective?, Trends in Plant Science, vol.11, pp.375-381, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-00091810
Global biodiversity scenarios for the year 2100, Science, vol.287, pp.1770-1774, 2000. ,
Ecological genomics of local adaptation, Nature reviews Genetics, vol.14, pp.807-820, 2013. ,
Sequencing pools of individuals-mining genome-wide polymorphism data without big funding, Nature reviews Genetics, vol.15, pp.749-763, 2014. ,
Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology, Annals of Botany, vol.99, pp.1043-1054, 2007. ,
It's about time: the temporal dynamics of phenotypic selection in the wild, Ecology Letters, vol.12, pp.1261-1276, 2009. ,
Interspecific interactions affect species and community responses to climate shifts, Oikos, vol.122, pp.358-366, 2013. ,
Adaptation genomics: the next generation, Trends in Ecology and Evolution, vol.25, pp.705-712, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-01945554
Metapopulation structure favors plasticity over local adaptation, The American naturalist, vol.160, pp.271-283, 2002. ,
Phenotypic plasticity for plant development, function and life history, Trends in Plant Science, vol.5, pp.537-542, 2000. ,
, The 1001 Genomes Consortium (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana, Cell, vol.166, pp.481-491
Climate change and the ecologist, Nature, vol.448, pp.550-552, 2007. ,
URL : https://hal.archives-ouvertes.fr/halsde-00283754
Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils, Nature Genetics, vol.42, pp.260-263, 2010. ,
Evolution of germination strategy in the invasive species Ulex europaeus, Journal of Plant Ecology, vol.10, pp.375-385, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01559962
Ecological genomics: understanding gene and genome function in the natural environment, Heredity, vol.100, pp.178-183, 2008. ,
Constraints on the evolution of adaptive phenotypic plasticity in plants, New Phytologist, vol.166, pp.49-60, 2005. ,
Pollen dispersal in an insect-pollinated wet meadow herb along an urban river, Landscape and Urban Planning, vol.95, pp.201-208, 2010. ,
Introduced species: a significant component of human-caused global change, New Zealand Journal of Ecology, vol.21, pp.1-16, 1997. ,
Genomic patterns of pleiotropy and the evolution of complexity, Proceedings of the National Academy of Sciences of the United States of America, vol.107, pp.18034-18039, 2010. ,
, The Anthropocene is functionally and stratigraphically distinct from the Holocene, vol.351, p.2622, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01453042
Evolution in a community context: on integrating ecological interactions and macroevolution, Trends in Ecology and Evolution, vol.32, pp.291-304, 2017. ,
Novel loci control variation in reproductive timing in Arabidopsis thaliana in natural environments, Genetics, vol.162, pp.1875-1884, 2002. ,
Density-dependent processes influencing the evolutionary dynamics of dispersal: a functional analysis of seed dispersal in Arabidopsis thaliana (Brassicaceae), American Journal of Botany, vol.92, pp.960-971, 2005. ,
The North American Pleistocene overkill hypothesis and the re-wilding debate, Diversity and Distributions, vol.16, pp.874-876, 2010. ,
DNA barcoding of Rhododendron (Ericaceae), the largest Chinese plant genus in biodiversity hotspots of the Himalaya-Hengduan Mountains, Molecular Ecology Resources, vol.15, pp.932-944, 2015. ,
Genomic signature of adaptation to climate in Medicago truncatula, Genetics, vol.196, pp.1263-1275, 2014. ,
Microbial hub taxa link host and abiotic factors to plant microbiome 825 variation, PLoS Biol, vol.14, p.1002352, 2016. ,
Wild plant species growing closely connected in a subalpine meadow 827 host distinct root-associated bacterial communities, PeerJ, vol.3, p.804, 2015. ,
Functional overlap of the Arabidopsis leaf and root microbiota, Nature, vol.829, issue.528, pp.364-369, 2015. ,
Emergence shapes the structure of the seed microbiota, Appl Environ, vol.831, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01153480
, , vol.81, pp.1257-1266
A framework to gage the epidemic potential of plant pathogens in 833 environmental reservoirs: the example of kiwifruit canker, Mol Plant Pathol, vol.16, pp.137-834, 2014. ,
The Pseudomonas viridiflava phylogroups in the P. syringae complex 836 are characterized by genetic variability and phenotypic plasticity of pathogenicity-related 837 traits, Environ Microbiol, vol.16, pp.2301-2315, 2014. ,
Molecular mechanisms underlying the 839 emergence of bacterial pathogens: an ecological perspective, Mol. Plant. Pathol, vol.16, pp.840-860, 2016. ,
Interactions between the microbiota and pathogenic 842 bacteria in the gut, Nature, vol.535, pp.85-93, 2016. ,
Role of the microbiota in immunity and inflammation, Cell, vol.844, issue.157, pp.121-141, 2014. ,
Linking sequence to function in soil bacteria: 846 sequence-directed isolation of novel bacteria contributing to soilborne plant disease 847 suppression, Appl Environ Microbiol, vol.75, pp.915-924, 2009. ,
Unraveling the plant microbiome: looking back and future perspectives, 2014. ,
, Front Microbiol, vol.5, p.148
A user's guide to a data base of the diversity of Pseudomonas syringae 851 and its application to classifying strains in this phylogenetic complex, PloS One, vol.9, pp.852-105547, 2014. ,
A synthetic community approach reveals plant genotypes 854 affecting the phyllosphere microbiota, PLoS Genet, vol.10, p.1004283, 2014. ,
Bacterial communities associated 856 with the leaves and the roots of Arabidopsis thaliana, PloS One, vol.8, p.56329, 2013. ,
Competition and the origins of novelty: experimental evolution of 858 niche-width expansion in a virus, Biol Lett, vol.9, p.20120616, 2013. ,
Host biology in light of the microbiome: Ten 860 principles of holobionts and hologenomes, PLoS Biol, vol.13, pp.1-23, 2015. ,
Investigation of the geographical scale of adaptive phenological 862 variation and its underlying genetics in Arabidopsis thaliana, Mol Ecol, vol.22, p.4240, 2013. ,
Structure and functions of the bacterial microbiota of plants, Annu 865 Rev Plant Biol, vol.64, pp.807-838, 2013. ,
Comprehensive list of names of plant pathogenic bacteria, 1980. ,
, J Plant Pathol, vol.92, pp.551-592
List of new names of plant pathogenic bacteria, J Plant, p.869, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-01210013
, , vol.94, pp.21-27
List of new names of plant pathogenic bacteria, J Plant 871 Pathol, vol.96, pp.223-226, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-01210013
Bacterial community assembly based on functional genes rather than 873 species, vol.108, pp.14288-14293, 2011. ,
Sparse PLS discriminant analysis: biologically 875 relevant feature selection and graphical displays for multiclass problems, Bmc Bioinf, pp.876-892, 2011. ,
Global patterns of 16S rRNA diversity at a depth of millions of 878 sequences per sample, vol.108, pp.4516-4522, 2011. ,
Partial least squares regression as an 880 alternative to current regression methods used in ecology, vol.118, pp.681-690, 2009. ,
Plant compartment and biogeography affect microbiome 882 composition in cultivated and native Agave species, New Phytol, vol.209, pp.798-811, 2016. ,
Seasonal community succession of the phyllosphere microbiome, 2015. ,
, Molecular plant-microbe interactions : MPMI, 28, pp.274-285
Plant diversity effects on soil food webs are stronger than those of 886 elevated CO2 and N deposition in a long-term grassland experiment, vol.887, pp.6889-6894, 2013. ,
Contrasting microbial biogeographical patterns between 889 anthropogenic subalpine grasslands and natural alpine grasslands, New Phytol, vol.890, pp.1196-1207, 2016. ,
DOI : 10.1111/nph.13690
Isolation and identification of Pseudomonas syringae facilitated by 892 a PCR targeting the whole P. syringae group, FEMS Microb Ecol, vol.92, 2016. ,
Survival trade-offs in plant roots during colonization by closely 895 related beneficial and pathogenic fungi, Nature Comm, vol.7, p.11362, 2016. ,
Associations with rhizosphere bacteria can confer an adaptive 897 advantage to plants, Nature Plants, vol.1, p.15051, 2015. ,
DOI : 10.1038/nplants.2015.51
URL : http://europepmc.org/articles/pmc4806546?pdf=render
Genome-wide association study of Arabidopsis thaliana leaf 899 microbial community, Nature Comm, vol.5, p.5320, 2014. ,
An atypical kinase under balancing selection confers broad901 spectrum disease resistance in Arabidopsis, PLoS Gen, vol.9, p.1003766, 2013. ,
DOI : 10.1371/journal.pgen.1003766
URL : https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1003766&type=printable
Protection of Arabidopsis thaliana against 903 leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model 904 system, Appl Enviro Microbiol, vol.77, pp.3202-3210, 2011. ,
Pseudomonas viridiflava and P. syringae-natural pathogens of 906 Arabidopsis thaliana. MPMI, 15, pp.1195-1203, 2002. ,
vegan: community ecology package. R package version 1, pp.16-16, 2009. ,
Control of pathogens and pathobionts by the gut microbiota, 2013. ,
, , vol.14, pp.685-690
Plant-microbe communications for symbiosis, 2010. ,
DOI : 10.1093/pcp/pcq125
URL : https://academic.oup.com/pcp/article-pdf/51/9/1377/5179580/pcq125.pdf
, Plant Cell Physiol, vol.51, pp.1377-1380
A conceptual framework for invasion in microbial communities, 2016. ,
, ISME J, vol.10, pp.2773-2775
Salicylic acid and jasmonic acid signaling 915 defense pathways reduce natural bacterial diversity on Arabidopsis thaliana, vol.916, pp.1512-1522, 2007. ,
Sparse PLS: Variable selection when integrating omics data, 2008. ,
, Appl Mol Biol, vol.7
Integrative mixture of experts to 920 combine clinical factors and gene markers, Bioinformatics, vol.26, pp.1192-1198, 2010. ,
Plant microbiome. Salicylic acid modulates colonization of the root 922 microbiome by specific bacterial taxa, Science, vol.349, pp.860-864, 2015. ,
Ecologically meaningful transformations for ordination 924 of species data, Oecologia, vol.129, pp.271-280, 2001. ,
Local and regional factors influencing bacterial 926 community assembly, Environ Microbiology Rep, vol.4, pp.1-9, 2012. ,
Defining the core Arabidopsis thaliana root microbiome, Nature, vol.928, issue.488, pp.86-90, 2012. ,
On the importance of patch attributes, environmental factors and past 930 human impacts as determinants of perennial plant species richness and diversity in 931 mediterranean semiarid steppes, Diver Distrib, vol.10, pp.21-29, 2004. ,
Swarm v2: highly-scalable and high-resolution amplicon clustering, 2015. ,
, PeerJ, vol.3, p.1420
Ecological succession and stochastic variation in the assembly of, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-01019120
, Arabidopsis thaliana phyllosphere communities. mBio, vol.5, pp.682-695
Resource pulses can alleviate the biodiversity-invasion relationship 937 in soil microbial communities, Ecology, vol.96, pp.915-926, 2015. ,
Top 10 plant pathogenic bacteria in molecular plant pathology, Mol 939 Plant Pathol, vol.13, pp.614-629, 2012. ,
Experimental evolution of a plant pathogen into a legume 941 symbiont, PLoS Biol, vol.8, p.1000280, 2010. ,
Mathematical modeling of primary succession of murine intestinal 943 microbiota, vol.111, pp.439-483, 2014. ,
IMG 4 version of the integrated microbial genomes 945 comparative analysis system, Nucleic Acids Res, vol.42, pp.560-567, 2014. ,
The rhizosphere microbiome: 947 significance of plant beneficial, plant pathogenic, and human pathogenic 948 microorganisms, FEMS Microbiol Rev, vol.37, pp.634-663, 2013. ,
Genetic mechanisms and evolutionary significance of 950 natural variation in Arabidopsis, Nature, vol.441, pp.947-952, 2006. ,
Demographic and genetic patterns of variation among populations 952 of Arabidopsis thaliana from contrasting native environments, PloS one, vol.4, p.7213, 2009. ,
Surprising niche for the plant pathogen Pseudomonas syringae, 2007. ,
, Infect. Genet. Evol, vol.7, pp.84-92
Gut microbiota diversity and human diseases: 956 should we reintroduce key predators in our ecosystem? Front Microbiol, vol.7, p.455, 2016. ,
DOI : 10.3389/fmicb.2016.00455
URL : https://www.frontiersin.org/articles/10.3389/fmicb.2016.00455/pdf
APE: Analyses of phylogenetics and evolution 958 in R language, Bioinformatics, vol.20, pp.289-290, 2004. ,
Demographic fate of Arabidopsis thaliana cohorts of autumn-and spring960 germinated plants along an altitudinal gradient, J Ecol, vol.100, pp.1009-1018, 2012. ,
Microbiome networks: a systems framework for identifying candidate 962 microbial assemblages for disease management, Phytopathology, vol.106, pp.1083-1096, 2016. ,
Multivariate analyses in microbial ecology, FEMS Microbiol Ecol, vol.62, pp.964-142, 2007. ,
The microbiome of the leaf surface of Arabidopsis protects 966 against a fungal pathogen, New Phytol, vol.210, pp.1033-1043, 2016. ,
Chapter Four-The genetics underlying natural variation in 968 the biotic interactions of Arabidopsis thaliana : the challenges of linking evolutionary 969 genetics and community ecology, Curr Top Dev Biol, pp.111-156, 2016. ,
Impact of initial pathogen density on resistance and 971 tolerance in a polymorphic disease resistance gene system in Arabidopsis thaliana, 2010. ,
, Genetics, vol.185, pp.283-291
Native root-associated bacteria rescue a plant from a sudden-wilt 974 disease that emerged during continuous cropping, vol.112, pp.5013-5020, 2015. ,
Quantitative divergence of the bacterial root microbiota in 976 42, 2014. ,
, Arabidopsis thaliana relatives, vol.111, pp.585-592
Introducing mothur: open-source, platform-independent, 978 community-supported software for describing and comparing microbial communities, 2009. ,
, Applied Environ Microbiol, vol.75, pp.7537-7541
MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol, 2013. ,
, Biol Evol, vol.30, pp.2725-2729
The importance of the microbiome of the plant holobiont, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01115639
, The New Phytol, vol.206, pp.1196-1206
Microbial species delineation using whole genome sequences, 2015. ,
, Nucleic Acids Res, vol.43, pp.6761-6771
Shifting the paradigm from pathogens to pathobiome: new 987 concepts in the light of meta-omics, Front Cell Infect Microbiol, vol.4, p.29, 2014. ,
Microbial life in the phyllosphere, Nat Rev Micro, vol.10, pp.828-840, 2012. ,
Host genotype and age shape the leaf and root microbiomes of a 990 wild perennial plant, Nature Comm, vol.7, p.12151, 2016. ,
DAMBE5: a comprehensive software package for data analysis in molecular 992 biology and evolution, Mol Biol Evol, vol.30, pp.1720-1728, 2013. ,
Superorganisms and holobionts. Microbe Magazine, vol.8, pp.152-153, 2013. ,
, Figure 1. Location of the 163 A. thaliana populations across the region Midi-Pyrénées (southwest of France), p.56
, Figure 13. Pathogenicity of Pseudomonas sp. strains isolated from the 163 A. thaliana populations of the region Midi1118
A) Mean bacterial growth across eight accessions collected in the region Midi-Pyrénées for two strains of P ,
, ) and two strains of P. syringae sensu stricto (0132-Psy-BAZI-AL 1120 and 0143-Psy-THOM-AL).B) Illustration of symptoms observed three days after inoculation for two strains of P
, Presence and absence of symptoms was observed on each of the eight accessions collected in the region Midi-Pyrénées for 1122 the strains 0111-Psy-RAYRB-BL and 0117-Psy-NAZA-AL