Hoffmann AA, Sgro CM. Climate change and evolutionary adaptation. Nature. 2011;470:479–85.
Article
CAS
PubMed
Google Scholar
Carroll SP, Jorgensen PS, Kinnison MT, Bergstrom CT, Denison RF, Gluckman P, et al. Applying evolutionary biology to address global challenges. Science. 2014;346:1245993.
Article
PubMed
PubMed Central
Google Scholar
Scheffers BR, De Meester L, Bridge TC, Hoffmann AA, Pandolfi JM, Corlett RT, et al. The broad footprint of climate change from genes to biomes to people. Science. 2016;354:aaf7671.
Article
PubMed
Google Scholar
Barrick JE, Lenski RE. Genome dynamics during experimental evolution. Nat Rev Genet. 2013;14:827–39.
Article
CAS
PubMed
PubMed Central
Google Scholar
Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nat Genet. 2010;42:260–3.
Article
CAS
PubMed
Google Scholar
Kang JQ, Zhang HT, Sun TS, Shi YH, Wang JQ, Zhang BC, et al. Natural variation of C-repeat-binding factor (CBFs) genes is a major cause of divergence in freezing tolerance among a group of Arabidopsis thaliana populations along the Yangtze River in China. New Phytol. 2013;199:1069–80.
Durvasula A, Fulgione A, Gutaker RM, Alacakaptan SI, Flood PJ, Neto C, et al. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2017;114:5213–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee CR, Svardal H, Farlow A, Exposito-Alonso M, Ding W, Novikova P, et al. On the post-glacial spread of human commensal Arabidopsis thaliana. Nat Commun. 2017;8:14458.
Article
CAS
PubMed
PubMed Central
Google Scholar
The 1001 Genomes Consortium. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell. 2016;166:481–91.
Article
Google Scholar
Cao J, Schneeberger K, Ossowski S, Gunther T, Bender S, Fitz J, et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011;43:956–63.
Article
CAS
PubMed
Google Scholar
Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J, Wilczek AM. A map of local adaptation in Arabidopsis thaliana. Science. 2011;334:86–9.
Article
CAS
PubMed
Google Scholar
Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperone FG, et al. Adaptation to climate across the Arabidopsis thaliana genome. Science. 2011;334:83–6.
Article
CAS
PubMed
Google Scholar
Horton MW, Hancock AM, Huang YS, Toomajian C, Atwell S, Auton A, et al. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel. Nat Genet. 2012;44:212–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, et al. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet. 2013;45:884–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, et al. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation. Elife. 2015;4:e05255.
Article
PubMed
PubMed Central
Google Scholar
Kawakatsu T, Huang SS, Jupe F, Sasaki E, Schmitz RJ, Urich MA, et al. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell. 2016;166:492–505.
Koornneef M, Alonso-Blanco C, Vreugdenhil D. Naturally occurring genetic variation in Arabidopsis thaliana. Annu Rev Plant Biol. 2004;55:141–72.
Article
CAS
PubMed
Google Scholar
Weigel D. Natural variation in Arabidopsis: from molecular genetics to ecological genomics. Plant Physiol. 2012;158:2–22.
Article
CAS
PubMed
Google Scholar
Weigel D, Nordborg M. Population genomics for understanding adaptation in wild plant species. Annu Rev Genet. 2015;49:315–38.
Article
CAS
PubMed
Google Scholar
Beck JB, Schmuths H, Schaal BA. Native range genetic variation in Arabidopsis thaliana is strongly geographically structured and reflects Pleistocene glacial dynamics. Mol Ecol. 2008;17:902–15.
Article
CAS
PubMed
Google Scholar
Platt A, Horton M, Huang YS, Li Y, Anastasio AE, Mulyati NW, et al. The scale of population structure in Arabidopsis thaliana. PLoS Genet. 2010;6:e1000843.
Article
PubMed
PubMed Central
Google Scholar
Yin P, Kang J, He F, Qu LJ, Gu H. The origin of populations of Arabidopsis thaliana in China, based on the chloroplast DNA sequences. BMC Plant Biol. 2010;10:22.
Article
PubMed
PubMed Central
Google Scholar
He F, Kang D, Ren Y, Qu LJ, Zhen Y, Gu H. Genetic diversity of the natural populations of Arabidopsis thaliana in China. Heredity (Edinb). 2007;99:423–31.
Article
CAS
Google Scholar
Gaut B. Arabidopsis thaliana as a model for the genetics of local adaptation. Nat Genet. 2012;44:115–6.
Article
CAS
PubMed
Google Scholar
Scheinfeldt LB, Tishkoff SA. Recent human adaptation: genomic approaches, interpretation and insights. Nat Rev Genet. 2013;14:692–702.
Article
PubMed
PubMed Central
Google Scholar
Ellegren H. Genome sequencing and population genomics in non-model organisms. Trends Ecol Evol. 2014;29:51–63.
Article
PubMed
Google Scholar
Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, et al. Patterns of population epigenomic diversity. Nature. 2013;495:193–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schiffels S, Durbin R. Inferring human population size and separation history from multiple genome sequences. Nat Genet. 2014;46:919–25.
Article
CAS
PubMed
PubMed Central
Google Scholar
Excoffier L, Dupanloup I, Huerta-Sanchez E, Sousa VC, Foll M. Robust demographic inference from genomic and SNP data. PLoS Genet. 2013;9:e1003905.
Article
PubMed
PubMed Central
Google Scholar
Gómez-Mena C, Pineiro M, Franco-Zorrilla JM, Salinas J, Coupland G, Martinez-Zapater JM. Early bolting in short days: an Arabidopsis mutation that causes early flowering and partially suppresses the floral phenotype of leafy. Plant Cell. 2001;13:1011–24.
Article
PubMed
PubMed Central
Google Scholar
Pineiro M, Gomez-Mena C, Schaffer R, Martinez-Zapater JM, Coupland G. EARLY BOLTING IN SHORT DAYS is related to chromatin remodeling factors and regulates flowering in Arabidopsis by repressing FT. Plant Cell. 2003;15:1552–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Proveniers M, Rutjens B, Brand M, Smeekens S. The Arabidopsis TALE homeobox gene ATH1 controls floral competency through positive regulation of FLC. Plant J. 2007;52:899–913.
Article
CAS
PubMed
Google Scholar
Zacharaki V, Benhamed M, Poulios S, Latrasse D, Papoutsoglou P, Delarue M, et al. The Arabidopsis ortholog of the YEATS domain containing protein YAF9a regulates flowering by controlling H4 acetylation levels at the FLC locus. Plant Sci. 2012;196:44–52.
Article
CAS
PubMed
Google Scholar
Mendez-Vigo B, Martinez-Zapater JM, Alonso-Blanco C. The flowering repressor SVP underlies a novel Arabidopsis thaliana QTL interacting with the genetic background. PLoS Genet. 2013;9:e1003289.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yuan W, Luo X, Li Z, Yang W, Wang Y, Liu R, et al. A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis. Nat Genet. 2016;48:1527–34.
Article
CAS
PubMed
Google Scholar
Zhai H, Ning W, Wu H, Zhang X, Lu S, Xia Z. DNA-binding protein phosphatase AtDBP1 acts as a promoter of flowering in Arabidopsis. Planta. 2016;243:623–33.
Article
CAS
PubMed
Google Scholar
Zhang L, Zhang X, Ju H, Chen J, Wang S, Wang H, et al. Ovate family protein1 interaction with BLH3 regulates transition timing from vegetative to reproductive phase in Arabidopsis. Biochem Biophys Res Commun. 2016;470:492–7.
Article
CAS
PubMed
Google Scholar
Huang X, Zhang Y, Zhang X, Shi Y. Long-chain base kinase1 affects freezing tolerance in Arabidopsis thaliana. Plant Sci. 2017;259:94–103.
Article
CAS
PubMed
Google Scholar
An L, Zhou Z, Sun L, Yan A, Xi W, Yu N, et al. A zinc finger protein gene ZFP5 integrates phytohormone signaling to control root hair development in Arabidopsis. Plant J. 2012;72:474–90.
Marzol E, Borassi C, Denita Juarez SP, Mangano S, Estevez JM. RSL4 takes control: multiple signals, one transcription factor. Trends Plant Sci. 2017;22:553–5.
Article
CAS
PubMed
Google Scholar
Stetter MG, Benz M, Ludewig U. Increased root hair density by loss of WRKY6 in Arabidopsis thaliana. PeerJ. 2017;5:e2891.
Salome PA, To JP, Kieber JJ, McClung CR. Arabidopsis response regulators ARR3 and ARR4 play cytokinin-independent roles in the control of circadian period. Plant Cell. 2006;18:55–69.
Article
CAS
PubMed
PubMed Central
Google Scholar
Le Roux C, Huet G, Jauneau A, Camborde L, Tremousaygue D, Kraut A, et al. A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity. Cell. 2015;161:1074–88.
Article
PubMed
Google Scholar
Sarris PF, Duxbury Z, Huh SU, Ma Y, Segonzac C, Sklenar J, et al. A plant immune receptor detects pathogen effectors that target WRKY transcription factors. Cell. 2015;161:1089–100.
Article
CAS
PubMed
Google Scholar
Palma K, Thorgrimsen S, Malinovsky FG, Fiil BK, Nielsen HB, Brodersen P, et al. Autoimmunity in Arabidopsis acd11 is mediated by epigenetic regulation of an immune receptor. PLoS Pathog. 2010;6:e1001137.
Munch D, Teh OK, Malinovsky FG, Liu Q, Vetukuri RR, El Kasmi F, et al. Retromer contributes to immunity-associated cell death in Arabidopsis. Plant Cell. 2015;27:463–79.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lachance J, Tishkoff SA. Population genomics of human adaptation. Annu Rev Ecol Evol Syst. 2013;44:123–43.
Article
PubMed
PubMed Central
Google Scholar
Jeong C, Di Rienzo A. Adaptations to local environments in modern human populations. Curr Opin Genet Dev. 2014;29:1–8.
Article
CAS
PubMed
Google Scholar
Weinig C, Ewers BE, Welch SM. Ecological genomics and process modeling of local adaptation to climate. Curr Opin Plant Biol. 2014;18:66–72.
Article
PubMed
Google Scholar
Yano K, Yamamoto E, Aya K, Takeuchi H, Lo PC, Hu L, et al. Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nat Genet. 2016;48:927–34.
Article
CAS
PubMed
Google Scholar
Lee JH, Ryu HS, Chung KS, Pose D, Kim S, Schmid M, et al. Regulation of temperature-responsive flowering by MADS-box transcription factor repressors. Science. 2013;342:628–32.
Article
CAS
PubMed
Google Scholar
Pose D, Verhage L, Ott F, Yant L, Mathieu J, Angenent GC, et al. Temperature-dependent regulation of flowering by antagonistic FLM variants. Nature. 2013;503:414–7.
Article
CAS
PubMed
Google Scholar
Wilczek AM, Cooper MD, Korves TM, Schmitt J. Lagging adaptation to warming climate in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2014;111:7906–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colautti RI, Barrett SC. Rapid adaptation to climate facilitates range expansion of an invasive plant. Science. 2013;342:364–6.
Article
CAS
PubMed
Google Scholar
Fan S, Hansen MEB, Lo Y, Tishkoff SA. Going global by adapting local: A review of recent human adaptation. Science. 2016;354:54–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee JH, Yoo SJ, Park SH, Hwang I, Lee JS, Ahn JH. Role of SVP in the control of flowering time by ambient temperature in Arabidopsis. Genes Dev. 2007;21:397–402.
Zou YP, Hou XH, Wu Q, Li ZW, Han TS, Niu XM, et al. Adaptation of Arabidopsis thaliana to the Yangtze River basin. NCBI SRA. 2017;BioProject Accession:PRJNA293798; SRP062811.
Doyle JJ, Doyle JL. A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochem Bull. 1987;19:11–5.
Google Scholar
Guo YL, Todesco M, Hagmann J, Das S, Weigel D. Independent FLC mutations as causes of flowering-time variation in Arabidopsis thaliana and Capsella rubella. Genetics. 2012;192:729–39.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
Article
PubMed
PubMed Central
Google Scholar
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19:1655–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38:904–9.
Article
CAS
PubMed
Google Scholar
Feisenstein J. PHYLIP-phylogeny inference package (version 3.2). Cladistics. 1989;5:164–6.
Google Scholar
Hu TT, Pattyn P, Bakker EG, Cao J, Cheng JF, Clark RM, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet. 2011;43:476–81.
Article
PubMed
PubMed Central
Google Scholar
Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F, Guo YL, et al. The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet. 2013;45:831–5.
Article
CAS
PubMed
Google Scholar
Berglund AC, Sjolund E, Ostlund G, Sonnhammer EL. InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res. 2008;36:D263–266.
Article
CAS
PubMed
Google Scholar
Ossowski S, Schneeberger K, Lucas-Lledo JI, Warthmann N, Clark RM, Shaw RG, et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science. 2010;327:92–4.
Article
CAS
PubMed
Google Scholar
Salomé PA, Bomblies K, Fitz J, Laitinen RA, Warthmann N, Yant L, et al. The recombination landscape in Arabidopsis thaliana F2 populations. Heredity (Edinb). 2012;108:447–55.
Article
Google Scholar
Phillips SJ, Anderson RP, Schapire RE. Maximum entropy modeling of species geographic distributions. Ecol Model. 2006;190:231–59.
Article
Google Scholar
Han TS, Wu Q, Hou XH, Li ZW, Zou YP, Ge S, et al. Frequent introgressions from diploid species contribute to the adaptation of the tetraploid Shepherd’s purse (Capsella bursa-pastoris). Mol Plant. 2015;8:427–38.
Article
CAS
PubMed
Google Scholar
DeGiorgio M, Huber CD, Hubisz MJ, Hellmann I, Nielsen R. SweepFinder2: increased sensitivity, robustness and flexibility. Bioinformatics. 2016;32:1895–7.
Article
CAS
PubMed
Google Scholar
Alachiotis N, Stamatakis A, Pavlidis P. OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. Bioinformatics. 2012;28:2274–5.
Article
CAS
PubMed
Google Scholar
Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics. 2005;21:3448–9.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25:2865–71.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zou YP, Hou XH, Wu Q, Li ZW, Han TS, Niu XM, et al. Adaptation of Arabidopsis thaliana to the Yangtze River basin. NCBI GenBank. 2017;GenBank accession number:MF663187-MF663188.