Abdel-Ghani AH, Parzies HK, Omary A, Geiger HH (2004) Estimating the outcrossing rate of barley landraces and wild barley populations collected from ecologically different regions of Jordan Theor Appl Genet 109(3):588–595
Google Scholar
Akerman A, Bürger R (2014) The consequences of gene flow for local adaptation and differentiation: a two-locus two-deme model J Math Biol 68(5):1135–1198
Google Scholar
Al-Asadi H, Petkova D, Stephens M, Novembre J (2019) Estimating recent migration and population-size surfaces PLoS Genet 15(1):e1007908
Google Scholar
Baker HG (1967) Support for Baker’s law-as a rule Evolution 21(4):853–856
Google Scholar
Baker K, Baker K, Bayer M, Cook N, Dreißig S, Dhillon T, Russell J, Hedley PE, Morris J, Ramsay L, Colas I et al. (2014) The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression Plant J 79(6):981–992
Google Scholar
Battey C, Ralph PL, Kern AD (2020) Space is the place: effects of continuous spatial structure on analysis of population genetic data Genetics 215(1):193–214
Google Scholar
Baum M, Grando S, Backes G, Jahoor A, Sabbagh A, Ceccarelli S (2003) QTLs for agronomic traits in the mediterranean environment identified in recombinant inbred lines of the cross’ Arta’ × H. spontaneum 41-1 Theor Appl Genet 107(7):1215–1225
Google Scholar
Bedada G, Westerbergh A, Nevo E, Korol A, Schmid KJ (2014) DNA sequence variation of wild barley Hordeum spontaneum (L.) across environmental gradients in Israel Heredity 112(6):646–655
Google Scholar
Berner D, Roesti M (2017) Genomics of adaptive divergence with chromosome-scale heterogeneity in crossover rate Mol Ecol 26(22):6351–6369
Google Scholar
Bhatia G, Patterson N, Sankararaman S, Price AL (2013) Estimating and interpreting FST: the impact of rare variants Genome Res 23(9):1514–1521
Google Scholar
Bohra A, Kilian B, Kilian B, Sivasankar S, Caccamo M, Mba, C, McCouch SR, Varshney RK (2021) Reap the crop wild relatives for breeding future crops. Trends Biotechnol. https://doi.org/10.1016/j.tibtech.2021.08.009
Bradburd GS, Coop GM, Ralph PL (2018) Inferring continuous and discrete population genetic structure across space. Genetics 210(1):33–52
Google Scholar
Bürger R, Akerman A (2011) The effects of linkage and gene flow on local adaptation: a two-locus continent–island model. Theor Popul Biol 80(4):272–288
Google Scholar
Cabreros I, Storey JD (2019) A likelihood-free estimator of population structure bridging admixture models and principal components analysis. Genetics 212(4):1009–1029
Google Scholar
Caldwell KS, Russell J, Langridge P, Powell W (2006) Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172(1):557–567
Google Scholar
Capblancq T, Luu K, Blum MG, Bazin E (2018) Evaluation of redundancy analysis to identify signatures of local adaptation. Mol Ecol Resour 18(6):1223–1233
Google Scholar
Caye K, Jumentier B, Lepeule J, François O (2019) LFMM 2: fast and accurate inference of gene-environment associations in genome-wide studies. Mol Biol Evol 36(4):852–860
Google Scholar
Contreras-Moreira B, Serrano-Notivoli R, Mohammed NE, Cantalapiedra CP, Beguería S, Casas AM, Igartua E (2019) Genetic association with high-resolution climate data reveals selection footprints in the genomes of barley landraces across the Iberian Peninsula. Mol Ecol 28(8):1994–2012
Google Scholar
Dawson IK, Russell J, Powell W, Steffenson B, Thomas WTB, Waugh R (2015) Barley: a translational model for adaptation to climate change. New Phytol 206(3):913–931
Google Scholar
Dray S, Legendre P, Peres-Neto PR (2006) Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (pcnm). Ecol Model 196(3-4):483–493
Dray S, Bauman D, Blanchet G, Borcard D, Clappe S, Guenard G, Jombart T, Larocque G, Legendre P, Madi N, Wagner HH (2019) adespatial: multivariate multiscale spatial analysis. R package version 0.3-7. https://CRAN.R-project.org/package=adespatial
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5):e19379
Google Scholar
Excoffier L, Hofer T, Foll M (2009) Detecting loci under selection in a hierarchically structured population. Heredity 103(4):285–298
Google Scholar
Fang Z, Gonzales AM, Clegg MT, Smith KP, Muehlbauer GJ, Steffenson BJ, Morrell PL (2014) Two genomic regions contribute disproportionately to geographic differentiation in wild barley. G34(7):1193–1203
Google Scholar
Fick SE, Hijmans RJ (2017) Worldclim 2: new 1-km spatial resolution climate surfaces for global land areas. Int J Climatol 37(12):4302–4315
Forester BR, Lasky JR, Wagner HH, Urban DL (2018) Comparing methods for detecting multilocus adaptation with multivariate genotype–environment associations. Mol Ecol 27(9):2215–2233
Google Scholar
Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR (2016) Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes. Mol Ecol 25(1):104–120
Google Scholar
Galkin E, Dalal A, Evenko A, Fridman E, Kan I, Wallach R, Moshelion M (2018) Risk-management strategies and transpiration rates of wild barley in uncertain environments. Physiol Plant 164(4):412–428
Google Scholar
Gautier M (2015) Genome-wide scan for adaptive divergence and association with population-specific covariates. Genetics 201(4):1555–1579
Google Scholar
Gibson MJ, Moyle LC (2020) Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species. Mol Ecol 29(12):2204–2217
Google Scholar
Günther T, Coop G (2013) Robust identification of local adaptation from allele frequencies. Genetics 195(1):205–220
Google Scholar
Gutaker RM, Groen SC, Bellis ES, Choi JY, Pires IS, Bocinsky RK, Slayton ER, Wilkins O, Castillo CC, Negrão S et al. (2020) Genomic history and ecology of the geographic spread of rice. Nat Plants 6(5):492–502
Google Scholar
Hämälä T, Savolainen O (2019) Genomic patterns of local adaptation under gene flow in arabidopsis lyrata. Mol Biol Evol 36(11):2557–2571
Harlan JR, Zohary D (1966) Distribution of wild wheats and barley. Science 153(3740):1074–1080
Google Scholar
Hartfield M, Bataillon T, Glémin S (2017) The evolutionary interplay between adaptation and self-fertilization. Trends Genet 33(6):420–431
Google Scholar
Hendrick MF, Finseth FR, Mathiasson ME, Palmer KA, Broder EM, Breigenzer P, Fishman L (2016) The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene underlying leaf trichome divergence in yellowstone mimulus guttatus. Mol Ecol 25(22):5647–5662
Google Scholar
Hengl T, Mendes de Jesus J, Heuvelink GBM, Ruiperez Gonzalez M, Kilibarda M, Blagotić A, Shangguan W, Wright MN, Geng X, Bauer-Marschallinger B et al. (2017) Soilgrids250m: Global gridded soil information based on machine learning. PLoS ONE 12(2):e0169748
Google Scholar
Herzig P, Herzig P, Maurer A, Draba V, Sharma R, Draicchio F, Bull H, Milne L, Thomas WTB, Flavell AJ, Pillen K (2018) Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping. J Exp Bot 69(7):1517–1531
Google Scholar
Hill W, Weir B (1988) Variances and covariances of squared linkage disequilibria in finite populations. Theor Popul Biol 33(1):54–78
Google Scholar
Hodgins KA, Yeaman S (2019) Mating system impacts the genetic architecture of adaptation to heterogeneous environments. New Phytol 224(3):1201–1214
Google Scholar
House GL, Hahn MW (2018) Evaluating methods to visualize patterns of genetic differentiation on a landscape. Mol Ecol Resour 18(3):448–460
Google Scholar
Hübner S, Korol AB, Schmid KJ (2015) Rna-seq analysis identifies genes associated with differential reproductive success under drought-stress in accessions of wild barley hordeum spontaneum. BMC Plant Biol15(1):1–14
Hübner S, Bdolach E, Ein-Gedy S, Schmid KJ, Korol A, Fridman E (2013) Phenotypic landscapes: phenological patterns in wild and cultivated barley. J Evol Biol 26(1):163–174
Google Scholar
Hübner S, Günther T, Flavell A, Fridman E, Graner A, Korol A, Schmid KJ (2012) Islands and streams: clusters and gene flow in wild barley populations from the Levant. Mol Ecol 21(5):1115–1129
Google Scholar
Hübner S, Höffken M, Oren E, Haseneyer G, Stein N, Graner A, Schmid K, Fridman E (2009) Strong correlation of wild barley (Hordeum spontaneum) population structure with temperature and precipitation variation. Mol Ecol 18(7):1523–1536
Google Scholar
Jakob SS, Rödder D, Engler JO, Shaaf S, Özkan H, Blattner FR, Kilian B (2014) Evolutionary history of wild barley (Hordeum vulgare subsp. spontaneum) analyzed using multilocus sequence data and paleodistribution modeling. Genome Biol Evol 6(3):685–702
Google Scholar
Jayakodi M, Padmarasu S, Haberer G, Bonthala VS, Gundlach H, Monat C, Lux T, Kamal N, Lang D, Himmelbach A, Ens J, Zhang X-Q, Angessa TT, Zhou G, Tan C, Hill C, Wang P, Schreiber M, Boston LB, Plott C, Jenkins J, Guo Y, Fiebig A, Budak H, Xu D, Zhang J, Wang C, Grimwood J, Schmutz J, Guo G, Zhang G, Mochida K, Hirayama T, Sato K, Chalmers KJ, Langridge P, Waugh R, Pozniak CJ, Scholz U, Mayer KFX, Spannagl M, Li C, Mascher M, Stein N (2020) The barley pan-genome reveals the hidden legacy of mutation breeding Nature 588:284–289. https://doi.org/10.1038/s41586-020-2947-8
Google Scholar
Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecol Lett 7(12):1225–1241
Kilian B, Özkan H, Kohl J, von Haeseler A, Barale F, Deusch O, Brandolini A, Yucel C, Martin W, Salamini F (2006) Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol Genet Genom 276(3):230–241
Google Scholar
Lasky JR, Des Marais DL, McKAY JK, Richards JH, Juenger TE, Keitt TH (2012) Characterizing genomic variation of arabidopsis thaliana: the roles of geography and climate. Mol Ecol 21(22):5512–5529
Google Scholar
Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE et al. (2015) Genome-environment associations in sorghum landraces predict adaptive traits. Sci Adv 1(6):e1400218
Google Scholar
Lawson DJ, Van Dorp L, Falush D (2018) A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots. Nat Commun 9(1):1–11
Google Scholar
Lee C-R, Mitchell-Olds T (2011) Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Mol Ecol 20(22):4631–4642
Google Scholar
Leek JT (2011) Asymptotic conditional singular value decomposition for high-dimensional genomic data. Biometrics 67(2):344–352
Google Scholar
Legendre P, Legendre L (2012) Canonical analysis. In: Numerical ecology, 3rd English edn, chap. 11. Elsevier Science BV, The Netherlands, pp 625–710
López-Goldar X, Agrawal AA (2021) Ecological interactions, environmental gradients, and gene flow in local adaptation Trends Plant Sci 26(8):796–809
Google Scholar
Lotterhos KE, Whitlock MC (2015) The relative power of genome scans to detect local adaptation depends on sampling design and statistical method. Mol Ecol 24(5):1031–1046
Google Scholar
Lundgren E, Ralph PL (2019) Are populations like a circuit? Comparing isolation by resistance to a new coalescent-based method. Mol Ecol Resour 19(6):1388–1406
Google Scholar
Makowski D, Ben-Shachar M, Lüdecke D (2019) bayestestR: describing effects and their uncertainty, existence and significance within the Bayesian framework. J Open Source Softw 4(40):1541
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J et al. (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544(7651):427–433
Google Scholar
Mascher M (2019) Pseudomolecules and annotation of the second version of the reference genome sequence assembly of barley cv. morex [morex v2]. https://doi.ipk-gatersleben.de:443/DOI/83e8e186-dc4b-47f7-a820-28ad37cb176b/d1067eba-1d08-42e2-85ec-66bfd5112cd8/2
McVean G (2009) A genealogical interpretation of principal components analysis. PLoS Genet 5(10):e1000686
Mee JA, Yeaman S (2019) Unpacking conditional neutrality: genomic signatures of selection on conditionally beneficial and conditionally deleterious mutations. Am Nat 194(4):529–540
Google Scholar
Milner SG, Jost M, Taketa S, Mazón ER, Himmelbach A, Oppermann M, Weise S, Knüpffer H, Basterrechea M, König P et al. (2019) Genebank genomics highlights the diversity of a global barley collection. Nat Genet 51(2):319–326
Google Scholar
Morrell PL, Toleno DM, Lundy KE, Clegg MT (2005) Low levels of linkage disequilibrium in wild barley (Hordeum vulgare ssp. spontaneum) despite high rates of self-fertilization. Proc Natl Acad Sci USA 102(7):2442–2447
Google Scholar
Navarro JAR, Willcox M, Burgueño J, Romay C, Swarts K, Trachsel S, Preciado E, Terron A, Delgado HV, Vidal V et al. (2017) A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat Genet 49(3):476
Nevo E, Zohary D, Brown A, Haber M (1979) Genetic diversity and environmental associations of wild barley, Hordeum spontaneum, in Israel. Evolution 33(3):815–833
Google Scholar
Nevo E, Beharav A, Meyer RC, Hackett CA, Forster BP, Russell JR, Powell W (2005) Genomic microsatellite adaptive divergence of wild barley by microclimatic stress in ‘Evolution Canyon’, Israel. Biol J Linn Soc84(2):205–224
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2019) vegan: community ecology package. R package version 2.5-6. https://CRAN.R-project.org/package=vegan
Pankin A, Altmüller J, Becker C, von Korff M (2018) Targeted resequencing reveals genomic signatures of barley domestication. New Phytol 218(3):1247–1259
Google Scholar
Pekel J-F, Cottam A, Gorelick N, Belward AS (2016) High-resolution mapping of global surface water and its long-term changes. Nature 540(7633):418–422
Google Scholar
Pembleton L, Cogan N, Forster J (2013) StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations Mol Ecol Res 13:946–952. https://doi.org/10.1111/1755-0998.12129
Google Scholar
Peterman WE (2018) Resistancega: an r package for the optimization of resistance surfaces using genetic algorithms. Methods Ecol Evol 9(6):1638–1647
Petkova D, Novembre J, Stephens M (2016) Visualizing spatial population structure with estimated effective migration surfaces. Nat Genet 48(1):94
Google Scholar
Pham A-T, Maurer A, Pillen K, Brien C, Dowling K, Berger B, Eglinton JK, March TJ (2019) Genome-wide association of barley plant growth under drought stress using a nested association mapping population. BMC Plant Biol 19(1):134
Google Scholar
Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7(2):e32253
Google Scholar
Pyhäjärvi T, Hufford MB, Mezmouk S, Ross-Ibarra J (2013) Complex patterns of local adaptation in teosinte. Genome Biol Evol 5(9):1594–1609
Google Scholar
Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R (2015) A practical guide to environmental association analysis in landscape genomics. Mol Ecol 24(17):4348–4370
Google Scholar
Renaut S, Grassa CJ, Yeaman S, Moyers BT, Lai Z, Kane NC, Bowers JE, Burke JM, Rieseberg LH (2013) Genomic islands of divergence are not affected by geography of speciation in sunflowers. Nat Commun 4(1):1–8
Russell J, Mascher M, Dawson IK, Kyriakidis S, Calixto C, Freund F, Bayer M, Milne I, Marshall-Griffiths T, Heinen S et al. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet 48(9):1024
Google Scholar
Samuk K, Samuk K, Owens GL, Delmore KE, Miller SE, Rennison DJ, Schluter D (2017) Gene flow and selection interact to promote adaptive divergence in regions of low recombination. Mol Ecol 26(17):4378–4390
Google Scholar
Sato K, Mascher M, Himmelbach A, Haberer G, Spannagl M, Stein N (2021) Chromosome-scale assembly of wild barley accession ‘OUH602’. G3 11(10):jkab244
Google Scholar
Schmid K, Kilian B. Russell J (2018) Barley domestication, adaptation and population genomics. In: The Barley Genome, Springer International Publishing: Cham, pp 317–336
Szkiba D, Kapun M, von Haeseler A, Gallach M (2014) SNP2GO: functional analysis of genome-wide association studies. Genetics 197(1):285–289
Google Scholar
Terrazas RA, Balbirnie-Cumming K, Morris J, Hedley PE, Russell J, Paterson E, Baggs EM, Fridman E, Bulgarelli D (2020) A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota. Sci Rep 10(1):1–13
Tiffin P, Ross-Ibarra J (2014) Advances and limits of using population genetics to understand local adaptation. Trends Ecol Evol 29(12):673–680
Google Scholar
Tsuda Y, Chen J, Stocks M, Källman T, Sønstebø JH, Parducci L, Semerikov V, Sperisen C, Politov D, Ronkainen T et al. (2016) The extent and meaning of hybridization and introgression between siberian spruce (picea obovata) and norway spruce (picea abies): cryptic refugia as stepping stones to the west? Mol Ecol 25(12):2773–2789
Google Scholar
Turner-Hissong SD, Mabry ME, Beissinger TM, Ross-Ibarra J, Pires JC (2020) Evolutionary insights into plant breeding Curr Opin Plant Biol 54:93–100. https://doi.org/10.1016/j.pbi.2020.03.003
Google Scholar
de Villemereuil P, Frichot É, Bazin É, François O, Gaggiotti OE (2014) Genome scan methods against more complex models: when and how much should we trust them? Mol Ecol 23(8):2006–2019
Google Scholar
Volis S (2011) Adaptive genetic differentiation in a predominantly self-pollinating species analyzed by transplanting into natural environment, crossbreeding and QST-FST test. New Phytol 192(1):237–248
Google Scholar
Volis S, Mendlinger S, Ward D (2002a) Differentiation in populations of Hordeum spontaneum along a gradient of environmental productivity and predictability: life history and local adaptation. Biol J Linn Soc 77(4):479–490
Volis S, Mendlinger S, Ward D (2002b) Adaptive traits of wild barley plants of Mediterranean and desert origin. Oecologia 133(2):131–138
Google Scholar
Volis S, Zaretsky M, Shulgina I (2010) Fine-scale spatial genetic structure in a predominantly selfing plant: role of seed and pollen dispersal. Heredity 105(4):384–393
Google Scholar
Volis S, Shulgina I, Ward D, Mendlinger S (2003) Regional subdivision in wild barley allozyme variation: adaptive or neutral? J Hered 94(4):341–351
Google Scholar
Volis S, Verhoeven K, Mendlinger S, Ward D (2004) Phenotypic selection and regulation of reproduction in different environments in wild barley. J Evol Biol 17(5):1121–1131
Google Scholar
Volis S, Yakubov B, Shulgina I, Ward D, Mendlinger S (2005) Distinguishing adaptive from nonadaptive genetic differentiation: comparison of q st and f st at two spatial scales. Heredity 95(6):466–475
Google Scholar
Volis S, Yakubov B, Shulgina I, Ward D, Zur V, Mendlinger S (2001) Tests for adaptive RAPD variation in population genetic structure of wild barley, Hordeum spontaneum Koch. Biol J Linn Soc 74(3):289–303
Wang X, Chen Z-H, Yang C, Zhang X, Jin G, Chen G, Wang Y, Holford P, Nevo E, Zhang G et al. (2018) Genomic adaptation to drought in wild barley is driven by edaphic natural selection at the Tabigha Evolution Slope. Proc Natl Acad Sci USA 115(20):5223–5228
Google Scholar
Wiegmann M, Wiegmann M, Maurer A, Pham A, March TJ, Al-Abdallat A, Thomas WTB, Bull HJ, Shahid M, Eglinton J, Baum M, Flavell AJ, Tester M, Pillen K (2019) Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues Sci Rep 9(1):6397. https://doi.org/10.1038/s41598-019-42673-1
Google Scholar
Yeaman S, Whitlock MC (2011) The genetic architecture of adaptation under migration–selection balance. Evolution 65(7):1897–1911
Google Scholar
Zheng X, Levine D, Shen J, Gogarten S, Laurie C, Weir B (2012) A high-performance computing toolset for relatedness and principal component analysis of snp data Bioinformatics 28(24):3326–3328. https://doi.org/10.1093/bioinformatics/bts606
Google Scholar
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