M. C. Whitlock, Modern approaches to local adaptation. The American 972 Naturalist. 2015;186. 973 2. Bradshaw AD. Ecological significance of genetic variation between 974 populations. Perspectives on plant population ecology, pp.213-241, 1984.

M. Bulmer, Multiple niche polymorphism, The American Naturalist, vol.976, pp.254-261, 1972.

J. A. Endler, Natural selection in the wild, p.354, 1986.

L. Gay, P. A. Crochet, D. A. Bell, and T. Lenormand, Comparing clines on molecular 979 and phenotypic traits in hybrid zones: A window on tension zone models, Evolution, vol.980, pp.2789-806, 2008.

R. Lande, Natural selection and random genetic drift in phenotypic evolution

, Evolution, vol.30, pp.314-348, 1976.

T. Lenormand, Gene flow and the limits to natural selection, Ecology and Evolution, vol.17, pp.183-192, 2002.

M. C. Whitlock and R. Gomulkiewicz, Probability of fixation in a heterogeneous 986 environment, Genetics, pp.1-40, 2005.

S. Yeaman and S. P. Otto, Establishment and maintenance of adaptive genetic 988 divergence under migration, selection and drift, Evolution, vol.67, p.10, 2011.

H. D. Rundle and P. Nosil, Ecological speciation, Ecology Letters, vol.8, p.11, 2005.

T. J. Kawecki and D. Ebert, Conceptual issues in local adaptation, Ecology Letters, vol.991, p.12, 2004.

J. Hereford, A quantitative survey of local adaptation and fitness trade-offs

R. Leimu and M. Fischer, A meta-analysis of local adaptation in plants, The American Naturalist, vol.173, pp.579-88, 2009.

P. Tiffin and J. Ross-ibarra, Advances and limits of using population genetics to 997 understand local adaptation, Trends in Ecology and Evolution, vol.29, p.16, 1997.

M. Slatkin, Rare alleles as indicators of gene flow, Evolution, vol.39, issue.1, p.17, 1985.

R. Lande, Neutral theory of quantitative genetic variance in an island model 1003 with local extinction and colonization, Evolution, vol.46, pp.381-390, 1992.

M. C. Whitlock, Neutral additive genetic variance in a metapopulation, Genetics 1005 Research, vol.74, pp.215-236, 1999.

K. Spitze, Population structure in Daphina obtusa: quantitative genetic and 1007 allozymic variation, Genetics Society of America, vol.135, pp.367-74, 1993.

S. Wright, The genetical structure of populations, Annals of Eugenics, vol.1009, pp.323-54, 1951.

E. Luquet, J. Léna, C. Miaud, S. Plénet, A. M. Roschanski et al., Phenotypic divergence of the common 1011 toad (Bufo bufo) along an altitudinal gradient: evidence for local adaptation, Heredity, vol.1012, p.1014, 2015.

H. Fdr, Evidence of divergent selection for drought and cold tolerance at 1015 landscape and local scales in Abies alba Mill. in the French Mediterranean Alps, Molecular Ecology, vol.25, pp.776-94, 1016.

T. Kawakami, T. J. Morgan, J. B. Nippert, T. W. Ocheltree, R. Keith et al., Natural selection drives clinal life history patterns in the perennial sunflower species, p.1019, 1018.

, Helianthus maximiliani. Molecular Ecology, vol.20, pp.2318-2346, 2011.

B. T. Moyers and L. H. Rieseberg, Remarkable life history polymorphism may be 1021 evolving under divergent selection in the silverleaf sunflower, Molecular Ecology, vol.1022, p.25, 2016.

M. Kirkpatrick and N. Barton, Chromosome inversions, local adaptation and 1024 speciation, Genetics, vol.1025, p.26, 2006.

D. B. Lowry and J. H. Willis, A widespread chromosomal inversion polymorphism 1026 contributes to a major life-history transition, local adaptation, and reproductive 1027 isolation, PLoS Biology, vol.8, 2010.

D. Legrand, N. Larranaga, R. Bertrand, S. Ducatez, O. Calvez et al., 1029 Evolution of a butterfly dispersal syndrome, vol.1030, p.28, 2016.

N. Bierne, J. Welch, E. Loire, F. Bonhomme, and P. David, Lewontin RC, Krakauer J. Distribution of gene frequency as a test of the 1034 theory of the selective neutrality of polymorphisms, Molecular Ecology, vol.1032, p.30, 1033.

M. A. Beaumont, R. A. Nichols, R. Vitalis, K. Dawson, and P. Boursot, Evaluating loci for use in the genetic analysis of 1036 population structure, Proceedings of the Royal Society B: Biological Sciences, vol.1037, p.32, 1996.

M. Foll and O. Gaggiotti, A genome scan method to identify selected loci 1041 appropriate for both dominant and codominant markers: A Bayesian perspective

, Genetics, vol.180, pp.977-93, 2008.

E. Lah and M. Foll, Detecting loci under selection in a 1044 hierarchically structured population, Heredity, vol.103, p.34, 2009.

M. Bonhomme, C. Chevalet, B. Servin, S. Boitard, J. Abdallah et al., Detecting selection in population trees: The Lewontin and Krakauer test extended, 1046.
URL : https://hal.archives-ouvertes.fr/hal-00842515

, Genetics, vol.186, pp.241-62, 2010.

T. Günther, G. Coop, K. E. Lotterhos, and M. C. Whitlock, Haasl RJ, Payseur BA. Fifteen years of genomewide scans for selection: 1054 trends, lessons and unaddressed genetic sources of complication, Genetics Society of America, vol.195, p.38, 1050.

L. Corre, V. Kremer, and A. , The genetic differentiation at quantitative trait loci 1057 under local adaptation, Molecular Ecology, vol.21, p.39, 2012.

X. Yi, Y. Liang, E. Huerta-sanchez, J. X. , X. P. Cuo et al.,

G. Coop, D. Witonsky, D. Rienzo, A. Pritchard, and J. K. , Using environmental 1062 correlations to identify loci underlying local adaptation, Genetics, vol.1060, p.41, 1061.

G. Guillot, S. Renaud, R. Ledevin, J. Michaux, and C. J. , A unifying model for 1064 the analysis of phenotypic, genetic, and geographic data, vol.61, pp.897-911, 2012.

E. Frichot, S. D. Schoville, G. Bouchard, and O. François, Testing for associations 1066 between loci and environmental gradients using latent factor mixed models

, Molecular Biology and Evolution, vol.30, p.43, 2013.

M. Gautier, S. Joost, A. Bonin, M. W. Bruford, L. Després et al., A 1071 spatial analysis method (SAM) to detect candidate loci for selection: Towards a 1072 landscape genomics approach to adaptation, Molecular Ecology, vol.201, p.46, 1070.

S. De-mita, A. C. Thuillet, L. Gay, N. Ahmadi, S. Manel et al., Detecting selection along environmental gradients: Analysis of eight methods and 1078 their effectiveness for outbreeding and selfing populations, Molecular Ecology, vol.1079, p.47, 1077.

S. Hoban, J. L. Kelley, K. E. Lotterhos, M. F. Antolin, G. Bradburd et al., 1081 Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future 1082 directions, The American Naturalist, vol.188, p.48, 2016.

N. Barton, J. Hermisson, M. Nordborg, A. Fournier-level, A. Korte et al., 1092 Inferences from the historical distribution of wild and domesticated maize provide 1093 ecological and evolutionary insight, Genetics, vol.334, pp.7-1094, 1086.

P. Bilinski, P. S. Albert, J. J. Berg, J. A. Birchler, M. N. Grote et al., Parallel 1095 altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

C. M. Diez, B. S. Gaut, E. Meca, E. Scheinvar, S. Montes-hernandez et al., Genome size variation in wild and cultivated maize along altitudinal gradients, PLoS Genetics, 2018.

T. Pyhäjärvi, M. B. Hufford, S. Mezmouk, J. Ross-ibarra, Z. Fang et al., Complex patterns of 1101 local adaptation in teosinte, Genome Biology and Evolution, vol.199, p.1103, 1100.

. Jdj, Megabase-scale inversion polymorphism in the wild ancestor of maize

, Genetics, vol.191, pp.883-94, 2012.

J. A. Aguirre-liguori, M. I. Tenaillon, A. Vázquez-lobo, and B. S. Gaut, , p.1106

J. P. Correa and S. Montes-hernandez, Connecting genomic patterns of local 1107 adaptation and niche suitability in teosintes, Molecular Ecology, vol.26, p.1109, 1108.

Y. Vigouroux, Signatures of local adaptation in lowland and highland teosintes 1110 from whole-genome sequencing of pooled samples, Molecular Ecology, vol.1111, pp.2738-56, 1112.

, Genetics, vol.189, pp.621-653, 2011.

G. J. Mckinney, A. Varian, J. Scardina, and K. M. Nichols, Genetic and morphological 1116 divergence in three strains of brook trout Salvelinus fontinalis commonly stocked in 1117 Lake Superior, PLoS ONE, vol.9, issue.12, pp.113809-1119, 1118.

M. Sohail, R. M. Maier, A. Ganna, A. Bloemendal, A. R. Martin et al.,

, Polygenic adaptation on height is overestimated due to uncorrected stratification in 1121 genome-wide association studies. eLife. 2019;8. 1122 62. Desrousseaux AD, Sandron F, Siberchicot A, Cierco-Ayrolles C, Mangin B. 1123 Package ' LDcorSV, vol.1124, p.63, 2017.

B. Mangin, A. Siberchicot, S. Nicolas, A. Doligez, P. This et al.,

, Novel measures of linkage disequilibrium that correct the bias due to population 1126 structure and relatedness, Heredity, vol.108, p.64, 2012.

O. Savolainen, M. Lascoux, and J. Merilä, Ecological genomics of local adaptation, Nature reviews Genetics, vol.14, p.65, 1128.

J. T. Anderson, J. H. Willis, and T. Mitchell-olds, Evolutionary genetics of plant 1130 adaptation, Trends in Genetics, vol.27, p.66, 2011.

A. H. Halbritter, S. Fior, I. Keller, R. Billeter, P. J. Edwards et al., 1132 Trait differentiation and adaptation of plants along elevation gradients, Journal of 1133 Evolutionary Biology, vol.31, issue.6, p.67, 2018.

C. Körner, A. D. Friend, F. I. Woodward, and V. R. Switsur, Field measurements of 1137 photosynthesis, stomatal conductance, leaf nitrogen and ? 13 C along altitudinal 1138 gradients in Scotland, Frontiers in Plant Science. 1140, vol.22, pp.117-1139, 1136.

H. Frohnmeyer, D. Staiger, S. G. Byars, W. Papst, and A. A. Hoffmann, Luo Y, Widmer A, Karrenberg S. The roles of genetic drift and natural 1148 selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis 1149 thaliana, Evolution, vol.1143, pp.220-228, 2007.

G. R. Guerin, H. Wen, A. J. Lowe, G. R. Guerin, and H. Wen, Leaf morphology shift 1151 linked to climate change, Population Ecology, vol.2012, p.74

G. Kofidis, A. M. Bosabalidis, and M. Moustakas, Contemporary seasonal and 1153 altitudinal variations of leaf structural features in oregano

B. Mendez-vigo, F. X. Pico, M. Ramiro, J. M. Martinez-zapater, and A. , Annals of Botany, vol.92, issue.5, pp.635-680, 1155.

C. Oleksyn, J. Modrzynski, J. Tjoelker, M. G. Zytkowaik, R. Reich et al., Karolewski 1159 P. Growth and physiology of Picea abies populations from elevational transects: 1160 common garden evidence for altitudinal ecotypes and cold adaptation. 1998:573-90. 1161 77. Soularue JP, Kremer A. Evolutionary responses of tree phenology to the 1162 combined effects of assortative mating, gene flow and divergent selection, Plant Physiology, vol.157, pp.485-94, 1158.

J. F. Doebley, Maize introgression into teosinte --a reappraisal, vol.71, p.79, 1984.

N. Lauter, C. Gustus, A. Westerbergh, J. Doebley, J. Smith et al., The inheritance and evolution 1167 of leaf pigmentation and pubescence in teosinte, Genetics Society of America, vol.1168, p.82, 1169.

H. Dittberner, A. Korte, T. Mettler-altmann, and A. Weber,

J. Meaux, J. E. Carlson, C. A. Adams, and K. E. Holsinger, Intraspecific variation in stomatal 1177 traits, leaf traits and physiology reflects adaptation along aridity gradients in a South 1178 African shrub, Molecular Ecology, vol.83, p.84, 1176.

C. Körner, R. Mayr, C. C. Bresson, Y. Vitasse, A. Kremer et al., Replicate 1186 altitudinal clines reveal that evolutionary flexibility underlies adaptation to drought 1187 stress in annual Mimulus guttatus, Plants 1181 and their Atmospheric Environment, vol.85, p.87, 1182.

C. Körner, M. Neumayer, S. P. Menendez-riedl, A. Smeets-scheel, E. S. Buckler et al., Jakobsson A, Eriksson O. A comparative study of seed number, seed size, 1191 seedling size and recruitment in grassland plants, Science, vol.182, p.90, 1190.

L. Moreau, A. Charcosset, and A. Gallais, Use of trial clustering to study QTL x 1195 environment effects for grain yield and related traits in maize. Theoretical and 1196 Applied Genetics, vol.110, pp.92-105, 2004.

E. Durand, S. Bouchet, P. Bertin, A. Ressayre, P. Jamin et al., Flowering time in maize: Linkage and epistasis at a major effect locus, Genetics, vol.1199, p.92, 1198.

D. Li, X. Wang, X. Zhang, Q. Chen, G. Xu et al., The genetic architecture 1201 of leaf number and its genetic relationship to flowering time in maize, New 1202 Phytologist, vol.210, pp.256-68, 2015.

J. A. Aguirre-liguori, B. S. Gaut, J. P. Jaramillo-correa, M. I. Tenaillon, S. Montes-1204--hernández et al., Divergence with gene flow is driven by local 1205 adaptation to temperature and soil phosphorus concentration in teosinte subspecies ( 1206 Zea mays parviglumis and Zea mays mexicana) Molecular Ecology. 2019:2814-30. 1207 94. Consortium G. 1,135 Genomes reveal the global pattern of polymorphism in 1208 Arabidopsis thaliana, Genetics, vol.166, issue.4, p.96, 2016.

J. Guo, Y. Wu, Z. Zhu, Z. Zheng, M. Trzaskowski et al., Global genetic 1212 differentiation of complex traits shaped by natural selection in humans, Communications, vol.9, issue.1, p.1865, 1213.

J. J. Berg, A. Harpak, N. Sinnott-armstrong, A. M. Joergensen, H. Mostafavi et al., Genetic diversity 1218 and selection in the maize starch pathway. Proceedings of the National Academy of 1219 Sciences of the United States of America, vol.1216, pp.1206-1215, 1217.

A. L. Weber, W. H. Briggs, J. Rucker, B. M. Baltazar, J. De et al.,

J. and F. P. , The genetic architecture of complex traits in teosinte (Zea mays ssp. 1224 parviglumis): New evidence from association mapping, Genetics, vol.180, pp.1221-1253, 2008.

S. Bouchet, B. Servin, P. Bertin, D. Madur, V. Combes et al., Adaptation of maize to temperate climates: Mid-density genome-wide association 1227 genetics and diversity patterns reveal key genomic regions, with a major contribution 1228 of the Vgt2 (ZCN8) locus, PLoS ONE, vol.8, 1226.

M. J. Sheehan, L. M. Kennedy, D. E. Costich, and T. P. Brutnell, Subfunctionalization of 1230 PhyB1 and PhyB2 in the control of seedling and mature plant traits in maize, Journal, vol.49, pp.338-53, 1231.

O. N. Danilevskaya, X. Meng, Z. Hou, E. V. Ananiev, and C. R. Simmons, A genomic 1233 and expression compendium of the expanded PEBP gene family from maize, Physiology, vol.146, pp.250-64, 1234.

X. Meng, M. G. Muszynski, and O. N. Danilevskaya, The FT-Like ZCN8 gene 1236 functions as a floral activator and is involved in photoperiod sensitivity in maize. The 1237 Plant Cell, vol.23, pp.942-60, 2011.

Y. X. Li, C. Li, P. J. Bradbury, X. Liu, F. Lu et al., Identification of 1239 genetic variants associated with maize flowering time using an extremely large multi-1240 genetic background population. The Plant journal : for cell and molecular biology, vol.86, pp.391-402, 1241.

J. Yu, X. Li, C. Zhu, C. Yeh, W. Wu et al., Genic and non-genic 1243 contributions to natural variation of quantitative traits in maize, Genome research, pp.2436-2480, 1244.

M. Wellenreuther and L. Bernatchez, Eco-evolutionary genomics of chromosomal 1246 inversions, Trends in Ecology and Evolution, vol.33, pp.427-467, 2018.

D. Ayala, A. Ullastres, and J. González, Adaptation through chromosomal 1248 inversions in Anopheles, Frontiers in Genetics, vol.5, pp.1-10, 2014.

J. Barth, P. R. Berg, P. R. Jonsson, S. Bonanomi, H. Corell et al., Genome architecture enables local adaptation of Atlantic cod despite high 1251 connectivity, Molecular Ecology, vol.26, pp.4452-66, 2017.

M. Lundberg, M. Liedvogel, K. Larson, H. Sigeman, M. Grahn et al., Genetic differences between willow warbler migratory phenotypes are few and cluster 1254 in large haplotype blocks, Evolution Letters, vol.2017, pp.155-68, 1253.

A. D. Twyford and J. Friedman, Adaptive divergence in the monkey flower Mimulus 1256 guttatus is maintained by a chromosomal inversion, Evolution, vol.69, pp.1476-86, 2015.

C. M. Díez, B. S. Gaut, E. Meca, E. Scheinvar, S. Montes-hernandez et al., Genome size variation in wild and cultivated maize along altitudinal 1259 gradients, New Phytologist, vol.199, issue.1, pp.264-76, 2013.

R. J. Hijmans, J. Van-etten, J. Cheng, M. Mattiuzzi, M. Sumner et al., Package 'raster ': geographic data analysis and modeling, 2018.

F. Husson, J. Josse, S. Le, and J. Mazet, Package ' FactoMineR '. An R package, p.96, 1263.
URL : https://hal.archives-ouvertes.fr/hal-00359835

C. M. Andorf, E. K. Cannon, J. L. Portwood, J. M. Gardiner, L. C. Harper et al., MaizeGDB update: New tools, data and interface for the maize model 1266 organism database, Nucleic Acids Research, vol.44, p.1268, 1267.

S. Barraud, Maize adaptation to temperate climate: Relationship between 1269 population structure and polymorphism in the Dwarf8 gene, Genetics, vol.1270, pp.2449-63, 2006.

E. Guichoux, S. Lagache, S. Wagner, P. Chaumeil, P. Léger et al., 1272 Current trends in microsatellite genotyping, Molecular Ecology Resources, vol.1273, pp.591-611, 2011.

M. Jakobsson, N. A. Rosenberg, G. Evanno, S. Regnaut, and J. Goudet, Detecting the number of clusters of 1277 individuals using the software STRUCTURE: A simulation study, Ecology, vol.14, pp.2611-2631, 1278.

O. J. Hardy and X. Vekemans, spagedi: a versatile computer program to analyse 1280 spatial genetic structure at the individual or population levels, Molecular Ecology, vol.2, pp.618-638, 1281.

B. A. Loiselle, V. L. Sork, J. D. Nason, and C. Graham, Spatial genetic structure of a 1283 tropical understory shrub, Psychotria officinalis (Rubiaceae), American Journal of 1284 Botany, vol.82, pp.1420-1425, 1995.

J. K. Pickrell and J. K. Pritchard, 123. Fitak RRs. optM: an R package to optimize the number of migration edges 1288 using threshold models, Journal of Heredity, vol.8, issue.11, 2012.

S. Jdj, T. A. Kato-yamakake, A. Sanmiguel, M. , H. Casillas-1290 et al., Distribución y caracterización del teocintle, p.165, 12911998.

D. Butler, B. R. Cullis, A. R. Gilmour, and B. J. Gogel, ASReml-R reference manual

, Holsinger KE, Weir BS. Genetics in geographically structured populations: 1295 defining, estimating and interpreting F(ST), Nature reviews Genetics, vol.1294, issue.126, pp.639-1296, 2007.

K. J. Gilbert and M. C. Whitlock, QST-FST comparisons with unbalanced half-sib 1298 designs, Molecular Ecology Resources, vol.15, pp.262-269, 2015.

M. Karhunen, J. Merilä, T. Leinonen, J. M. Cano, and O. Ovaskainen, driftsel: An R 1300 package for detecting signals of natural selection in quantitative traits, Molecular 1301 Ecology Resources, vol.13, pp.746-54, 2013.

J. D. Hadfield, MCMC methods for multi-response generalized linear mixed 1303 models: the MCMCglmm R package, Journal of Statistical Software, p.33, 2010.

K. Semagn, R. Babu, S. Hearne, and M. Olsen, Single nucleotide polymorphism 1305 genotyping using Kompetitive Allele Specific PCR (KASP): Overview of the 1306 technology and its application in crop improvement, Molecular Breeding, vol.33, pp.721-50, 2002.

T. Günther and G. Coop, A Short Manual for Bayenv2.0, 2016.

D. Villemereuil, P. Gaggiotti, and O. E. , A new FST-based method to uncover local 1311 adaptation using environmental variables, Methods in Ecology and Evolution, 2015.

R. Rincent, L. Moreau, H. Monod, E. Kuhn, A. E. Melchinger et al., Recovering power in association mapping panels with variable levels of linkage 1314 disequilibrium, Genetics, vol.197, pp.375-87, 1313.

G. S. Bradburd, P. L. Ralph, and G. M. Coop, Disentangling the effects of geographic 1316 and ecological isolation on genetic differentiation, Evolution, vol.67, pp.3258-73, 2013.

J. W. Lichstein, Multiple regression on distance matrices: A multivariate spatial 1318 analysis tool, Plant Ecology, vol.188, pp.117-148, 2007.

S. C. Goslee and D. L. Urban, Journal of Statistical Software The ecodist package for 1320 dissimilarity-based analysis of ecological data, 2007.

. Cc-by-nc-nd, International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint, 2019.