
Agarwal M, Hao YJ, Kapoor A, Dong CH, Fujii H, Zheng XW et al. (2006) A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance. J Biol Chem 281:37636–37645
Ahrens CW, Rymer PD, Stow A, Bragg J, Dillon S, Umbers KDL et al. (2018) The search for loci under selection: trends, biases and progress. Mol Ecol 27:1342–1356
Akaji Y, Hirobe M, Miyazaki Y, Makimoto T, Kinoshita S, Hattori I et al. (2017) Survival and growth of Fagus crenata seedlings in relation to biological and microtopographical factors in a cool temperate broadleaf forest. J For Res 22:294–302
Akima H, Gebhardt A (2016) akima: interpolation of irregularly and regularly spaced data. R package version 0.6-2. https://CRAN.R-project.org/package=akima
Asuka Y, Tani N, Tsumura Y, Tomaru N (2004a) Development and characterization of microsatellite markers for Fagus crenata Blume. Mol Ecol Notes 4:101–103
Asuka Y, Tomaru N, Nisimura N, Tsumura Y, Yamamoto S (2004b) Heterogeneous genetic structure in a Fagus crenata population in an old-growth beech forest revealed by microsatellite markers. Mol Ecol 13:1241–1250
Barberis IM, Batista WB, Pire EF, Lewis JP, Leon JC (2002) Woody population distribution and environmental heterogeneity in a Chaco forest, Argentina. J Veg Sci 13:607–614
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate—a practical and powerful approach to multiple testing. J R Stat Soc Ser B-Stat Methodol 57:289–300
Bivand R, Piras G (2015) Comparing implementations of estimation methods for spatial econometrics. J Stat Softw 63:1–36
Bolker BM, Brooks ME, Clark CJ, Geange SW, Poulsen JR, Stevens MHH et al. (2009) Generalized linear mixed models: a practical guide for ecology and evolution. Trends Ecol Evol 24:127–135
Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, Patil N et al. (1999) Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet 22:231–238
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140
Csillery K, Lalague H, Vendramin GG, Gonzalez-Martinez SC, Fady B, Oddou-Muratorio S (2014) Detecting short spatial scale local adaptation and epistatic selection in climate-related candidate genes in European beech (Fagus sylvatica) populations. Mol Ecol 23:4696–4708
Davis MW (2017) ApE: a plasmid Editor v2.0.53. http://biologylabs.utah.edu/Jorgensen/wayned/ape/
Denekamp M, Smeekens SC (2003) Integration of wounding and osmotic stress signals determines the expression of the AtMYB102 transcription factor gene. Plant Physiol 132:1415–1423
Dray S, Bauman D, Blanchet G, Borcard D, Clappe S, Guenard G et al. (2016) adespatial: multivariate multiscale spatial analysis. R package version 0.2-0. https://CRAN.R-project.org/package=adespatial
Dray S, Legendre P, Peres-Neto PR (2006) Spatial modelling: a comprehensive framework for principal coordinate analysis of neighbour matrices (PCNM). Ecol Model 196:483–493
Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573–581
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR (2016) Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes. Mol Ecol 25:104–120
Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J, Wilczek AM (2011) A map of local adaptation in Arabidopsis thaliana. Science 334:86–89
Gabriel KR, Sokal RR (1969) A new statistical approach to geographic variation analysis. Syst Biol 18:259–278
Golldack D, Li C, Mohan H, Probst N (2014) Tolerance to drought and salt stress in plants: unraveling the signaling networks. Front Plant Sci 5:151
Hanaoka S, Yuzurihara J, Asuka Y, Tomaru N, Tsumura Y, Kakubari Y et al. (2007) Pollen-mediated gene flow in a small, fragmented natural population of Fagus crenata. Can J Bot 85:404–413
Hardy OJ, Vekemans X (2002) SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620
Harms KE, Condit R, Hubbell SP, Foster RB (2001) Habitat associations of trees and shrubs in a 50-ha neotropical forest plot. J Ecol 89:947–959
Hartl DL, Clark AG (2007) Principles of population genetics. Sinauer Associates, Inc., Sunderland, U.S.A
Hijmans RJ (2017) raster: geographic data analysis and modeling. R package version 2.6-7. https://CRAN.R-project.org/package=raster
Inanaga M, Nakanishi A, Torimaru T, Nishimura N, Tomaru N (2014) Distance-dependent but genetically random mating in a Japanese beech (Fagus crenata) population. Botany 92:795–803
Ingvarsson PK (2008) Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula. Genetics 180:329–340
Ito M, Shiratake T (1983) Kaetsusannchi Gankyoujisan syuuhen no chikei chishitsu – Karikomiike heitanchi no keiseikatei to Kogannkyoujiko no kousatsu [Topograhy and geology around Mt. Gankyouji in Kaetsu Mountains. – Discussion on the process shaping the flat surface on Karikomiike pond and Kogankyoujiko pond -]. Bull Fukui City Mus Nat Hist 30:9–18 (in Japanese)
Japan National Land Agency (1988) Soil map: Echizenkatsuyama – Hakusan (in Japanese)
Katiyar A, Smita S, Lenka SK, Rajwanshi R, Chinnusamy V, Bansal KC (2012) Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis. BMC Genom 13:544
Krajmerova D, Hrivnak M, Ditmarova L, Jamnicka G, Kmet J, Kurjak D et al. (2017) Nucleotide polymorphisms associated with climate, phenology and physiological traits in European beech (Fagus sylvatica L.). New Forests 48:463–477
Kruskal JB (1964) Nonmetric multidimensional scaling: a numerical method. Psychometrika 29:115–129
Kutnar L, Nagel TA, Kermavnar J (2019) Effects of disturbance on understory vegetation across Slovenian forest ecosystems. Forests 10:1048
Leck MA, Simpson RL, Parker VT (2008) Why seedlings? In: Leck MA, Parker VT, Simpson RL (eds) Seedling ecology and evolution. Cambridge University Press, Cambridge, UK, p 3–12
Leonhardt N, Kwak JM, Robert N, Waner D, Leonhardt G, Schroeder JI (2004) Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant. Plant Cell 16:596–615
Liang J, He JX (2018) Protective role of anthocyanins in plants under low nitrogen stress. Biochem Biophys Res Commun 498:946–953
Linhart YB, Grant MC (1996) Evolutionary significance of local genetic differentiation in plants. Annu Rev Ecol Syst 27:237–277
Loiselle BA, Sork VL, Nason J, Graham C (1995) Spatial genetic-structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot 82:1420–1425
Makie G, Kisanuki H, Torimaru T (2017) Hakusan kokuritsu kouen Karikomiike ni okeru buna tennenrin no gunsyuukouzou [Community structure of a beech forest at Karikomiike pond in Hakusan national park]. Chubu For Res 65:25–27 (in Japanese)
Manabe T, Nishimura N, Miura M, Yamamoto S (2000) Population structure and spatial patterns for trees in a temperate old-growth evergreen broad-leaved forest in Japan. Plant Ecol 151:181–197
Matsuda S, Wakamatsu N, Jouyu H, Makita H, Akada S (2011) An extensive analysis of R2R3-MYB regulatory genes from Fagus crenata. Tree Genet Genomes 7:307–321
Metcalfe P, Beven K, Freer J (2018) dynatopmodel: Implementation of the dynamic TOPMODEL hydrological model. R package version 1.2.1. https://CRAN.R-project.org/package=dynatopmodel
Mukai Y (2008) Buna no jyuhun no bunshiseitaigaku: jikahuwagousei to kinkoujyakusei [Molecular ecology of beech pollination: self incompatibility and inbreeding depression]. In: Terazawa K, Koyama H (eds) Applied ecology for restration of beech forests. Bun-ichi Sogo Shuppan Co., Tokyo (in Japanese)
Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325
Oddou-Muratorio S, Bontemps A, Klein EK, Chybicki I, Vendramin GG, Suyama Y (2010) Comparison of direct and indirect genetic methods for estimating seed and pollen dispersal in Fagus sylvatica and Fagus crenata. For Ecol Manag 259:2151–2159
Oksanen JF, Blanchet G, Friendly M, Kindt R, Legendre P, McGlinn D et al. (2018) vegan: Community Ecology Package. R package version 2.5-2. https://CRAN.R-project.org/package=vegan
Paz-Ares J, Ghosal D, Wienand U, Peterson PA, Saedler H (1987) The regulatory c1 locus of Zea mays encodes a protein with homology to myb proto-oncogene products and with structural similarities to transcriptional activators. Embo J 6:3553–3558
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. Plos One 7:e37135
R Development Core Team (2018) R v.3.5.2: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Radula MW, Szymura TH, Szymura M (2018) Topographic wetness index explains soil moisture better than bioindication with Ellenberg’s indicator values. Ecol Indic 85:172–179
Rousset F (2008) GENEPOP ‘007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour 8:103–106
Sasaki T, Koyama A, Koyanagi T, Furukawa T, Uchida K (2015) Data analysis of plant community structure and diversity, 1st edn. Kyoritsu Shuppan Co., Ltd, Tokyo, Japan (in Japaneses)
Schafer M, Brutting C, Xu SQ, Ling ZH, Steppuhn A, Baldwin IT et al. (2017) NaMYB8 regulates distinct, optimally distributed herbivore defense traits. J Integr Plant Biol 59:844–850
Senno T (1979) On structure of beech (Fagus crenata Blume) stands in Mt.Hakusan. Sci Rep Kyoto Prefect University, Agriculture 31:125–136 (in Japanese with English summary)
Shin N, Nakamura F (2005) Effects of fluvial geomorphology on riparian tree species in Rekifune River, northern Japan. Plant Ecol 178:15–28
Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4:447–456
Suyama Y, Matsuki Y (2015) MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform. Sci Rep 5:12
Takahashi K, Uemura S, Suzuki JI, Hara T (2003) Effects of understory dwarf bamboo on soil water and the growth of overstory trees in a dense secondary Betula ermanii forest, northern Japan. Ecol Res 18:767–774
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Torimaru T, Akada S, Ishida K, Narita M, Higaki D (2018) Species habitat associations in an old-growth beech forest community organised by landslide disturbances. J For Res 23:98–104
Tsumura Y, Uchiyama K, Moriguchi Y, Kimura MK, Ueno S, Ujino-Ihara T (2014) Genetic differentiation and evolutionary adaptation in Cryptomeria japonica. G3-Genes Genomes Genet 4:2389–2402
Vekemans X, Hardy OJ (2004) New insights from fine-scale spatial genetic structure analyses in plant populations. Mol Ecol 13:921–935
Wagner HH, Chavez-Pesqueira M, Forester BR (2017) Spatial detection of outlier loci with Moran eigenvector maps. Mol Ecol Resour 17:1122–1135
Wagner HH, Dray S (2015) Generating spatially constrained null models for irregularly spaced data using Moran spectral randomization methods. Methods Ecol Evol 6:1169–1178
Wang IJ, Bradburd GS (2014) Isolation by environment. Mol Ecol 23:5649–5662
Weir B, Cockerham C (1984) Estimating F-statics for the analysis of population structure. Evolution 38:1358–1370
Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM (2009) Expansion and diversification of the Populus R2R3-MYB family of transcription factors. Plant Physiol 149:981–993
Yamamoto S, Nishimura N, Matsui K (1995) Natural disturbance and tree species coexistence in an old-growth beech – Dwarf bamboo forest, southwestern Japan. J Veg Sci 6:875–886
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