Tree Genetics & Genomes

, 14:29 | Cite as

The genomics of local adaptation in trees: are we out of the woods yet?

  • Brandon M. Lind
  • Mitra Menon
  • Constance E. Bolte
  • Trevor M. Faske
  • Andrew J. Eckert
Part of the following topical collections:
  1. Adaptation


There is substantial interest in uncovering the genetic basis of the traits underlying adaptive responses in tree species, as this information will ultimately aid conservation and industrial endeavors across populations, generations, and environments. Fundamentally, the characterization of such genetic bases is within the context of a genetic architecture, which describes the mutlidimensional relationship between genotype and phenotype through the identification of causative variants, their relative location within a genome, expression, pleiotropic effect, environmental influence, and degree of dominance, epistasis, and additivity. Here, we review theory related to polygenic local adaptation and contextualize these expectations with methods often used to uncover the genetic basis of traits important to tree conservation and industry. A broad literature survey suggests that most tree traits generally exhibit considerable heritability, that underlying quantitative genetic variation (QST) is structured more so across populations than neutral expectations (FST) in 69% of comparisons across the literature, and that single-locus associations often exhibit small estimated per-locus effects. Together, these results suggest differential selection across populations often acts on tree phenotypes underlain by polygenic architectures consisting of numerous small to moderate effect loci. Using this synthesis, we highlight the limits of using solely single-locus approaches to describe underlying genetic architectures and close by addressing hurdles and promising alternatives towards such goals, remark upon the current state of tree genomics, and identify future directions for this field. Importantly, we argue, the success of future endeavors should not be predicated on the shortcomings of past studies and will instead be dependent upon the application of theory to empiricism, standardized reporting, centralized open-access databases, and continual input and review of the community’s research.


Trees GWAS Genetic architecture Polygenic local adaptation 



The authors would like to thank S. González-Martínez for inviting this review, Chris Friedline for stimulating conversations when developing content, and Justin Bagley, Jill Wegrzyn, and two anonymous reviewers for providing helpful comments to earlier versions of this manuscript. Brandon Lind is supported through a Dissertation Fellowship provided by the Graduate School of Virginia Commonwealth University. Andrew Eckert is supported through the National Science Foundation (EF-1442486) and the United States Department of Agriculture (USDA 2016-67013-24469).

Author contributions

BML and AJE conceived the review, with contributions from MM, CEB, and TMF. BML, MM, CEB, and TMF contributed to the literature search and survey which was analyzed by BML. CEB summarized QST and FST comparisons. BML wrote the manuscript with contributions from MM and AJE. All authors contributed to the editing of the manuscript.

Supplementary material

11295_2017_1224_MOESM1_ESM.xlsx (484 kb)
ESM 1 (XLSX 484 kb)
11295_2017_1224_MOESM2_ESM.xlsx (238 kb)
ESM 2 (XLSX 237 kb)
11295_2017_1224_MOESM3_ESM.docx (622 kb)
ESM 3 (DOCX 621 kb)


  1. Adams WT, Joly RJ (1980) Linkage relationships among twelve allozyme loci in loblolly pine. J Hered 71:199–202. CrossRefGoogle Scholar
  2. Alberto FJ, Aitken SN, Alía R (2013) Potential for evolutionary responses to climate change–evidence from tree populations. Glob Chang Biol 19:1645–1661. PubMedPubMedCentralCrossRefGoogle Scholar
  3. Ali OA, O’Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C, Miller MR (2016) RAD capture (Rapture): flexible and efficient sequence-based genotyping. Genetics 202:389–400. PubMedCrossRefGoogle Scholar
  4. Álvarez-Castro JM, Carlborg O (2007) A unified model for functional and statistical epistasis and its application in quantitative trait loci analysis. Genetics 176:1151–1167. PubMedPubMedCentralCrossRefGoogle Scholar
  5. Anderson JT, Lee C-R, Rushworth CA et al (2012) Genetic trade-offs and conditional neutrality contribute to local adaptation. Mol Ecol 22:699–708. PubMedPubMedCentralCrossRefGoogle Scholar
  6. Arnold SJ (1992) Constraints on phenotypic evolution. Am Nat 140:S85–S107. PubMedCrossRefGoogle Scholar
  7. Ashander J, Chevin L-M, Baskett ML (2016) Predicting evolutionary rescue via evolving plasticity in stochastic environments. Proc R Soc B Biol Sci 283:20161690–20161610. CrossRefGoogle Scholar
  8. Ávila V, Pérez-Figueroa A, Caballero A et al (2014) The action of stabilizing selection, mutation, and drift on epistatic quantitative traits. Evolution 68:1974–1987. PubMedCrossRefGoogle Scholar
  9. Bailey SF, Bataillon T (2016) Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature? Mol Ecol 25:203–218. PubMedCrossRefGoogle Scholar
  10. Barrett R, Schluter D (2008) Adaptation from standing genetic variation. Trends Ecol Evol 23:38–44. PubMedCrossRefGoogle Scholar
  11. Barton NH (1990) Pleiotropic models of quantitative variation. Genetics 124:773–782PubMedPubMedCentralGoogle Scholar
  12. Barton NH (1999) Clines in polygenic traits. Genet Res 74:223–236. PubMedCrossRefGoogle Scholar
  13. Barton NH (2017) How does epistasis influence the response to selection? Heredity 118:96–109. PubMedCrossRefGoogle Scholar
  14. Barton NH, Etheridge AM, Véber A (2016) The infinitesimal model. bioRxiv 1–54. doi:
  15. Beavis W (1994) The power and deceit of QTL experiments: lessons from comparative QTL studies. Proceedings of the forty-ninth annual corn and sorghum industry research conference. American Seed Trade Association, Chicago, pp 250–266Google Scholar
  16. Bérénos C, Ellis PA, Pilkington JB, Pemberton JM (2014) Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches. Mol Ecol 23:3434–3451. PubMedPubMedCentralCrossRefGoogle Scholar
  17. Berg JJ, Coop G (2014) A population genetic signal of polygenic adaptation. PLoS Genet 10:e1004412. PubMedPubMedCentralCrossRefGoogle Scholar
  18. Bernardo R, Yu JM (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47:1082–1090. CrossRefGoogle Scholar
  19. Berry AJ, Ajioka JW, Kreitman M (1991) Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics 129:1111–1117PubMedPubMedCentralGoogle Scholar
  20. Bessega C, Pometti C, Ewens M et al (2015) Evidences of local adaptation in quantitative traits in Prosopis alba (Leguminosae). Genetica 143:31. PubMedCrossRefGoogle Scholar
  21. Blanquart F, Kaltz O, Nuismer SL, Gandon S (2013) A practical guide to measuring local adaptation. Ecol Lett 16:1195–1205. PubMedCrossRefGoogle Scholar
  22. Bontemps A, Lefèvre F, Davi H, Oddou-Muratorio S (2016) In situ marker-based assessment of leaf trait evolutionary potential in a marginal European beech population. J Evol Biol 29:514–527.
  23. Boshier D, Broadhurst L, Cornelius J et al (2015) Is local best? Examining the evidence for local adaptation in trees and its scale. Environ Evid 4:1–10. CrossRefGoogle Scholar
  24. Bower AD, Aitken SN (2008) Ecological genetics and seed transfer guidelines for Pinus albicaulis (Pinaceae). Am J Bot 95:66–76PubMedCrossRefGoogle Scholar
  25. Boyle EA, Li YI, Pritchard JK (2017) An expanded view of complex traits: from polygenic to omnigenic. Cell 169:1177–1186. PubMedCrossRefGoogle Scholar
  26. Brandvain Y, Wright SI (2016) The limits of natural selection in a non-equilibrium world. Trends Genet 32:201–210. PubMedCrossRefGoogle Scholar
  27. Breiman L (2001) Random Forests. Mach Learn 45:5–32. CrossRefGoogle Scholar
  28. Budde KB, Heuertz M, Hernandez-Serrano A et al (2014) In situ genetic association for serotiny, a fire-related trait, in Mediterranean maritime pine (Pinus pinaster). New Phytol 201:230–241. PubMedCrossRefGoogle Scholar
  29. Bulmer MG (1980) The mathematical theory of quantitative genetics. Genet Res 19:17–25. CrossRefGoogle Scholar
  30. Bürger R (1999) Evolution of genetic variability and the advantage of sex and recombination in changing environments. Genetics 153:1055–1069PubMedPubMedCentralGoogle Scholar
  31. Bürger R, Akerman A (2011) The effects of linkage and gene flow on local adaptation: a two-locus continent-island model. Theor Popul Biol 80:272–288. PubMedPubMedCentralCrossRefGoogle Scholar
  32. Bürger R, Lynch M (1995) Evolution and extinction in a changing environment: a quantitative-genetic analysis. Evolution 49:151–163. PubMedCrossRefGoogle Scholar
  33. Burghardt LT, Young ND, Tiffin P (2017) A guide to genome-wide association mapping in plants. Curr Protoc Plant Biol.
  34. Caballero A, Tenesa A, Keightley PD (2015) The nature of genetic variation for complex traits revealed by GWAS and regional heritability mapping analyses. Genetics 201:1601–1613PubMedPubMedCentralCrossRefGoogle Scholar
  35. Ćalić I, Bussotti F, Martínez-García PJ, Neale DB (2015) Recent landscape genomics studies in forest trees. Tree Genet Genomes 12:3. CrossRefGoogle Scholar
  36. Carlborg Ö, Haley CS (2004) Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5:618–625. PubMedCrossRefGoogle Scholar
  37. Carrasco A, Wegrzyn JL, Durán R, Fernández M, Donoso A, Rodriguez V, Neale DB, Valenzuela S (2017) Expression profiling in Pinus radiata infected with Fusarium circinatum. Tree Genet Genomes 13:1665. CrossRefGoogle Scholar
  38. Carter AJR, Hermisson J, Hansen TF (2005) The role of epistatic gene interactions in the response to selection and the evolution of evolvability. Theor Popul Biol 68:179–196. PubMedCrossRefGoogle Scholar
  39. Castellanos MC, González‐Martínez SC, Pausas JG (2015) Field heritability of a plant adaptation to fire in heterogeneous landscapes. Mol Ecol 24:5633-42.
  40. Catchen JM, Hohenlohe PA, Bernatchez L et al (2017) Unbroken: RADseq remains a powerful tool for understanding the genetics of adaptation in natural populations. Mol Ecol Resour 17:362–365. PubMedCrossRefGoogle Scholar
  41. Charlesworth B (2013) Background selection 20 years on: The Wilhelmine E. Key 2012 Invitational Lecture. J Hered 104:161–171PubMedCrossRefGoogle Scholar
  42. Charlesworth B, Charlesworth D (2010) Elements of evolutionary genetics. Roberts and Company Publishers, Greenwood Village 734 pp.Google Scholar
  43. Chaves JA, Cooper EA, Hendry AP, Podos J, De León LF, Raeymaekers JAM, MacMillan WO, Uy JAC (2016) Genomic variation at the tips of the adaptive radiation of Darwin’s finches. Mol Ecol 25:5282–5295. PubMedCrossRefGoogle Scholar
  44. Cheplick GP (2015) Approaches to plant evolutionary ecology. Oxford University Press, OxfordGoogle Scholar
  45. Cheverud JM, Routman EJ (1995) Epistasis and its contribution to genetic variance components. Genetics 139:1455–1461PubMedPubMedCentralGoogle Scholar
  46. Chevin L-M (2012) Genetic constraints on adaptation to a changing environment. Evolution 67:708–721. PubMedCrossRefGoogle Scholar
  47. Chevin L-M, Hoffmann AA (2017) Evolution of phenotypic plasticity in extreme environments. Philos Trans Roy Soc B: Biol Sci 372:20160138–20160112. CrossRefGoogle Scholar
  48. Chevin L-M, Hospital F (2008) Selective sweep at a quantitative trait locus in the presence of background genetic variation. Genetics 180:1645–1660. PubMedPubMedCentralCrossRefGoogle Scholar
  49. Chevin L-M, Lande R (2011) Adaptation to marginal habitats by evolution of increased phenotypic plasticity. J Evol Biol 24:1462–1476. PubMedCrossRefGoogle Scholar
  50. Chevin L-M, Lande R, Mace GM (2010b) Adaptation, plasticity, and extinction in a changing environment: towards a predictive theory. PLoS Biol 8:e1000357. PubMedPubMedCentralCrossRefGoogle Scholar
  51. Chevin L-M, Martin G, Lenormand T (2010a) Fisher’s model and the genomics of adaptation: restricted pleiotropy, heterogeneous mutation, and parallel evolution. Evolution 64:3213–3231. PubMedCrossRefGoogle Scholar
  52. Civelek M, Lusis AJ (2014) Systems genetics approaches to understand complex traits. Nat Rev Genet 15:34–48. PubMedCrossRefGoogle Scholar
  53. Cockerham CC (1954) An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 39:859–882PubMedPubMedCentralGoogle Scholar
  54. Cohen D, Bogeat-Triboulot M-B, Tisserant E, Balzergue S, Martin-Magniette M-L, Lelandais G, Ningre N, R, J-P, Tamby J-P, Le Thiec D, Hummel I (2010) Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics 11:630.
  55. Collins S, de Meaux J, Acquisti C (2007) Adaptive walks toward a moving optimum. Genetics 176:1089–1099. PubMedPubMedCentralCrossRefGoogle Scholar
  56. Comeault AA, Soria-Carrasco V, Gompert Z et al (2014) Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae. Am Nat 183:711–727. PubMedCrossRefGoogle Scholar
  57. Comeault AA, Flaxman SM, Riesch R et al (2015) Selection on a genetic polymorphism counteracts ecological speciation in a stick insect. Curr Biol 25:1975–1981. PubMedCrossRefGoogle Scholar
  58. Cornelius J (1994) Heritabilities and additive genetic coefficients of variation in forest trees. Can J For Res 24:372–379. CrossRefGoogle Scholar
  59. Costanza R, d’Arge R, De Groot R et al (1997) The value of the world’s ecosystem services and natural capital. Nature 387:253–260. CrossRefGoogle Scholar
  60. Cowen L, Ideker T, Raphael BJ, Sharan R (2017) Network propagation: a universal amplifier of genetic associations. Nat Ecol Evol 18:551–562. Google Scholar
  61. Crnokrak P, Merilä J (2002). Genetic population divergence: markers and traits. Trends Ecol Evol 17:501.
  62. Cronn R, Dolan PC, Jogdeo S, Wegrzyn JL, Neale DB, St. Clair JB, Denver DR (2017) Transcription through the eye of a needle: daily and annual cycles of gene expression variation in Douglas Fir needles. bioRxiv.
  63. Crow JF (2008) Maintaining evolvability. J Genet 87:349–353. PubMedCrossRefGoogle Scholar
  64. Crow JF (2010) On epistasis: why it is unimportant in polygenic directional selection. Philos T Roy Soc B 365:1241–1244. CrossRefGoogle Scholar
  65. Cruickshank TE, Hahn MW (2014) Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol 23:3133–3157. PubMedCrossRefGoogle Scholar
  66. Csilléry K, Lalagüe H, Vendramin GG, González-Martínez 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.
  67. De La Torre AR, Li Z, Van de Peer Y, Ingvarsson PK (2017) Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. Mol Biol Evol 34:1363–1377. CrossRefGoogle Scholar
  68. De Mita S, Thuillet A-C, Gay L, Ahmadi N, Manel S, Ronfort J, Vigouroux Y (2013) Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations. Mol Ecol 22:1383–1399. PubMedCrossRefGoogle Scholar
  69. de Villemereuil P, Gaggiotti OE, Mouterde M, Till-Bottraud I (2015) Common garden experiments in the genomic era: new perspectives and opportunities. Heredity 116:249–254. PubMedPubMedCentralCrossRefGoogle Scholar
  70. de Visser JAGM, Cooper TF, Elena SF (2011) The causes of epistasis. P R Soc B-Biol Sci 278:3617–3624. CrossRefGoogle Scholar
  71. de Vladar HP, Barton N (2014) Stability and response of polygenic traits to stabilizing selection and mutation. Genetics 197:749–767.
  72. Devey ME, Fiddler TA, Liu BH, Knapp SJ, Neale DB (1994) An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree. Theor Appl Genet 88:273–278. PubMedGoogle Scholar
  73. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997–1004PubMedCrossRefGoogle Scholar
  74. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB (2010) Rare variants create synthetic genomewide associations. PLoS Biol 8:e1000294. PubMedPubMedCentralCrossRefGoogle Scholar
  75. Dittmar EL, Oakley CG, Conner JK, Gould BA, Schemske DW (2016) Factors influencing the effect size distribution of adaptive substitutions. P R Soc B-Biol Sci 283:3065–3068. Google Scholar
  76. Donohue K, Rubio de Casas R, Burghardt L, Kovach K, Willis CG (2010) Germination, post-germination adaptation, and species ecological ranges. Annu Rev Ecol Evol Syst 41:293–319. CrossRefGoogle Scholar
  77. Du J, Groover A (2010) Transcriptional regulation of secondary growth and wood formation. J Integr Plant Biol. 52:17–27. PubMedCrossRefGoogle Scholar
  78. Dungey HS (2001) Pine hybrids—a review of their use performance and genetics. For Ecol Manag 148:243–258. CrossRefGoogle Scholar
  79. East EM (1910) A Mendelian interpretation of variation that is apparently continuous. Am Nat 44:65–82. CrossRefGoogle Scholar
  80. Eckert AJ, Pande B, Ersoz ES, Wright MH, Rashbrook VK, Nicolet CM, Neale DB (2009) High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.) Tree Genet Genomes 5:225–234. CrossRefGoogle Scholar
  81. Eckert AJ, Wegrzyn JL, Cumbie WP et al (2012) Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome. New Phytol 193:890–902. PubMedCrossRefGoogle Scholar
  82. Eckert AJ, Bower AD, Jermstad KD, Wegrzyn JL, Knaus BJ, Syring JV, Neale DB (2013b) Multilocus analyses reveal little evidence for lineage-wide adaptive evolution within major clades of soft pines (Pinus subgenus Strobus). Mol Ecol 22:5635–5650. PubMedCrossRefGoogle Scholar
  83. Eckert AJ, Wegryzn JL, Liechty JD, Lee JM, Cumbie WP, Davis JM, Goldfarb B, Loopstra CA, Palle SR, Quesada T, Langley CH, Neale DB (2013a) The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (Pinus taeda, Pinaceae). Genetics 195:1353–1372.
  84. Eckert AJ, Maloney PE, Vogler DR et al (2015) Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae). Tree Genet Genomes 11:1–17. CrossRefGoogle Scholar
  85. Ehret GB, Lamparter D, Hoggart CJ, Whittaker JC, Beckmann JS, Kutalik Z, Genetic Investigation of Anthropometric Traits Consortium (2012) A multi-SNP locus-association method reveals a substantial fraction of the missing heritability. Am J Hum Genet 91:863–871.
  86. Ersoz ES, Wright MH, González-Martínez SC, Langley CH, Neale DB (2010) Evolution of disease response genes in loblolly pine: insights from candidate genes. PLoS ONE 5:e14234. PubMedPubMedCentralCrossRefGoogle Scholar
  87. Evans LM, Kaluthota S, Pearce DW, Allan GJ, Floate K, Rood SB, Whitham TG (2016) Bud phenology and growth are subject to divergent selection across a latitudinal gradient in Populus angustifolia and impact adaptation across the distributional range and associated arthropods. Ecol Evol 6:4565–4581. PubMedPubMedCentralCrossRefGoogle Scholar
  88. Eyre-Walker A (2010) Genetic architecture of a complex trait and its implications for fitness and genomewide association studies. Proc Natl Acad Sci 1752-1756.
  89. Eyre-Walker A, Keightley PD (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8:610–618. PubMedCrossRefGoogle Scholar
  90. Falconer DS (1989) Introduction to quantitative genetics, 3d edn. Longman, New YorkGoogle Scholar
  91. Feltus FA (2014) Systems genetics: a paradigm to improve discovery of candidate genes and mechanisms underlying complex traits. Plant Sci 223:45–48. PubMedCrossRefGoogle Scholar
  92. Feder JL, Nosil P (2010) The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. Evolution 64:1729–1747. PubMedCrossRefGoogle Scholar
  93. Feder JL, Egan SP, Nosil P (2012b) The genomics of speciation-with-gene-flow. Trends Genet 28:342–350. PubMedCrossRefGoogle Scholar
  94. Feder JL, Gejji R, Yeaman S, Nosil P (2012) Establishment of new mutations under divergence and genome hitchhiking. Philos T Roy Soc B 367:461–474.
  95. Feldman M, Lewontin R (1975) The heritability hang-up. Science 190:1163–1168. PubMedCrossRefGoogle Scholar
  96. Felsenstein J (1976) The theoretical population genetics of variable selection and migration. Annu Rev Genet 10:253–280. PubMedCrossRefGoogle Scholar
  97. Fisher RA (1918) The correlation between relatives on the supposition of Mendelian inheritance. Trans Roy Soc Edinb 52:399–433CrossRefGoogle Scholar
  98. Fisher RA (1930) The genetical theory of natural selection: a complete variorum edition. Oxford University Press, OxfordCrossRefGoogle Scholar
  99. Forester BR, Lasky JR, Wagner HH, Urban DL (2017) Using genotype-environment associations to identify multilocus local adaptation. bioRxiv 1–24. doi:
  100. Franks SJ, Weber JJ, Aitken SN (2013) Evolutionary and plastic responses to climate change in terrestrial plant populations. Evol Appl 7:123–139. PubMedPubMedCentralCrossRefGoogle Scholar
  101. Friedline CJ, Lind BM, Hobson EM, Harwood DE, Mix AD, Maloney PE, Eckert AJ (2015) The genetic architecture of local adaptation I: the genomic landscape of foxtail pine (Pinus balfouriana Grev. & Balf.) as revealed from a high-density linkage map. Tree Genet Genomes 11:49.
  102. Gagnaire P-A, Gaggiotti OE (2016) Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches. Curr Zool 62:603–616. PubMedPubMedCentralCrossRefGoogle Scholar
  103. Gazal S, Finucane HK, Furlotte NA, Loh P, Palamara PF, Liu X, Schoech A, Bulik-Sullivan B, Neale BM, Gusev A, Price A (2017) Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection. Nat Gen 49:1421-1427
  104. Gibson G (2012) Rare and common variants: twenty arguments. Nat Rev Genet 13:135–145. PubMedPubMedCentralCrossRefGoogle Scholar
  105. Gilbert KJ, Whitlock MC (2015) Q STF ST comparisons with unbalanced half-sib designs. Mol Ecol Resour 15:262–267. PubMedCrossRefGoogle Scholar
  106. Goddard ME, Wray NR, Verbyla K, Visscher PM (2009) Estimating effects and making predictions from genome-wide marker data. Stat Sci 24:517–529. CrossRefGoogle Scholar
  107. Gompert Z, Jahner JP, Scholl CF, Wilson JS, Lucas LK, Soria-Carrasco V, Fordyce JA, Nice CC, Buerkle CA, Forister ML (2015) The evolution of novel host use is unlikely to be constrained by trade-offs or a lack of genetic variation. Mol Ecol 24:2777–2793. PubMedCrossRefGoogle Scholar
  108. Gompert Z, Egan SP, Barrett RDH, Feder JL, Nosil P (2016) Multilocus approaches for the measurement of selection on correlated genetic loci. Mol Ecol 26:1–18. Google Scholar
  109. Goodnight CJ (1988) Epistasis and the effect of founder events on the additive genetic variance. Evolution 42:441–454. PubMedCrossRefGoogle Scholar
  110. Göring HHH, Terwilliger JD, Blangero J (2001) Large upward bias in estimation of locus-specific effects from genomewide scans. Am J Hum Genet 69:1357–1369. PubMedPubMedCentralCrossRefGoogle Scholar
  111. Grandtner MM (2005) Elsevier’s dictionary of trees: Volume 1: North America. ElsevierGoogle Scholar
  112. Grattapaglia D (2017) Status and perspectives of genomic selection in forest tree breeding. In: Sorrells ME (ed) Genomic selection for crop improvement. Springer, Cham, pp 199–257CrossRefGoogle Scholar
  113. Grattapaglia D, Resende MDV (2011) Genomic selection in forest tree breeding. Tree Genet Genomes 7:241–255. CrossRefGoogle Scholar
  114. Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-test cross: mapping strategy and RAPD markers. Genetics 137:1121–1137PubMedPubMedCentralGoogle Scholar
  115. Griswold CK (2015) Additive genetic variation and evolvability of a multivariate trait can be increased by epistatic gene action. J Theor Biol 387:241–257. PubMedCrossRefGoogle Scholar
  116. Guan Y, Stephens M (2011) Bayesian variable selection regression for genome-wide association studies and other large-scale problems. Ann Appl Stat 5:1780–1815. CrossRefGoogle Scholar
  117. Haldane JBS (1930) A mathematical theory of natural and artificial selection. (Part VI, Isolation.). 26:220–230Google Scholar
  118. Hall D, Hallingbäck HR, Wu HX (2016) Estimation of number and size of QTL effects in forest tree traits. Tree Genet Genomes 12:1–17. CrossRefGoogle Scholar
  119. Hansen TF (2003) Is modularity necessary for evolvability? Biosystems 69:83–94. PubMedCrossRefGoogle Scholar
  120. Hansen TF (2006) The evolution of genetic architecture. Annu Rev Ecol Evol Syst 37:123–157. CrossRefGoogle Scholar
  121. Hansen TF (2013) Why epistasis is important for selection and adaptation. Evolution 67:3501–3511. PubMedCrossRefGoogle Scholar
  122. Hansen TF, Wagner GP (2001) Modeling genetic architecture: a multilinear theory of gene interaction. Theor Popul Biol 59:61–86. PubMedCrossRefGoogle Scholar
  123. Hansen TF, Pelabon C, Houle D (2011) Heritability is not evolvability. Evol Biol 38:258–277CrossRefGoogle Scholar
  124. Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12. CrossRefGoogle Scholar
  125. Hemani G, Knott S, Haley C (2013) An evolutionary perspective on epistasis and the missing heritability. PLoS Genet 9:e1003295. PubMedPubMedCentralCrossRefGoogle Scholar
  126. Henderson CR (1975) Best linear unbiased estimation and prediction under a selection model. Biometrics 31:423–447. PubMedCrossRefGoogle Scholar
  127. Hendry AP (2002) < = ≠ > ?. Trends Ecol Evol 17:502–502. CrossRefGoogle Scholar
  128. Hendry AP (2016) Key questions on the role of phenotypic plasticity in eco-evolutionary dynamics. J Hered 107:25–41. PubMedCrossRefGoogle Scholar
  129. Hereford J (2009) A quantitative survey of local adaptation and fitness trade-offs. Am Nat 173:579–588. PubMedCrossRefGoogle Scholar
  130. Hermisson J (2009) Who believes in whole-genome scans for selection? Heredity 103:283–284. PubMedCrossRefGoogle Scholar
  131. Hermisson J, Pennings PS (2005) Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169:2335–2352. PubMedPubMedCentralCrossRefGoogle Scholar
  132. Hermisson J, Pennings PS (2017) Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation. Methods Ecol Evol 8:700–716. CrossRefGoogle Scholar
  133. Hermisson J, Hansen TF, Wagner GP (2003) Epistasis in polygenic traits and the evolution of genetic architecture under stabilizing selection. Am Nat 161:708–734. PubMedCrossRefGoogle Scholar
  134. Hill WG (2010) Understanding and using quantitative genetic variation. Philos T Roy Soc B 365:73–85Google Scholar
  135. Hill WG, Goddard ME, Visscher PM (2008) Data and theory point to mainly additive genetic variance for complex traits. PLoS Genet 4:e1000008. PubMedPubMedCentralCrossRefGoogle Scholar
  136. Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95–108. PubMedCrossRefGoogle Scholar
  137. Hoban S, Kelley JL, Lotterhos KE et al (2016) Finding the genomic basis of local adaptation: Pitfalls, practical solutions, and future directions. Am Nat 188:379–397. PubMedPubMedCentralCrossRefGoogle Scholar
  138. Hodgins KA, Yeaman S, Nurkowski KA et al (2016) Expression divergence is correlated with sequence evolution but not positive selection in conifers. Mol Biol Evol 33:1502–1516. PubMedCrossRefGoogle Scholar
  139. Hoffmann AA, Rieseberg LH (2008) Revisiting the impact of inversions in evolution: From population genetic markers to drivers of adaptive shifts and speciation? Annu Rev Ecol Evol Syst 39:21–42. PubMedPubMedCentralCrossRefGoogle Scholar
  140. Holliday JA, Wang T, Aitken SN (2012) Predicting adaptive phenotypes from multilocus genotypes in Sitka spruce (Picea sitchensis) using random forest. G3-Genes Genom Genet 2:1085–1903.
  141. Holliday JA, Zhou L, Bawa R, Zhang M, Oubida RW (2016) Evidence for extensive parallelism but divergent genomic architecture of adaptation along altitudinal and latitudinal gradients in Populus trichocarpa. New Phytol 209:1240–1251. PubMedCrossRefGoogle Scholar
  142. Holliday JA, Aitken SN, Cooke JEK, Fady B, González-Martínez SC, Heuertz M, Jaramillo-Correa JP, Lexer C, Staton M, Whetten RW, Plomion C (2017) Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Mol Ecol 26:706–717. PubMedCrossRefGoogle Scholar
  143. Hornoy B, Pavy N, Gérardi S, Beaulieu J, Bousquet J (2015) Genetic adaptation to climate in white spruce involves small to moderate allele frequency shifts in functionally diverse genes. Genome Biol Evol 7:3269–3285. PubMedPubMedCentralCrossRefGoogle Scholar
  144. Howe GT, Aitken SN, Neale DB, Jermstad KD, Wheeler NC, Chen THH (2003) From genotype to phenotype: unraveling the complexities of cold adaptation in forest trees. Can J Bot 81:1247–1266. CrossRefGoogle Scholar
  145. Huang W, Mackay TFC (2016) The genetic architecture of quantitative traits cannot be inferred from variance component analysis. PLoS Genet 12:e1006421. PubMedPubMedCentralCrossRefGoogle Scholar
  146. Huber CD, Durvasula A, Hancock AM, Lohmueller KE (2017). Gene expression drives the evolution of dominance. bioRxiv.
  147. Ingvarsson PK, Hvidsten TR, Street NR (2016) Towards integration of population and comparative genomics in forest trees. New Phytol 212:338–344. PubMedCrossRefGoogle Scholar
  148. Innan H, Kim Y (2004) Pattern of polymorphism after strong artificial selection in a domestication event. Proc Natl Acad Sci 101:10667–10672. PubMedPubMedCentralCrossRefGoogle Scholar
  149. Isik F, Kumar S, Martínez-García PJ, Iwata H, Yamamoto T (2015) Acceleration of forest and fruit tree domestication by genomic selection. Adv Bot Res 74:93–124. CrossRefGoogle Scholar
  150. Iwata H et al (2011) Prospects for genomic selection in conifer breeding: a simulation study of Cryptomeria japonica. Tree Genet Genomes 7:747–758. CrossRefGoogle Scholar
  151. Jain K, Stephan W (2015) Response of polygenic traits under stabilizing selection and mutation when loci have unequal effects. G3-Genes Genom Genet 5:1065–1074.
  152. Jain K, Stephan W (2017) Rapid adaptation of a polygenic trait after a sudden environmental shift. Genetics 206:389–406. PubMedCrossRefGoogle Scholar
  153. Jansen RC, Tesson BM, Fu J, Yan Y, McIntyre LM (2009) Defining gene and QTL networks. Curr Opin Plant Biol 12:241–246. PubMedCrossRefGoogle Scholar
  154. Jensen JD (2014) On the unfounded enthusiasm for soft selective sweeps. Nat Commun 5:5281. PubMedCrossRefGoogle Scholar
  155. Jensen JD, Kim Y, DuMont VB, Aquadro CF, Bustamante CD (2005) Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170:1401–1410. PubMedPubMedCentralCrossRefGoogle Scholar
  156. Jiao WB, Schneeberger K (2017) The impact of third generation genomic technologies on plant genome assembly. Curr Opin Plant Biol 36:64–70. PubMedCrossRefGoogle Scholar
  157. Johnson RC, Nelson GW, Troyer JL, Lautenberger JA, Kessing BD, Winkler CA, O’Brien SJ (2010) Accounting for multiple comparisons in a genome-wide association study (GWAS). BMC Genomics 11:724Google Scholar
  158. Jones AG, Bürger R, Arnold SJ (2014) Epistasis and natural selection shape the mutational architecture of complex traits. Nat Commun 5:3709. PubMedPubMedCentralGoogle Scholar
  159. Joo JWJ, Hormozdiari F, Han B, Eskin E (2016) Multiple testing correction in linear mixed models. Genome Biol 17:62Google Scholar
  160. Josephs EB, Lee YW, Stinchcombe JR, Wright SI (2015) Association mapping reveals the role of purifying selection in the maintenance of genomic variation in gene expression. Proc Natl Acad Sci 112:15390–15395. PubMedPubMedCentralCrossRefGoogle Scholar
  161. Josephs EB, Wright SI, Stinchcombe JR, Schoen DJ (2017) The relationship between selection, network connectivity, and regulatory variation within a population of Capsella grandiflora. Genome Biol Evol 9:1099–1109. PubMedCentralCrossRefGoogle Scholar
  162. Josephs EB, Stinchcombe JR, Wright SI (2017a) What can genome-wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits? New Phytol 214:21–33. PubMedCrossRefGoogle Scholar
  163. Kaplan NL, Hudson RR, Langley CH (1989) The “hitchhiking effect” revisited. Genetics 123:887–899PubMedPubMedCentralGoogle Scholar
  164. Kawecki TJ (2008) Adaptation to marginal habitats. Annu Rev Ecol Evol Syst 39:321–342. CrossRefGoogle Scholar
  165. Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecol Lett 7:1225–1241. CrossRefGoogle Scholar
  166. Keightley PD, Eyre-Walker A (2010) What can we learn about the distribution of fitness effects of new mutations from DNA sequence data? Philos T Roy Soc B 365:1187–1193. CrossRefGoogle Scholar
  167. Kempthorne O (1954) The correlation between relatives in a random mating population. P Roy Soc B-Biol Sci 143:103–113. CrossRefGoogle Scholar
  168. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  169. Kinloch BB Jr, Parks GK, Fowler CW (1970) White pine blister rust: simply inherited resistance in sugar pine. Science 167:193–195. PubMedCrossRefGoogle Scholar
  170. Kirkpatrick M, Barton NH (1997) Evolution of a species’ range. Am Nat 150:1–23. PubMedCrossRefGoogle Scholar
  171. Kirkpatrick M, Barton NH (2006) Chromosome inversions, local adaptation and speciation. Genetics 173:419–434. PubMedPubMedCentralCrossRefGoogle Scholar
  172. Kopp M, Hermisson J (2009a) The genetic basis of phenotypic adaptation I: fixation of beneficial mutations in the moving optimum model. Genetics 182:233–249. PubMedPubMedCentralCrossRefGoogle Scholar
  173. Kopp M, Hermisson J (2009b) The genetic basis of phenotypic adaptation II: the distribution of adaptive substitutions in the moving optimum model. Genetics 183:1453–1476. PubMedPubMedCentralCrossRefGoogle Scholar
  174. Kopp M, Matuszewski S (2013) Rapid evolution of quantitative traits: theoretical perspectives. Evol Appl 7:169–191. PubMedPubMedCentralCrossRefGoogle Scholar
  175. Kremer A, Le Corre V (2012) Decoupling of differentiation between traits and their underlying genes in response to divergent selection. Heredity 108:375–385. PubMedCrossRefGoogle Scholar
  176. Kremer A, Ronce O, Robledo-Arnuncio JJ, Guillaume F, Bohrer G, Nathan R, Bridle JR, Gomulkiewicz KEK, Ritlan K, Kuparinen A, Gerber S, Schueler S (2012) Long-distance gene flow and adaptation of forest trees to rapid climate change. Ecol Lett 15:378–392. PubMedPubMedCentralCrossRefGoogle Scholar
  177. Krutovsky KV, Neale DB (2005) Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir. Genetics 171:2029–2041. PubMedPubMedCentralCrossRefGoogle Scholar
  178. Lamichhaney S, Berglund J, Almén MS, Maqbool K, Grabherr M, Martinez-Barrio A, Promerová M, Rubin CJ, Wang C, Zamani N, Grant BR, Grant PR, Webster MT, Andersson L (2015) Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518:371–375. PubMedCrossRefGoogle Scholar
  179. Lamy JB, Bouffier L, Burlett R, Plomion C, Cochard H, Delzon S (2011) Uniform selection as a primary force reducing population genetic differentiation of cavitation resistance across a species range. PLoS ONE 6:e23476. PubMedPubMedCentralCrossRefGoogle Scholar
  180. Lamy JB, Plomion C, Kremer A, Delzon S (2012) < as a signature of canalization. Mol Ecol 21:5646–5655. PubMedCrossRefGoogle Scholar
  181. Lande R (1980) The genetic covariance between characters maintained by pleiotropic mutations. Genetics 94:203–215PubMedPubMedCentralGoogle Scholar
  182. Lande R (2009) Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation. J Evol Biol 22:1435–1446. PubMedCrossRefGoogle Scholar
  183. Lande R, Arnold S (1983) The measurement of selection on correlated characters. Evolution 37:1210–1226. PubMedCrossRefGoogle Scholar
  184. Langlet O (1971) Two hundred years genecology. Taxon 20:653–721. CrossRefGoogle Scholar
  185. Latta RG (1998) Differentiation of allelic frequencies at quantitative trait loci affecting locally adaptive traits. Am Nat 151:283–292. PubMedCrossRefGoogle Scholar
  186. Latta RG (2003) Gene flow, adaptive population divergence and comparative population structure across loci. New Phytol 161:51–58. CrossRefGoogle Scholar
  187. Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB (2016) The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards. Mol Ecol 25:306–323. PubMedCrossRefGoogle Scholar
  188. Lauteri M, Pliura A, Monteverdi MC, Brugnoli E, Villani F, Eriksson G (2004) Genetic variation in carbon isotope discrimination in six European populations of Castanea sativa Mill. originating from contrasting localities. J Evol Biol 17:1286–1296. PubMedCrossRefGoogle Scholar
  189. Le Corre V, Kremer A (2012) The genetic differentiation at quantitative trait loci under local adaptation. Mol Ecol 21:1548–1566. PubMedCrossRefGoogle Scholar
  190. Le Corre V, Kremer A (2003) Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection. Genetics 164:1205–1219PubMedPubMedCentralGoogle Scholar
  191. Le Rouzic A, Álvarez-Castro JM (2016) Epistasis-induced evolutionary plateaus in selection responses. Am Nat 188:E134–E150. PubMedCrossRefGoogle Scholar
  192. Leempoel K, Duruz S, Rochat E, Widmer I, OrozcoterWengel P, Joost S (2017) Simple rules for an efficient use of Geographic Information Systems in molecular ecology. Front Ecol Evol 5:33. CrossRefGoogle Scholar
  193. Legendre P, Legendre LF (2012) Numerical ecology (Vol. 24). ElsevierGoogle Scholar
  194. Leimu R, Fischer M (2008) A meta-analysis of local adaptation in plants. PLoS ONE 3:e4010. PubMedPubMedCentralCrossRefGoogle Scholar
  195. Leinonen PH, Sandring S, Quilot B et al (2009) Local adaptation in European populations of Arabidopsis lyrata (Brassicaceae). Am J Bot 96:1129–1137. PubMedCrossRefGoogle Scholar
  196. Leinonen T, McCairns RJS, O'Hara RB, Merilä J (2013) Comparisons: evolutionary and ecological insights from genomic heterogeneity. Nat Rev Genet 14:179–190. PubMedCrossRefGoogle Scholar
  197. Leiserson M, Eldridge JV, Ramachandran S (2013) Network analysis of GWAS data. Curr Opin Genet Dev 23:602–610. PubMedCrossRefGoogle Scholar
  198. Leitch AR, Leitch IJ (2012) Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol 194:629–646. PubMedCrossRefGoogle Scholar
  199. Lenormand T (2002) Gene flow and the limits to natural selection. Trends Ecol Evol 17:183–189. CrossRefGoogle Scholar
  200. Lewontin RC, Krakauer J (1973) Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphismsGoogle Scholar
  201. Li Y, Suontoma M, Burdon RD, Dungey HS (2017) Genotype by environment interactions in forest tree breeding: Review of methodology and perspectives on research and application. Tree Genet Genomes 13:60. CrossRefGoogle Scholar
  202. Lind BM, Friedline CJ, Wegrzyn JL, Maloney PE, Vogler DR, Neale DB, Eckert AJ (2017) Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA. Mol Ecol 26:3168–3185. PubMedCrossRefGoogle Scholar
  203. Liu J-J Williams H, Li XR, Schoettle AW, Sniezko RA, Murray M, Zamany A, Roke G, Chen H (2017) Profiling methyl jasmonate-responsive transcriptome for understanding induced systemic resistance in whitebark pine (Pinus albicaulis). Plant Mol Biol 95:359–374.
  204. Liu J-J, Schoettle AW, Sniezko RA et al (2016) Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping. BMC Genomics 17:753. PubMedPubMedCentralCrossRefGoogle Scholar
  205. Loehle C (1988) Tree life history strategies: the role of defenses. Can J For Res 18:209–222CrossRefGoogle Scholar
  206. Long AD, Langley CH (1999) The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res 9:720–731PubMedPubMedCentralGoogle Scholar
  207. Lopez GA, Potts BM, Vaillancourt RE, Apiolaza LA (2003) Maternal and carryover effects on early growth of Eucalyptus globulus. Can J For Res 33(11):2108–2115. CrossRefGoogle Scholar
  208. Lotterhos KE, Whitlock MC (2014) Evaluation of demographic history and neutral parameterization on the performance of F ST outlier tests. Mol Ecol 23:2178–2192. PubMedPubMedCentralCrossRefGoogle Scholar
  209. Lotterhos KE, Whitlock MC (2015) The relative power of genome scans to detect local adaptation depends on sampling design and statistical method. Mol Ecol 24:1031–1046. PubMedCrossRefGoogle Scholar
  210. Lotterhos KE, Hodges K, Yeaman S, Degner J, Aitken S (2017) Modular environmental pleiotropy of genes involved in local adaptation to climate despite physical linkage. bioRxiv.
  211. Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A (2016) Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 17:142–152. PubMedPubMedCentralCrossRefGoogle Scholar
  212. Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A (2017) Responsible RAD: Striving for best practices in population genomic studies of adaptation. Mol Ecol Resour 17:366–369. PubMedCrossRefGoogle Scholar
  213. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer, SunderlandGoogle Scholar
  214. Mackay T (2001) The genetic architecture of quantitative traits. Annu Rev Genet 35:303–339PubMedCrossRefGoogle Scholar
  215. Mackay TFC (2014) Epistasis and quantitative traits: using model organisms to study gene-gene interactions. Nat Rev Genet 15:22–33. PubMedCrossRefGoogle Scholar
  216. Mackay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10:565–577. PubMedCrossRefGoogle Scholar
  217. MacPherson A, Hohenlohe PA, Nuismer SL (2015) Trait dimensionality explains widespread variation in local adaptation. P Roy Soc B-Biol Sci 282:20141570. CrossRefGoogle Scholar
  218. Mahalovich MF, Hipkins VD (2011) Molecular genetic variation in whitebark pine (Pinus albicaulis Engelm.) in the Inland West. In: Keane RE, Tomback DF, Murray MP, Smith CM (eds) The future of high-elevation, five-needle white pines in Western North America: Proceedings of the High Five Symposium. 28–30 June 2010; Missoula, MT. Proceedings RMRS-P-63. U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station, Fort Collins 376 pGoogle Scholar
  219. Mähler N, Wang J, Terebieniec BK, Ingvarsson PK, Street NR, Hvidsten TR (2017) Gene co-expression network connectivity is an important determinant of selective constraint. PLoS Genet 13:e1006402. PubMedPubMedCentralCrossRefGoogle Scholar
  220. Mahler DL, Weber MG, Wagner CE, Ingram T (2017) Pattern and process in the comparative study of convergent evolution. Am Nat 190:S13–S28. PubMedCrossRefGoogle Scholar
  221. Mäki-Tanila A, Hill WG (2014) Influence of gene interaction on complex trait variation with multilocus models. Genetics 198:355–367. PubMedPubMedCentralCrossRefGoogle Scholar
  222. Martin G, Lenormand T (2006) A general multivariate extension of Fisher’s geometrical model and the distribution of mutation fitness effects across species. Evolution 60:893–816. PubMedCrossRefGoogle Scholar
  223. Martin G, Lenormand T (2008) The distribution of beneficial and fixed mutation fitness effects close to an optimum. Genetics 179:907–916. PubMedPubMedCentralCrossRefGoogle Scholar
  224. Matuszewski S, Hermisson J, Kopp M (2014) Fisher’s geometric model with a moving optimum. Evolution 68:2571–2588. PubMedPubMedCentralCrossRefGoogle Scholar
  225. Matuszewski S, Hermisson J, Kopp M (2015) Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum. Genetics 200:1255–1274.
  226. Mátyás C (1996) Climatic adaptation of trees: rediscovering provenance tests. Euphytica 92:45–54CrossRefGoogle Scholar
  227. Maynard Smith JH, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genet Res 23:23–35CrossRefGoogle Scholar
  228. McCandlish DM, Stoltzfus A (2014) Modeling evolution using the probability of fixation: history and implications. Q Rev Biol 89:225–252. PubMedCrossRefGoogle Scholar
  229. McKay JK, Latta RG (2002) Adaptive population divergence: markers, QTL and traits. Trends Ecol Evol 17:285–291. CrossRefGoogle Scholar
  230. McKinney GJ, Larson WA, Seeb LW, Seeb JE (2017) RADseq provides unprecedented insights into molecular ecology and evolutionary genetics: comment on Breaking RAD by Lowry et al. (2016). Mol Ecol Resour 17:356–361. PubMedCrossRefGoogle Scholar
  231. Mei W, Stetter MG, Gates DJ, Stitzer MC, Ross-Ibarra J (2017) Adaptation in plant genomes: bigger is different. bioRxiv.
  232. Meier JI, Sousa VC, Marques DA, Selz OM Wagner CE, Excoffier L, Seehausen O (2017) Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Mol Ecol 26:123–141.
  233. Messer PW, Petrov DA (2013) Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol 28:659–669. PubMedCrossRefGoogle Scholar
  234. Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829PubMedPubMedCentralGoogle Scholar
  235. Mitton JB, Williams CG (2006) Gene flow in conifers. In: Williams CG (ed) Landscapes, genomics, and tansgenic conifers. Springer Netherlands, Dordrecht, pp 147–168CrossRefGoogle Scholar
  236. Mitton JB, Grant MC, Yoshino AM (1998) Variation in allozymes and stomatal size in pinyon (Pinus edulis, Pinaceae), associated with soil moisture. Am J Bot 85:1262–1265. PubMedCrossRefGoogle Scholar
  237. Mizrachi E, Verbeke L, Christie N et al (2017) Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. Proc Natl Acad Sci 114:1195–1200.
  238. Moreno G (1994) Genetic architecture, genetic behavior, and character evolution. Annu Rev Ecol Syst 25:31–44. CrossRefGoogle Scholar
  239. Morgenstern EK (1996) Geographic variation in forest trees: genetic basis and application of knowledge in silviculture. UBC Press, VancouverGoogle Scholar
  240. Morse AM, Peterson DG, Islam-Faridi MN et al (2009) Evolution of genome size and complexity in Pinus. PLoS ONE 4:e4332. PubMedPubMedCentralCrossRefGoogle Scholar
  241. Moser G, Lee SH, Hayes BJ, Goddard ME, Wray NR, Visscher PM (2015) Simultaneous discovery, estimation and prediction analysis of complex traits using a Bayesian mixture model. PLoS Genet 11:e1004969. PubMedPubMedCentralCrossRefGoogle Scholar
  242. Namkoong G (1979) Introduction to quantitative genetics in forestry. Technical Bulletin No. 1588. USDA Forest Service, Washington, D. C. 342 ppGoogle Scholar
  243. Neale DB, Kremer A (2011) Forest tree genomics: growing resources and applications. Nat Rev Genet 12:111–122. PubMedCrossRefGoogle Scholar
  244. Neale DB, Savolainen O (2004) Association genetics of complex traits in conifers. Trends Plant Sci 9:325–330. PubMedCrossRefGoogle Scholar
  245. Neale DB, Langley CH, Salzberg SL, Wegrzyn JL (2013) Open access to tree genomes: the path to a better forest. Genome Biol 14(6):120. PubMedPubMedCentralCrossRefGoogle Scholar
  246. Neale DB, Martínez-García PJ, La Torre De AR, Montanari S, Wei X-X (2017) Novel in-sights into tree biology and genome evolution as revealed through genomics. Annu Rev Plant Biol 68:457–483. PubMedCrossRefGoogle Scholar
  247. Nelson RM, Pettersson ME, Carlborg Ö (2013) A century after Fisher: time for a new paradigm in quantitative genetics. Trends Genet 29:669–676. PubMedCrossRefGoogle Scholar
  248. Nilsson-Ehle H (1909) Kreuzungsuntersuchungen an Hafer und Weizen. Lunds Universitets Arsskrift 5:1–122Google Scholar
  249. Nystedt B, Street NR, Wetterbom A, Zuccolo A, Lin Y-C, Scofield DG, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hällman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Käller, Luthman J, Lysholm F, Nittylä T, Olson Å, Rilakovic N, Ritland C, Rosselló, Sena J, Svensson T, Talavera-López C, Theißen G, Tuominen H, Vanneste K, Wu Z-Q, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Gil RG, Hvidsten TR, de Jong P, MacKay J, Morgante M, Ritland K, Sundberg B, Thompson SL, de Peer YV, Andersson B, Nilsson O, Ingvarsson PK, Lundeberg J, Jansson S (2013) The Norway spruce genome sequence and conifer genome evolution. Nature 497:570– 584.
  250. Ohta T (1982) Linkage disequilibrium with the island model. Genetics 101:139–155PubMedPubMedCentralGoogle Scholar
  251. Ohta T (1992) The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23:263–286. CrossRefGoogle Scholar
  252. Ohta T (1996) The current significance and standing of neutral and nearly neutral theories. BioEssays 18:673–684PubMedCrossRefGoogle Scholar
  253. Oldfield S, Lusty C, MacKinven A (1998) The world list of threatened trees. World Conservation PressGoogle Scholar
  254. Orr HA (1998) The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. Evolution 52:935. PubMedCrossRefGoogle Scholar
  255. Orr HA (2000) Adaptation and the cost of complexity. Evolution 54:13–20. PubMedCrossRefGoogle Scholar
  256. Orr HA (2001) The “sizes” of mutations fixed in phenotypic evolution: a response to Clarke and Arthur. Evol Dev 3:121–123. PubMedCrossRefGoogle Scholar
  257. Orr HA (2003) The distribution of fitness effects among beneficial mutations. Genetics 163:1519–1526. PubMedPubMedCentralGoogle Scholar
  258. Orr HA (2005) The genetic theory of adaptation: a brief history. Nat Rev Genet 6:119–127. PubMedCrossRefGoogle Scholar
  259. Orr HA (2006) The distribution of fitness effects among beneficial mutations in Fisher's geometric model of adaptation. J Theor Biol 238:279–285. PubMedCrossRefGoogle Scholar
  260. Ortiz-Barrientos D, Engelstädter J, Rieseberg LH (2016) Recombination rate evolution and the origin of species. Trends Ecol Evol 31:226–236. PubMedCrossRefGoogle Scholar
  261. Ovaskainen O, Karhunen M, Zheng CH, Cano Arias JM, Merilä J (2011) A new method to uncover signatures of divergent and stabilizing selection in quantitative traits. Genetics 189:621–632PubMedPubMedCentralCrossRefGoogle Scholar
  262. Paaby AB, Rockman MV (2013) The many faces of pleiotropy. Trends Genet 29:66–73. PubMedCrossRefGoogle Scholar
  263. Paixão T, Barton NH (2016) The effect of gene interactions on the long-term response to selection. Proc Natl Acad Sci 113:4422–4427.
  264. Palmé AE, Pyhajarvi T, Wachowiak W, Savolainen O (2009) Selection on nuclear genes in a Pinus phylogeny. Mol Biol Evol 26:893–905. PubMedCrossRefGoogle Scholar
  265. Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA (2012) Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol Ecol 21:2991–3005. PubMedCrossRefGoogle Scholar
  266. Parchman TL, Jahner JP, Uckele K, Galland LM (forthcoming) RADseq approaches and applications for forest tree geneticsGoogle Scholar
  267. Patterson HD, Thompson R (1971) Recovery of interblock information when block sizes are unequal. Biometrika 58:545–554CrossRefGoogle Scholar
  268. Pavlidis P, Metzler D, Stephan W (2012) Selective sweeps in multilocus models of quantitative traits. Genetics 192:225–239. PubMedPubMedCentralCrossRefGoogle Scholar
  269. Pennings PS, Hermisson J (2006a) Soft sweeps III: the signature of positive selection from recurrent mutation. PLoS Genet 2:e186. PubMedPubMedCentralCrossRefGoogle Scholar
  270. Pennings PS, Hermisson J (2006b) Soft sweeps II--Molecular population genetics of adaptation from recurrent mutation or migration. Mol Biol Evol 23:1076–1084. PubMedCrossRefGoogle Scholar
  271. Petit RJ, Hampe A (2006) Some evolutionary consequences of being a tree. Annu Rev Ecol 37:187–214CrossRefGoogle Scholar
  272. Phillips PC (2008) Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9:855–2527 867. PubMedPubMedCentralCrossRefGoogle Scholar
  273. Pickrell JK, Berisa T, Liu JZ, Ségurel L (2016) Detection and interpretation of shared genetic influences on 42 human traits. Nat Genet 48:709–717. PubMedPubMedCentralCrossRefGoogle Scholar
  274. Piepho HP, Möhring J, Melchinger AE, Büchse A (2008) BLUP for phenotypic selection in plant breeding and variety testing. 2533. Euphytica 161:209–228. CrossRefGoogle Scholar
  275. Platt A, Vilhjalmsson BJ, Nordborg M (2010) Conditions under which genome-wide association studies will be positively misleading. Genetics 186:1045–1052PubMedPubMedCentralCrossRefGoogle Scholar
  276. Plomion C, Bastien C, Bogeat-Triboulot M-B, Bouffier L, Déjardin A, Duplessis S, Fady B, Geuertz M, Le Gac A-L, Le Provost G, Legué V, Lelu-Walter M-A, Leplé J-C, Maury S, Morel A, Oddou-Muratorio S, Pilate G, Sanchez L, Scotti I, Scotti-Saintagne C, Segura V, T J-F, Vacher C (2016) Forest tree genomics: 10 achievements from the past 10 years and future prospects. Ann For Sci 73:77–103.
  277. Postma FM, Ågren J (2016) Early life stages contribute strongly to local adaptation in Arabidopsis thaliana. Proc Natl Acad Sci 113:7590–7595. PubMedPubMedCentralCrossRefGoogle Scholar
  278. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904–909. PubMedCrossRefGoogle Scholar
  279. Pritchard JK, Di Rienzo A (2010) Adaptation – not by sweeps alone. Nat Rev Genet 11:665–667.
  280. Prout T, Barker JSF (1993) F statistics in Drosophila buzzatii: selection, population size and inbreeding. Genetics 134:369–375PubMedPubMedCentralGoogle Scholar
  281. Prunier J, Laroche J, Beaulieu J, Bousquet J (2011) Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce. Mol Ecol 20:1702–1716. PubMedCrossRefGoogle Scholar
  282. Prunier J, Verta J-P, MacKay JJ (2015) Conifer genomics and adaptation: at the crossroads of genetic diversity and genome function. New Phytol 209:44–62. PubMedCrossRefGoogle Scholar
  283. Quesada T, Li Z, Dervinis C, Bocock PN, Tuskan GA, Casella G, Davis JM, Kirst M (2008) Comparative analysis of the transcriptomes of Populus trichocarpa and Arabidopsis thaliana suggests extensive evolution of gene expression regulation in angiosperms. New Phytol 180:408–420. PubMedCrossRefGoogle Scholar
  284. Ralph P, Coop G (2010) Parallel adaptation: one or many waves of advance of an advantageous allele? Genetics 186:647–668. PubMedPubMedCentralCrossRefGoogle Scholar
  285. Rausher MD, Delph LF (2015) Commentary: When does understanding phenotypic evolution require identification of the underlying genes? Evolution 69:1655–1664. PubMedCrossRefGoogle Scholar
  286. Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holdregger R (2015) A practical guide to environmental association analysis in landscape genomics. Mol Ecol 24:4348–4370. PubMedCrossRefGoogle Scholar
  287. Remington DL (2015) Alleles versus mutations: Understanding the evolution of genetic architecture requires a molecular perspective on allelic origins. Evolution 69:3025–3038. PubMedCrossRefGoogle Scholar
  288. Resende MFR Jr, Muñoz P, Acosta JJ, Peter GF, Davis JM, Grattapaglia D, Resende MDV, Kirst M (2012a) Accelerating the domestication of trees using genomic selection: accuracy of prediction models across ages and environments. New Phytol 193:617–624. PubMedCrossRefGoogle Scholar
  289. Resende MDV, Resende MFR Jr, Sansaloni CP, Petroli CD, Missiaggia AA, Aguiar AM, Abad JM, Takahashi EK, Rosado AM, Faria DA, Pappas GJ Jr, Kilian A, Grattapaglia D (2012b) Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees. New Phytol 194:116–128. PubMedCrossRefGoogle Scholar
  290. Resende MFR, Muñoz P, Resende MDV, Garrick DJ, Fernando RL, Davis JM, Jokela EJ, Martin TA, Peter GF (2012c) Kirst M. Accuracy of genomic selection methods in a standard data set of loblolly pine (Pinus taeda L.) Genetics 190:1503–1510.
  291. Riesch R, Muschick M, Lindtke D, Villoutreix R, Comeault AA, Farkas TE, Lucek K, Hellen E, Soria-Carrasco V, Dennis SR, de Carvalho CF, Safran RJ, Sandoval CP, Feder J, Gries R, Crespi BJ, Gries G, Gompert Z, Nosil P (2017) Transitions between phases of genomic differentiation during stick-insect speciation. Nat Ecol Evol 1:0082. CrossRefGoogle Scholar
  292. Ritland K, Ritland C (1996) Inferences about quantitative inheritance based on natural population structure in the yellow monkeyflower, Mimulus guttatus. Evolution 50:1074–1082. PubMedCrossRefGoogle Scholar
  293. Ritland K, Krutovsky KV, Tsumura Y, Pelgas B, Isabel N, Bousquet J (2011) Genetic mapping in conifers. In: Genetics, genomics and breeding of conifers, pp. 196–238Google Scholar
  294. Rockman MV (2012) The QTN program and the alleles that matter for evolution: All that’s gold does not glitter. Evolution 66:1–17. PubMedCrossRefGoogle Scholar
  295. Rodíguez-Quilón I, Santos-del-Blanco L, Serra-Varela MJ, Koskela J, González-Martínez SC, Alía R (2016) Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species. Ecol Appl 26:2254–2266Google Scholar
  296. Romero IG, Ruvinsky I, Gilad Y (2012) Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet 13:505–516. PubMedPubMedCentralCrossRefGoogle Scholar
  297. Roschanski AM, Csilléry K, Liepelt S, Oddou-Muratorio S, Ziegenhagen B, Huard F, Ullrich KK, Postolache D, Vendramin GG, Fady B (2016) Evidence of divergent selection at landscape and local scales in Abies alba Mill. in the French Mediterranean Alps. Mol Ecol 25:776–794. PubMedCrossRefGoogle Scholar
  298. Savolainen O, Pyhäjärvi T, Knürr T (2007) Gene flow and local adaptation in trees. Annu Rev Ecol Evol Syst 38:595–619. CrossRefGoogle Scholar
  299. Savolainen O, Lascoux M, Merilä J (2013) Ecological genomics of local adaptation. Nat Rev Genet 14:807–820. PubMedCrossRefGoogle Scholar
  300. Schoville SD, Bonin A, Francois O et al (2012) Adaptive genetic variation on the landscape: methods and cases. Annu Rev Ecol Evol Syst 43:23–43. CrossRefGoogle Scholar
  301. Schrider DR, Kern AD (2016) S/HIC: Robust identification of soft and hard sweeps using machine learning. PLoS Genet 12:e1005928–e1005931. PubMedPubMedCentralCrossRefGoogle Scholar
  302. Schrider DR, Mendes FK, Hahn MW, Kern AD (2015) Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps. Genetics 200:267–284. PubMedPubMedCentralCrossRefGoogle Scholar
  303. Schrider DR, Shanku AG, Kern AD (2016) Effects of linked selective sweeps on demographic inference and model selection. Genetics 204:1207–1223. PubMedPubMedCentralCrossRefGoogle Scholar
  304. Searle SR, Casella G, McCulloch CE (1992) Variance components. Wiley, New York 528 ppCrossRefGoogle Scholar
  305. Silva-Junior O, Faria DA, Grattapaglia D (2015) A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species. New Phytol 206:1527–1540. PubMedCrossRefGoogle Scholar
  306. Simons YB, Bullaughey K, Hudson RR, Sella G (2017) A model for the genetic architecture of quantitative traits under stabilizing selection. arXiv 1–76.
  307. Siol M, Wright S, Barrett S (2010) The population genomics of plant adaptation. New Phytol 188:313–332. PubMedCrossRefGoogle Scholar
  308. Slate J (2005) Quantitative trait locus mapping in natural populations: progress, caveats and future directions. Mol Ecol 14:363–379. PubMedCrossRefGoogle Scholar
  309. Slatkin M (1975) Gene flow and selection in a two-locus system. Genetics 81:787–802PubMedPubMedCentralGoogle Scholar
  310. Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science 236:787–793. PubMedCrossRefGoogle Scholar
  311. Smith SD (2016) Pleiotropy and the evolution of floral integration. New Phytol 209:80–85. PubMedCrossRefGoogle Scholar
  312. Sork VL, Aitken SN, Dyer RJ, Eckert AJ, Legendre P, Neale DB (2013) Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate. Tree Genet Genomes 9:901–911. CrossRefGoogle Scholar
  313. Sork VL, Squire K, Gugger PF, Steele SE, Levy ED, Eckert AJ (2016) Landscape genomic analysis of candidate genes for climate adaptation in a California endemic oak.
  314. Speed D, Balding DJ (2014) MultiBLUP: improved SNP-based predic- tion for complex traits. Genome Res 24:1550–1557. PubMedPubMedCentralCrossRefGoogle Scholar
  315. Spencer CCA, Su Z, Donnelly P, Marchini J (2009) Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet 5:e1000477. PubMedPubMedCentralCrossRefGoogle Scholar
  316. Spitze K (1993) Population structure in Daphnia obtusa: quantitative genetic and allozyme variation. Genetics 135:367–374PubMedPubMedCentralGoogle Scholar
  317. St Clair JB, Mandel NL, Vance-Borland KW (2005) Genecology of Douglas fir in western Oregon and Washington. Ann Bot 96:1199–1214. PubMedPubMedCentralCrossRefGoogle Scholar
  318. Stephan W (2010) Genetic hitchhiking versus background selection: the controversy and its implications. Philos T Roy Soc B 365:1245–1253. CrossRefGoogle Scholar
  319. Stephan W (2015) Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation. Mol Ecol 25:79–88. PubMedCrossRefGoogle Scholar
  320. Stephens M, Balding DJ (2009) Bayesian statistical methods for genetic association studies. Nat Rev Genet 10:681–690. PubMedCrossRefGoogle Scholar
  321. Stinchcombe JR, Hoekstra HE (2008) Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits. Heredity 100:158–170. PubMedCrossRefGoogle Scholar
  322. Stölting KN, Paris M, Meier C, Heinze B, Castiglione S, Bartha D, Lexer C (2015) Genome-wide patters of differentiation and spatially varying selection between postglacial recolonization lineage of Populus alba (Salicaceae), a widespread forest tree. New Phytol 207:723–734. PubMedCrossRefGoogle Scholar
  323. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci 100:9440–9445. PubMedPubMedCentralCrossRefGoogle Scholar
  324. Strickler SR, Bombarely A, Mueller LA (2012) Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am J Bot 99:257–266. PubMedCrossRefGoogle Scholar
  325. Suren H, Hodgins KA, Yeaman S, Nurkowski KA, Smets P, Rieseberg LH, Aitken SN, Holliday JA (2016) Exome capture from the spruce and pine giga-genomes. Mol Ecol 16:1136–1146. CrossRefGoogle Scholar
  326. Tan B, Grattapaglia D, Wu HX, Ingvarsson PK (2017) Genomic prediction reveals significant non-additive effects for growth in hybrid Eucalyptus. bioRxiv, 1–35.
  327. Temesgen B, Brown GR, Harry DE, Kinlaw CS, Sewell MM (2001) Neale DB. Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.) Theor Appl Genet 102:664–675.
  328. Tenaillon O (2014) The utility of Fisher’s geometric model in evolutionary genetics. Annu Rev Ecol Evol Syst 45:179–201. PubMedPubMedCentralCrossRefGoogle Scholar
  329. Thavamanikumar S, Southerton SG, Bossinger G, Thumma BR (2013) Dissection of complex traits in forest trees—Opportunities for marker-assisted selection. Tree Genet Genomes 9:627–639. CrossRefGoogle Scholar
  330. Tiffin P, Ross-Ibarra J (2014) Advances and limits of using population genetics to understand local adaptation. Trends Ecol Evol 29:673–680. PubMedCrossRefGoogle Scholar
  331. Tigano A, Friesen VL (2016) Genomics of local adaptation with gene flow. Mol Ecol 25:2144–2164. PubMedCrossRefGoogle Scholar
  332. Timpson NJ, Greenwood CMT, Soranzo N, Soranzo Lawson DJ, Richars JB (2018) Genetic architecture: the shape of the genetic contribution to human traits and disease. Nature Rev Genet 19:110–124. PubMedCrossRefGoogle Scholar
  333. Turelli M, Barton NH (1994) Genetic and statistical analyses of strong selection on polygenic traits: what, me normal? Genetics 138:913–941PubMedPubMedCentralGoogle Scholar
  334. Vasquez-Gross HA, Yu JJ, Figueroa B, Gessler DD, Neale DB, Wegrzyn JL (2013) CartograTree: connecting tree genomes, phenotypes and environment. Mol Ecol Resour 13:528–537. PubMedCrossRefGoogle Scholar
  335. Via S, Lande R (1985) Genotype-environment interaction and the evolution of phenotypic plasticity. Evolution 39:505–522. PubMedCrossRefGoogle Scholar
  336. Vialette-Guiraud ACM, Andres-Robin A, Chambrier P, Tavares R, Scutt CP (2016) The analysis of Gene Regulatory Networks in plant evo-devo. J Exp Bot 67:2549–2563. PubMedCrossRefGoogle Scholar
  337. Vitezica ZG, Legarra A, Toro MA, Varona L (2017) Orthogonal estimates of variances for additive, dominance, and epistatic effects in populations. Genetics 206:1297–1307. PubMedCrossRefGoogle Scholar
  338. Vizcaíno-Palomar N, Revuelta-Eugercios B, Zavala MA, Alia R, González-Martínez SC (2014) The role of population origin and microenvironment in seedling emergence and early survival in Mediterranean maritime pine (Pinus pinaster Aiton). PLoS ONE 9:e109132. PubMedPubMedCentralCrossRefGoogle Scholar
  339. Wachowiak W, Trivedi U, Perry A, Cavers S (2015) Comparative transcriptomics of a complex of four European pine species. BMC Genomics 16:234. PubMedPubMedCentralCrossRefGoogle Scholar
  340. Wadgymar SM, Lowry DB, Gould BA, Byron CN, Mactavish RM, Anderson JT (2017) Identifying targets and agents of selection: innovative methods to evaluate the processes that contribute to local adaptation. Methods Ecol Evol 8:738–749. CrossRefGoogle Scholar
  341. Wagner GP, Altenberg L (1996) Perspective: complex adaptations and the evolution of evolvability. Evolution 50:967. PubMedCrossRefGoogle Scholar
  342. Wagner GP, Zhang J (2011) The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms. Nat Rev Genet 12:204–213. PubMedCrossRefGoogle Scholar
  343. Wagner GP, Pavlicev M, Cheverud JM (2007) The road to modularity. Nat Rev Genet 8:921–931. PubMedCrossRefGoogle Scholar
  344. Wagner GP, Kenney-Hunt JP, Pavlicev M, Peck JR, Waxman D, Cheverud JM (2008) Pleiotropic scaling of gene effects and the ‘cost of complexity’. Nature 452:470–472. PubMedCrossRefGoogle Scholar
  345. Wang Z, Liao BY, Zhang J (2010) Genomic patterns of pleiotropy and the evolution of complexity. Proc Natl Acad Sci 107:18034–18039. PubMedPubMedCentralCrossRefGoogle Scholar
  346. Wang L, Beissinger TM, Lorant A, Ross-Ibarra C, Ross-Ibarra J, Hufford M (2017) The interplay of demography and selection during maize domestication and expansion. bioRxiv.
  347. Wegrzyn JL, Lee JM, Tearse BR, Neale DB (2008) TreeGenes: a forest tree genome database. Int J Plant Genomics 2008:1–7. CrossRefGoogle Scholar
  348. Wegrzyn JL, Main D, Figueroa B, Choi M, Yu J, Neale DB, Jung S, Lee T, Stanton M, Zheng P, Ficklin S, Cho I, Peace C, Evans K, Volk G (2012) Uniform standards for genome databases in forest and fruit trees. Tree Genet Genomes 8:549–557. CrossRefGoogle Scholar
  349. Welch JJ, Waxman D (2003) Modularity and the cost of complexity. Evolution 57:1723–1713. PubMedCrossRefGoogle Scholar
  350. Wellenreuther M, Hansson B (2016) Detecting polygenic evolution: problems, pitfalls, and promises. Trends Genet 32:155–164. PubMedCrossRefGoogle Scholar
  351. Whitlock MC (1999) Neutral additive genetic variance in a metapopulation. Genet Res 74:215–221. PubMedCrossRefGoogle Scholar
  352. Whitlock MC (2003) Fixation probability and time in subdivided populations. Genetics 164:767–779PubMedPubMedCentralGoogle Scholar
  353. Whitlock MC, Gilbert KJ (2012) QST in a hierarchically structured population. Mol Ecol Resour 12:481–483. PubMedCrossRefGoogle Scholar
  354. Whitlock MC, Guillaume F (2009) Testing for spatially divergent selection: comparing Q ST to F ST. Genetics 183:1055–1063. PubMedPubMedCentralCrossRefGoogle Scholar
  355. Whitlock MC, Lotterhos KE (2015) Reliable detection of loci responsible for local adaptation: Inference of a null model through trimming the distribution of F ST. Am Nat 186:S24–S36. PubMedCrossRefGoogle Scholar
  356. Whitlock MC, Phillips PC, Moore FB, Tonsor SJ (1995) Multiple fitness peaks and epistasis. Annu Rev Ecol Syst 26:601–629.
  357. Wong CK, Bernardo R (2008) Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations. Theor Appl Genet 116:815–824. PubMedCrossRefGoogle Scholar
  358. Wortley AH, Scotland RW (2004) Synonymy, sampling and seed plant numbers. Taxon 53(2):478–480. CrossRefGoogle Scholar
  359. Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159PubMedPubMedCentralGoogle Scholar
  360. Wright S (1932) The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress on Genetics 1:356–366.Google Scholar
  361. Xu S (2003) Theoretical basis of the beavis effect. Genetics 165:2259–2268. PubMedPubMedCentralGoogle Scholar
  362. Yang J, Benyamin B, McEvoy BP et al (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42:565–569. PubMedPubMedCentralCrossRefGoogle Scholar
  363. Yang J, Mezmouk S, Baumgarten A, Buckler ES, Guill KE, McMullen MD, Ross-Ibarra J (2017) Incomplete dominance of deleterious alleles contribute substantially to trait variation and heterosis in maize. bioRxiv.
  364. Yeaman S (2013) Genomic rearrangements and the evolution of clusters of locally adaptive loci. Proc Natl Acad Sci 110:E1743–E1751. PubMedPubMedCentralCrossRefGoogle Scholar
  365. Yeaman S (2015) Local adaptation by alleles of small effect. Am Nat 186:S74–S89. PubMedCrossRefGoogle Scholar
  366. Yeaman S, Jarvis A (2006) Regional heterogeneity and gene flow maintain variance in a quantitative trait within populations of lodgepole pine. Proc R Soc B Biol Sci 273:1587–1593. CrossRefGoogle Scholar
  367. Yeaman S, Otto SP (2011) Establishment and maintenance of adaptive genetic divergence under migration, selection, and drift. Evolution 65:2123–2129. PubMedCrossRefGoogle Scholar
  368. Yeaman S, Whitlock MC (2011) The genetic architecture of adaptation under migration-selection balance. Evolution 65:1897–1911. PubMedCrossRefGoogle Scholar
  369. Yeaman S, Hodgins KA, Lotterhos KE et al (2016) Convergent local adaptation to climate in distantly related conifers. Science 353:1431–1433. PubMedCrossRefGoogle Scholar
  370. Yoder JB, Tiffin P (2017) Effects of gene action, marker density, and timing of selection on the performance of landscape genomic scans of local adaptation. J Hered 109:16–28. PubMedCrossRefGoogle Scholar
  371. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2005) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208. PubMedCrossRefGoogle Scholar
  372. Zhang X-S (2012) Fisher’s geometric model of fitness landscape and variance in fitness within a changing environment. Evolution 66:2350–2368. PubMedCrossRefGoogle Scholar
  373. Zhang M, Zhou L, Bawa R, Suren H, Holliday JA (2016) Recombination rate variation, hitchhiking, and demographic history shape deleterious load in poplar. Mol Biol Evol 33:2899–2910. PubMedCrossRefGoogle Scholar
  374. Zhong S, Dekkers JC, Fernando RL, Jannink JL (2009) Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182:355–364. PubMedPubMedCentralCrossRefGoogle Scholar
  375. Zhou X, Carbonetto P, Stephens M (2013) Polygenic modeling with Bayesian sparse linear mixed models. PLoS Genet 9(2):e1003264. PubMedPubMedCentralCrossRefGoogle Scholar
  376. Zinkgraf M, Liu L, Groover A, Filkov V (2017) Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions. New Phytol 214:1464–1478. PubMedCrossRefGoogle Scholar
  377. Zöllner S, Pritchard JK (2007) Overcoming the Winner’s curse: estimating penetrance parameters from case-control data. Am J Hum Genet 80:605–615. PubMedPubMedCentralCrossRefGoogle Scholar
  378. Zuk O, Hechter E, Sunyaev SR (2012) The mystery of missing heritability: genetic interactions create phantom heritability. Proc Natl Acad Sci 109:1193–1198.

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Integrative Life SciencesVirginia Commonwealth UniversityRichmondUSA
  2. 2.Department of BiologyVirginia Commonwealth UniversityRichmondUSA

Personalised recommendations