REFERENCES
Adams HD, Kolb TE. 2004 . Drought responses of conifers in
ecotone forests of northern Arizona: tree ring growth and leaf δ 13 C.Oecologia. 140 : 217– 225.
Aitken SA, Yeaman S, Holliday JA, Wang T, Curtis-McLane S.
2008. Adaptation, migration or extirpation: climate change outcomes
for tree populations. Evolutionary Applications . 1:95-111.
Barabási AL, Oltvai ZN. 2004. Network biology: understanding
the cell’s functional organization. Nat Rev Genet.5(2): 101–13.
Barghi N, Hermission J, Schlotterer C. 2020 . Polygenic
adaptation: a unifying framework to understand positive selection.Nature Review Genetics. 21 (12):769-781.
Bates D, Mächler M, Bolker B, Walker S. 2015 . Fitting Linear
Mixed-Effects Models Using lme4. Journal of Statistical Software ,67 (1), 1–48.
Battlay P, Yeaman S, Hodgins KA . 2023 . Impacts of
pleiotropy and migration on repeated genetic adaptation. BioRxiv.
https://doi.org/10.1101/2021.09.13.459985
Bisbee J. 2014. Cone morphology of the Pinus
ayacahuite-flexilis complex of the southwestern United States and
Mexico . Bulletin of the Cupressus conservation project, 3, 3–33.
Blödner, C., T. Skroppa, O. Johnson and A. Polle. 2005.Freezing tolerance in two Norway spruce (Picea abies [L.] Karst.)
progenies is physiologically correlated with drought tolerance. J.
Plant Physiol . 162 :549–558.
Browne L, Wright JW, Fitz-Gibbon S, Gugger PF, Sork VL. 2019.Adaptational lag to temperature in valley oak (Quercus lobata) can be
mitigated by genome-informed assisted gene flow. Proc Natl Acad
Sci USA. 116 (50):25179-25185.
Bucholz ER, Waring KM, Kolb TE, Swenson JK, and Whipple AV.
2020. Water relations and drought response of Pinus
strobiformis . Canadian Journal of Forest Research .50(9) : 905-916.
Chevin L, Collins S, Lefèvre F. 2013 . Phenotypic plasticity and
evolutionary demographic responses to climate change: taking theory out
to the field. Funct. Ecol . 27 : 967–979.
Clausen Jens, Keck David D, Hiesey William M. 1948 .Experimental studies on the nature of species. III: Environmental
responses of climatic races of Achillea . 581; Washington, D.C.:
Carnegie Institution of Washington.
Cork JM, Purugganan MD. 2004. The evolution of molecular
genetic pathways and networks. Bioessays. 26(5): 479-84.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E et al.
2011. The Variant Call Format and VCFtools, Bioinformatics .27(15) :2156-8
Dayan DI, Crawford DL, Oleksiak MF. 2015. Phenotypic plasticity
in gene expression contributes to divergence of locally adapted
populations of Fundulus heteroclitus. Molecular Ecology .24(13) :3345-59.
Des Marais DL, Guerrero RF, Lasky JR, Scarpino SV. 2017.Topological features of a gene co-expression network predict patterns of
natural diversity in environmental response. Proceedings of Royal
Society of Biological Science s. 284(1856) :20170914
Etterson JR, Shaw RG. 2001 . Constraint to adaptive evolution in
response to global warming. Science 294 : 151–154.
Falconer DS & Mackay T. 1996 . Introduction to
Quantitative Genetics . Longman, New York.
Fagny M, Austerlitz F. 2021. Polygenic Adaptation: Integrating
Population Genetics and Gene Regulatory Networks. Trends in
Genetics. 37 (7):631-638.
Fisher RA. 1930. The genetic theory of natural
selection . Oxford: The Carendon Press.
Fitzpatrick MC, Chhatre VE, Soolanayakanahally RY, Keller SR.
2021. Experimental support for genomic prediction of climate
maladaptation using the machine learning approach Gradient Forests.Molecular Ecology Resources . 21 (8):2749-2765.
Franks SJ, Weber JJ, Aitken SN. 2014 . Evolutionary and plastic
responses to climate change in terrestrial plant populations.Evol. Appl. 7 : 123–139.
Geber MA, Eckhart VM. 2005. Experimental studies of adaptation
in Clarkia xantiana. II. Fitness variation across a sucoldpecies border.Evolution 59(3) :521–31.
Ghalambor CK, McKay JK, Carroll SP, Reznick DN. 2007. Adaptive
versus non-adaptive phenotypic plasticity and the potential for
contemporary adaptation in new environments. Functional ecology.2007. 21(3 ):394-407.
Goodrich BA, Waring KM & Kolb TE. 2016. Genetic variation inPinus strobiformis growth and drought tolerance from southwestern
US populations. Tree Physiology . 36: 1219-1235.
Goudet J. 2005 . hierfstat, a package for R to compute and test
hierarchical F-statistics. Molecular Ecology Notes , 5 ,
184–186.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA et
al. 2013. Trinity: reconstructing a full-length transcriptome without
a genome from RNA-Seq data. Nature Biotechnology. 29(7) : 644–652.
Grote S. 2020. GOfuncR: Gene ontology enrichment using
FUNC . R package version 1.10.0.
Haas, B., Papanicolaou, A., Yassour, M. et al. 2014.De novo transcript sequence reconstruction from RNA-Seq:
reference generation and analysis with Trinity. Nature Protocols .8: 1-43.
Hämälä T, Gorton AJ, Moeller DA, Tiffin P. 2021. Pleiotropy
facilitates local adaptation to distant optima in common ragweed
(Ambrosia artemisiifolia ). PLOS Genetics 16(3) :
e1008707.
Hampe A. & Petit RJ. 2005 . Conserving biodiversity under
climate change: the rear edge matters. Ecology Letters .8: 461–467.
Hart AJ, Ginzburg S, Xu M, et al. 2020. EnTAP: Bringing
faster and smarter functional annotation to non‐model eukaryotic
transcriptomes. Molecular Ecology Resources . 20 :
591-604.
Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999). From
molecular to modular cell biology. Nature . 402 : C47-52.
Hoffman GE and Schadt EE. 2016. variancePartition: interpreting
drivers of variation in complex gene expression studies. BMC
Bioinformatics 17 : 483.
Holliday JA, Ralph SG, White R, Bohlmann J, Aitken SN. 2008.Global monitoring of autumn gene expression within and among
phenotypically divergent populations of Sitka spruce (Picea sitchensis).New Phytologist . 178 :103–22.
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. Canadian Journal of Botany81 : 1247–1266.
Jordan IK, Mariño-Ramírez L, Wolf YI & Koonin EV. 2004.Conservation and Coevolution in the Scale-Free Human Gene Coexpression
Network. Molecular Biology and Evolution ,21(11) :2058–2070.
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
Biology Evolution . 9(4): 1099–1109.
Kong, R, Henry, H. 2019. Cross acclimation effects of spring
freezing and summer drought on plant functional groups and ecosystem
properties. Environmental and Experimental Botany . 164 :
52-57.
Kulmuni J, Wiley B & Otto S 2023. On the fast track: hybrids
adapt more rapidly than parental populations in a novel
environment, Evolution Letters . 1-9
Krueger F. Trim Galore!: 2015. A wrapper tool around
Cutadapt and FastQC to consistently apply quality and adapter trimming
to FastQ files.http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Lande R. 1980. The Genetic Covariance between Characters
Maintained by Pleiotropic Mutations. Genetics . 94 (1),
203–215.
Langlet O. 1971. Two hundred years of genecology. Taxon20 :653–721
Langfelder P, Horvath S. 2008. WGCNA: an R package for weighted
correlation network analysis. BMC Bioinformatics . 9 :559.
Langfelder P, Luo R, Oldham MC, Horvath S. 2011. Is My Network
Module Preserved and Reproducible? PLoS Computational Biology .7(1): e1001057.
Langmead B & Salzberg S. 2012. Fast gapped-read alignment with
Bowtie 2. Nature
Methods. 9 :357-359.
Lata C., Muthamilarasan M., Prasad M. 2015. Drought Stress
Responses and Signal Transduction in Plants. In: Pandey G. (eds)Elucidation of Abiotic Stress Signaling in Plants. Springer, New
York, NY.
Law CW, Chen Y, Shi W, Smyth GK 2014. voom: precision weights
unlock linear model analysis tools for RNA-seq read counts. Genome
Biology. 15: R29.
Leder EH, McCairns RJ, Leinonen T, Cano JM, Viitaniemi HM,
Nikinmaa M, Primmer CR, Merilä J. 2015. The Evolution and Adaptive
Potential of Transcriptional Variation in Sticklebacks—Signatures of
Selection and Widespread Heritability. Molecular Biology and
Evolution . 32(3) :674–689.
Leinonen T, O’Hara RB, Cano JM and Merilä J. 2008. Comparative
studies of quantitative trait and neutral marker divergence: a
meta-analysis. Journal of Evolutionary Biolog y.21 :1–17.
Lind BM, Menon M, Bolte CE, Faske TM & Eckert AJ. 2018 .The
genomics of local adaptation in trees: Are we out of the woods yet?.Tree genetics & genomes. 14(2): 29.
Lindtke D, Gompert Z, Lexer C, Buerkle CA. 2014 . Unexpected
ancestry of Populus seedlings from a hybrid zone implies a large role of
postzygotic selection in the maintenance of species. Molecular
Ecology. 23 : 4316-4330.
MacPherson, A., P. A. Hohenlohe, and S. L. Nuismer. (2015).Trait dimensionality explains widespread variation in local adaptation.Proc. R. Soc. B 282 : 20141570.
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 Genetics .13(4) :e1006402.
Marowa P, Ding A, Kong Y. 2016. Expansins: roles in plant
growth and potential applications in crop improvement. Plant Cell
Reports. 5(5) :949-965.
Mayol M, Riba M, Gonzalez-Martinez SC et al. 2015 . Adapting
through glacial cycles: insights from a long-lived tree (Taxus baccata).New Phytologist . 208 : 973–986.
Mei W, Stetter MG, Gates D, Stitzer MC, Ross-Ibarra J. 2018.Adaptation in plant genomes: bigger is different. American journal
of botany . 104 (1): 16-19.
Menon M, Landguth E, Leal-Saenz A et al. 2019. Tracing
the footprints of a moving hybrid zone under a demographic history of
speciation with gene flow. Evolutionary Applications .13(1): 195-209.
Menon M, Bagley JC, Page GFM. et al. 2021. Adaptive
evolution in a conifer hybrid zone is driven by a mosaic of recently
introgressed and background genetic variants. Communications
Biol ogy. 4: 160
Menon M, Bagley JC, Friedline CJ, Whipple AV, et al.2018 . The role of hybridization during ecological divergence of
southwestern white pine (Pinus strobiformis ) and limber pine
(P. flexilis ). Molecular Ecol ogy. 27 : 1245–1260.
Moler, E.R.V., 2020. Climate change studies of Southwestern
White Pine: Phenotypic and life history trait responses to temperature
manipulations during seed development and seedling growth.