References
Aitken, S.N., Yeaman, S., Holliday, J.A., Wang, T. & Curtis‐McLane, S.
(2008). Adaptation, migration or extirpation: climate change outcomes
for tree populations. Evolutionary Applications , 1, 95–111.
Alberto, F.J., Aitken, S.N., Alía, R., González‐Martínez, S.C.,
Hänninen, H., Kremer, A., et al. (2013). Potential for
evolutionary responses to climate change – evidence from tree
populations. Global Change Biology , 19, 1645–1661.
Anderson, J.T., Panetta, A.M. & Mitchell-Olds, T. (2012). Evolutionary
and Ecological Responses to Anthropogenic Climate Change: Update on
Anthropogenic Climate Change. Plant Physiology , 160, 1728–1740.
Andrews, K.R., Good, J.M., Miller, M.R., Luikart, G. & Hohenlohe, P.A.
(2016). Harnessing the power of RADseq for ecological and evolutionary
genomics. Nat Rev Genet , 17, 81–92.
Andrus, R.A., Harvey, B.J., Rodman, K.C., Hart, S.J. & Veblen, T.T.
(2018). Moisture availability limits subalpine tree establishment.Ecology , 99, 567–575.
Auld, J.R., Agrawal, A.A. & Relyea, R.A. (2010). Re-evaluating the
costs and limits of adaptive phenotypic plasticity. Proceedings of
the Royal Society B: Biological Sciences , 277, 503–511.
Bales, R.C., Hopmans, J.W., O’Geen, A.T., Meadows, M., Hartsough, P.C.,
Kirchner, P., et al. (2011). Soil Moisture Response to Snowmelt
and Rainfall in a Sierra Nevada Mixed-Conifer Forest. Vadose Zone
Journal , 10, 786–799.
Bateman, A., Martin, M.J., O’Donovan, C., Magrane, M., Alpi, E.,
Antunes, R., et al. (2017). UniProt: the universal protein
knowledgebase. Nucleic Acids Res , 45, D158–D169.
Beaulieu, J., Doerksen, T., Clément, S., MacKay, J. & Bousquet, J.
(2014). Accuracy of genomic selection models in a large population of
open-pollinated families in white spruce. Heredity , 113,
343–352.
Bell, G. & Gonzalez, A. (2009). Evolutionary rescue can prevent
extinction following environmental change. Ecology Letters , 12,
942–948.
Berg, N. & Hall, A. (2015). Increased Interannual Precipitation
Extremes over California under Climate Change. Journal of
Climate , 28, 6324–6334.
Beuerle, T. & Pichersky, E. (2002). Purification and characterization
of benzoate:coenzyme A ligase from Clarkia breweri. Arch Biochem
Biophys , 400, 258–264.
Brodribb, T.J., McAdam, S.A.M., Jordan, G.J. & Martins, S.C.V. (2014).
Conifer species adapt to low-rainfall climates by following one of two
divergent pathways. PNAS , 111, 14489–14493.
Brunner, I. & Godbold, D.L. (2007). Tree roots in a changing world.Journal of Forest Research , 12, 78–82.
Buckley, T.N. (2005). The control of stomata by water balance. New
Phytologist , 168, 275–292.
Cao, S., Guo, M., Wang, C., Xu, W., Shi, T., Tong, G., et al.(2019). Genome-wide characterization of aspartic protease (AP) gene
family in Populus trichocarpa and identification of the potential PtAPs
involved in wood formation. BMC Plant Biology , 19, 276.
Caye, K., Jumentier, B., Lepeule, J. & François, O. (2019). LFMM 2:
Fast and Accurate Inference of Gene-Environment Associations in
Genome-Wide Studies. Mol Biol Evol , 36, 852–860.
Cingolani, P., Platts, A., Wang, L.L., Coon, M., Nguyen, T., Wang, L.,et al. (2012). A program for annotating and predicting the
effects of single nucleotide polymorphisms, SnpEff. Fly , 6,
80–92.
Conkle, M.T. & Critchfield, W.B. (1988). Genetic variation and
hybridization of ponderosa pine. In: Ponderosa Pine: the species
and its management, Washington State University Cooperative Extension,
1988: p. 27-43 .
Creelman, R.A. & Mullet, J.E. (1995). Jasmonic acid distribution and
action in plants: regulation during development and response to biotic
and abiotic stress. PNAS , 92, 4114–4119.
Cregg, B.M. & Zhang, J.W. (2001). Physiology and morphology of Pinus
sylvestris seedlings from diverse sources under cyclic drought stress.Forest Ecology and Management , 154, 131–139.
Davey, J.W., Hohenlohe, P.A., Etter, P.D., Boone, J.Q., Catchen, J.M. &
Blaxter, M.L. (2011). Genome-wide genetic marker discovery and
genotyping using next-generation sequencing. Nature Reviews
Genetics , 12, 499–510.
Dillon, S., McEvoy, R., Baldwin, D.S., Rees, G.N., Parsons, Y. &
Southerton, S. (2014). Characterisation of Adaptive Genetic Diversity in
Environmentally Contrasted Populations of Eucalyptus camaldulensis
Dehnh. (River Red Gum). PLOS ONE , 9, e103515.
Eckert, A.J., Bower, A.D., Wegrzyn, J.L., Pande, B., Jermstad, K.D.,
Krutovsky, K.V., et al. (2009). Association Genetics of Coastal
Douglas Fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I.
Cold-Hardiness Related Traits. Genetics , 182, 1289–1302.
Eckert, A.J., van Heerwaarden, J., Wegrzyn, J.L., Nelson, C.D.,
Ross-Ibarra, J., Gonzalez-Martinez, S.C., et al. (2010). Patterns
of Population Structure and Environmental Associations to Aridity Across
the Range of Loblolly Pine (Pinus taeda L., Pinaceae). Genetics ,
185, 969–982.
Eckert, A.J., Maloney, P.E., Vogler, D.R., Jensen, C.E., Mix, A.D. &
Neale, D.B. (2015). Local adaptation at fine spatial scales: an example
from sugar pine (Pinus lambertiana, Pinaceae). Tree Genetics &
Genomes , 11, 42.
Elshire, R.J., Glaubitz, J.C., Sun, Q., Poland, J.A., Kawamoto, K.,
Buckler, E.S., et al. (2011). A robust, simple
genotyping-by-sequencing (GBS) approach for high diversity species.PLoS ONE , 6, 1–10.
Ettinger, A.K. & HilleRisLambers, J. (2013). Climate isn’t everything:
Competitive interactions and variation by life stage will also affect
range shifts in a warming world. American Journal of Botany , 100,
1344–1355.
Fettig, C.J., Mortenson, L.A., Bulaon, B.M. & Foulk, P.B. (2019). Tree
mortality following drought in the central and southern Sierra Nevada,
California, U.S. Forest Ecology and Management , 432, 164–178.
Flint, L.E., Flint, A.L., Thorne, J.H. & Boynton, R. (2013). Fine-scale
hydrologic modeling for regional landscape applications: the California
Basin Characterization Model development and performance. Ecol
Process , 2, 1–21.
Frichot, E. & François, O. (2015). LEA: An R package for landscape and
ecological association studies. Methods in Ecology and Evolution ,
6, 925–929.
Frichot, E., Schoville, S.D., Bouchard, G. & François, O. (2013).
Testing for Associations between Loci and Environmental Gradients Using
Latent Factor Mixed Models. Mol Biol Evol , 30, 1687–1699.
Fyfe, J.C., Derksen, C., Mudryk, L., Flato, G.M., Santer, B.D., Swart,
N.C., et al. (2017). Large near-term projected snowpack loss over
the western United States. Nat Commun , 8, 14996.
Gernandt, D.S., Hernández-León, S., Salgado-Hernández, E. & Pérez de La
Rosa, J.A. (2009). Phylogenetic relationships of Pinus subsection
Ponderosae inferred from rapidly evolving cpDNA regions.Systematic Botany , 34, 481–491.
Graham, R.T. & Jain, T.B. (2005). Ponderosa pine ecosystems. In:
Ritchie, Martin W.; Maguire, Douglas A.; Youngblood, Andrew, tech.
coordinators. Proceedings of the Symposium on Ponderosa Pine: Issues,
Trends, and Management, 2004 October 18-21, Klamath Falls, OR. Gen.
Tech. Rep PSW-GTR-198. Albany, CA: Pacific Southwest Research Station,
Forest Service, U.S. Department of Agriculture: 1-32. , 198, 1–32.
Griffin, D. & Anchukaitis, K.J. (2014). How unusual is the 2012–2014
California drought? Geophysical Research Letters , 41, 9017–9023.
Hamanishi, E.T. & Campbell, M.M. (2011). Genome-wide responses to
drought in forest trees. Forestry (Lond) , 84, 273–283.
Hamilton, J.A., Lexer, C. & Aitken, S.N. (2013). Differential
introgression reveals candidate genes for selection across a spruce
(Picea sitchensis × P. glauca) hybrid zone. New Phytologist , 197,
927–938.
Hancock, A.M., Brachi, B., Faure, N., Horton, M.W., Jarymowycz, L.B.,
Sperone, F.G., et al. (2011). Adaptation to climate across the
Arabidopsis thaliana genome. Science , 334, 83–86.
Harrisson, K.A., Pavlova, A., Telonis‐Scott, M. & Sunnucks, P. (2014).
Using genomics to characterize evolutionary potential for conservation
of wild populations. Evolutionary Applications , 7, 1008–1025.
Harvey, J.E., Smiljanić, M., Scharnweber, T., Buras, A., Cedro, A.,
Cruz-García, R., et al. (2020). Tree growth influenced by warming
winter climate and summer moisture availability in northern temperate
forests. Global Change Biology , 26, 2505–2518.
Hoffmann, A.A. & Sgrò, C.M. (2011). Climate change and evolutionary
adaptation. Nature , 470, 479–485.
Holliday, J.A., Ritland, K. & Aitken, S.N. (2010). Widespread,
ecologically relevant genetic markers developed from association mapping
of climate-related traits in Sitka spruce (Picea sitchensis). New
Phytologist , 188, 501–514.
Housset, J.M., Nadeau, S., Isabel, N., Depardieu, C., Duchesne, I.,
Lenz, P., et al. (2018). Tree rings provide a new class of
phenotypes for genetic associations that foster insights into adaptation
of conifers to climate change. New Phytologist , 218, 630–645.
Irvine, J., Perks, M.P., Magnani, F. & Grace, J. (1998). The response
of Pinus sylvestris to drought: stomatal control of transpiration and
hydraulic conductance. Tree Physiology , 18, 393–402.
Isik, F. (2014). Genomic selection in forest tree breeding: the concept
and an outlook to the future. New Forests , 45, 379–401.
Isik, F., Bartholomé, J., Farjat, A., Chancerel, E., Raffin, A.,
Sanchez, L., et al. (2016). Genomic selection in maritime pine.Plant Sci , 242, 108–119.
Jaramillo-Correa, J.-P., Rodríguez-Quilón, I., Grivet, D., Lepoittevin,
C., Sebastiani, F., Heuertz, M., et al. (2015). Molecular proxies
for climate maladaptation in a long-lived tree (Pinus pinaster Aiton,
Pinaceae). Genetics , 199, 793–807.
Johansen, A.D. & Latta, R.G. (2003). Mitochondrial haplotype
distribution, seed dispersal and patterns of postglacial expansion of
ponderosa pine. Molecular Ecology , 12, 293–298.
Kim, S.J., Ryu, M.Y. & Kim, W.T. (2012). Suppression of Arabidopsis
RING-DUF1117 E3 ubiquitin ligases, AtRDUF1 and AtRDUF2, reduces
tolerance to ABA-mediated drought stress. Biochemical and
Biophysical Research Communications , 420, 141–147.
Kitzmiller, J.H. (2005). Provenance Trials of Ponderosa Pine in Northern
California. Forest Science , 51, 595–607.
Kolb, T.E., Grady, K.C., McEttrick, M.P. & Herrero, A. (2016).
Local-Scale Drought Adaptation of Ponderosa Pine Seedlings at Habitat
Ecotones. Forest Science , 62, 641–651.
Kurek, I., Aviezer, K., Erel, N., Herman, E. & Breiman, A. (1999). The
wheat peptidyl prolyl cis-trans-isomerase FKBP77 is heat induced and
developmentally regulated. Plant Physiol , 119, 693–704.
Lai, J., Yu, B., Cao, Z., Chen, Y., Wu, Q., Huang, J., et al.(2015). Two homologous protein S-acyltransferases, PAT13 and PAT14,
cooperatively regulate leaf senescence in Arabidopsis. Journal of
Experimental Botany , 66, 6345–6353.
Langlet, O. (1971). Two Hundred Years Genecology. Taxon , 20,
653–721.
Lee, H.K., Cho, S.K., Son, O., Xu, Z., Hwang, I. & Kim, W.T. (2009).
Drought Stress-Induced Rma1H1, a RING Membrane-Anchor E3 Ubiquitin
Ligase Homolog, Regulates Aquaporin Levels via Ubiquitination in
Transgenic Arabidopsis Plants. The Plant Cell , 21, 622–641.
Li, H. (2011). A statistical framework for SNP calling, mutation
discovery, association mapping and population genetical parameter
estimation from sequencing data. Bioinformatics , 27, 2987–2993.
Li, H. & Durbin, R. (2009). Fast and accurate short read alignment with
Burrows-Wheeler transform. Bioinformatics , 25, 1754–1760.
Lu, M., Loopstra, C.A. & Krutovsky, K.V. (2019). Detecting the genetic
basis of local adaptation in loblolly pine (Pinus taeda L.) using whole
exome-wide genotyping and an integrative landscape genomics analysis
approach. Ecology and Evolution , 9, 6798–6809.
Lyzenga, W.J. & Stone, S.L. (2012). Abiotic stress tolerance mediated
by protein ubiquitination. Journal of Experimental Botany , 63,
599–616.
Maddi, A., Dettman, A., Fu, C., Seiler, S. & Free, S.J. (2012). WSC-1
and HAM-7 Are MAK-1 MAP Kinase Pathway Sensors Required for Cell Wall
Integrity and Hyphal Fusion in Neurospora crassa. PLOS ONE , 7,
e42374.
Maguire, K.C., Shinneman, D.J., Potter, K.M. & Hipkins, V.D. (2018).
Intraspecific Niche Models for Ponderosa Pine (Pinus ponderosa) Suggest
Potential Variability in Population-Level Response to Climate Change.Systematic Biology , 67, 965–978.
Mahony, C.R., MacLachlan, I.R., Lind, B.M., Yoder, J.B., Wang, T. &
Aitken, S.N. (2020). Evaluating genomic data for management of local
adaptation in a changing climate: A lodgepole pine case study.Evolutionary Applications , 13, 116–131.
Markesteijn, L. & Poorter, L. (2009). Seedling root morphology and
biomass allocation of 62 tropical tree species in relation to drought-
and shade-tolerance. Journal of Ecology , 97, 311–325.
Moran, E., Lauder, J., Musser, C., Stathos, A. & Shu, M. (2017a). The
genetics of drought tolerance in conifers. New Phytol , 216,
1034–1048.
Moran, E.V., DeSilva, R., Canning, C. & Wright, J.W. (In review). Sugar
pine association genetics and performance in a post-fire restoration
planting. Ecological Applications .
Moran, E.V., Lauder, J., Musser, C., Stathos, A. & Shu, M.J. (2017b).
The genetics of drought tolerance in conifers. New Phytologist ,
216, 1034–1048.
Namroud, M.-C., Beaulieu, J., Juge, N., Laroche, J. & Bousquet, J.
(2008). Scanning the genome for gene single nucleotide polymorphisms
involved in adaptive population differentiation in white spruce.Mol Ecol , 17, 3599–3613.
Neale, D.B. & Kremer, A. (2011). Forest tree genomics: growing
resources and applications. Nature Reviews Genetics , 12,
111–122.
Neale, D.B. & Savolainen, O. (2004). Association genetics of complex
traits in conifers. Trends in Plant Science , 9, 325–330.
Neale, D.B., Wegrzyn, J.L., Stevens, K.A., Zimin, A.V., Puiu, D.,
Crepeau, M.W., et al. (2014). Decoding the massive genome of
loblolly pine using haploid DNA and novel assembly strategies.Genome Biol , 15, R59.
Oney, B., Reineking, B., O’Neill, G. & Kreyling, J. (2013).
Intraspecific variation buffers projected climate change impacts on
Pinus contorta. Ecology and Evolution , 3, 437–449.
Parker, J. (1949). EFFECTS OF VARIATIONS IN THE ROOT-LEAF RATIO ON
TRANSPIRATION RATE. Plant Physiol , 24, 739–743.
Patterson, N., Price, A.L. & Reich, D. (2006). Population Structure and
Eigenanalysis. PLoS Genetics , 2, e190.
Poland, J.A., Brown, P.J., Sorrells, M.E. & Jannink, J.-L. (2012).
Development of High-Density Genetic Maps for Barley and Wheat Using a
Novel Two-Enzyme Genotyping-by-Sequencing Approach. PLOS ONE , 7,
e32253.
Poland, J.A. & Rife, T.W. (2012). Genotyping-by-Sequencing for Plant
Breeding and Genetics. The Plant Genome , 5, 92–102.
Potter, K.M., Hipkins, V.D., Mahalovich, M.F. & Means, R.E. (2013).
Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa
(Pinaceae): range-wide evolutionary history and implications for
conservation. Am. J. Bot. , 100, 1562–1579.
Potter, K.M., Hipkins, V.D., Mahalovich, M.F. & Means, R.E. (2015).
Nuclear genetic variation across the range of ponderosa pine (Pinus
ponderosa): Phylogeographic, taxonomic and conservation implications.Tree Genetics & Genomes , 11, 38.
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: SNPs and
climate adaptation. Molecular Ecology , 20, 1702–1716.
Rapacciuolo, G., Maher, S.P., Schneider, A.C., Hammond, T.T., Jabis,
M.D., Walsh, R.E., et al. (2014). Beyond a warming fingerprint:
individualistic biogeographic responses to heterogeneous climate change
in California. Global Change Biology , 20, 2841–2855.
Renard, S.M., McIntire, E.J.B. & Fajardo, A. (2016). Winter conditions
– not summer temperature – influence establishment of seedlings at
white spruce alpine treeline in Eastern Quebec. Journal of
Vegetation Science , 27, 29–39.
Rice, K.J. & Emery, N.C. (2003). Managing microevolution: restoration
in the face of global change. Frontiers in Ecology and the
Environment , 1, 469–478.
Rochette, N.C. & Catchen, J.M. (2017). Deriving genotypes from RAD-seq
short-read data using Stacks. Nature Protocols , 12, 2640–2659.
Ryan, M.G. (2011). Tree responses to drought. Tree Physiology ,
31, 237–239.
Ryu, M.Y., Cho, S.K. & Kim, W.T. (2010). The Arabidopsis C3H2C3-Type
RING E3 Ubiquitin Ligase AtAIRP1 Is a Positive Regulator of an Abscisic
Acid-Dependent Response to Drought Stress. Plant Physiology , 154,
1983–1997.
Savolainen, O., Lascoux, M. & Merilä, J. (2013). Ecological genomics of
local adaptation. Nature Reviews Genetics , 14, 807–820.
Seiler, J.R. & Johnson, J.D. (1988). Physiological and Morphological
Responses of Three Half-Sib Families of Loblolly Pine to Water-Stress
Conditioning. Forest Science , 34, 487–495.
Serreze, M.C., Clark, M.P., Armstrong, R.L., McGinnis, D.A. & Pulwarty,
R.S. (1999). Characteristics of the western United States snowpack from
snowpack telemetry (SNO℡) data. Water Resources Research , 35,
2145–2160.
Shu, M. (2020). Association genetics of drought tolerance in ponderosa
pine (Pinus ponderosa ). PhD. UC Merced, Merced, CA.
Sork, V.L., Aitken, S.N., Dyer, R.J., Eckert, A.J., Legendre, P. &
Neale, D.B. (2013). Putting the landscape into the genomics of trees:
approaches for understanding local adaptation and population responses
to changing climate. Tree Genetics & Genomes , 9, 901–911.
Stone, S.L. (2014). The role of ubiquitin and the 26S proteasome in
plant abiotic stress signaling. Frontiers in plant science , 5,
135.
Suren, H., Hodgins, K.A., Yeaman, S., Nurkowski, K.A., Smets, P.,
Rieseberg, L.H., et al. (2016). Exome capture from the spruce and
pine giga-genomes. Molecular Ecology Resources , 16, 1136–1146.
Taeger, S., Sparks, T.H. & Menzel, A. (2015). Effects of temperature
and drought manipulations on seedlings of Scots pine provenances.Plant Biology , 17, 361–372.
Uchiyama, K., Iwata, H., Moriguchi, Y., Ujino-Ihara, T., Ueno, S.,
Taguchi, Y., et al. (2013). Demonstration of Genome-Wide
Association Studies for Identifying Markers for Wood Property and Male
Strobili Traits in Cryptomeria japonica. PLOS ONE , 8, e79866.
UniProt: a hub for protein information. (2015). Nucleic Acids
Res , 43, D204–D212.
Van Kleunen, M. & Fischer, M. (2005). Constraints on the evolution of
adaptive phenotypic plasticity in plants. New Phytologist , 166,
49–60.
Wang, J., Zhao, Q., Hastie, T. & Owen, A.B. (2017). CONFOUNDER
ADJUSTMENT IN MULTIPLE HYPOTHESIS TESTING. Ann Stat , 45,
1863–1894.
Weiss, M., Sekhwal, M.K., Neale, D.B. & De La Torre, A.R. (2022).
Genomics of Climate Adaptation in Pinus Lambertiana. In: The Pine
Genomes , Compendium of Plant Genomes (ed. De La Torre, A.R.). Springer
International Publishing, Cham, pp. 51–65.
Williams, C.G. (Ed.). (2009). The Dynamic Wind-Pollinated Mating System.
In: Conifer Reproductive Biology . Springer Netherlands,
Dordrecht, pp. 125–135.
Willyard, A., Cronn, R. & Liston, A. (2009). Reticulate evolution and
incomplete lineage sorting among the ponderosa pines. Molecular
Phylogenetics and Evolution , 52, 498–511.
Wright, J.W. (2007). Local adaptation to serpentine soils in Pinus
ponderosa. Plant Soil , 293, 209–217.
Wu, D., Shu, M. & Moran, E.V. (2023). Heritability of plastic trait
changes in drought-exposed ponderosa pine seedlings. Ecosphere ,
14, e4454.
Xuereb, A., Stahlke, A., Bermingham, M., Brown, M., Nonaka, E., Razgour,
O., et al. (2017). Effect of missing data and sample size on the
performance of genotype-environment association methods.
Yeaman, S., Hodgins, K.A., Lotterhos, K.E., Suren, H., Nadeau, S.,
Degner, J.C., et al. (2016). Convergent local adaptation to
climate in distantly related conifers. Science , 353, 1431–1433.
Ying, C.C. & Liang, Q. (1994). Geographic pattern of adaptive variation
of lodgepole pine (Pinus contorta Dougl.) within the species’ coastal
range: field performance at age 20 years. Forest Ecology and
Management , 67, 281–298.
Zeng, X., Xu, Y., Jiang, J., Zhang, F., Ma, L., Wu, D., et al.(2018). Identification of cold stress responsive microRNAs in two winter
turnip rape (Brassica rapa L.) by high throughput sequencing. BMC
Plant Biol , 18, 52.
Zettlemoyer, M.A. & Peterson, M.L. (2021). Does Phenological Plasticity
Help or Hinder Range Shifts Under Climate Change? Frontiers in
Ecology and Evolution , 9.
Zimin, A., Stevens, K.A., Crepeau, M.W., Holtz-Morris, A., Koriabine,
M., Marçais, G., et al. (2014). Sequencing and Assembly of the
22-Gb Loblolly Pine Genome. Genetics , 196, 875–890.
Zu, T., Verna, J. & Ballester, R. (2001). Mutations in WSC genes for
putative stress receptors result in sensitivity to multiple stress
conditions and impairment of Rlm1-dependent gene expression in
Saccharomyces cerevisiae. Mol Gen Genomics , 266, 142–155.