References
- ADAMS, R. M., C. ROSENZWEIG, R. M. PEART, J. T. RITCHIE, B. A. MCCARL, J. D. GLYER, R. B. CURRY, J. W. JONES, K. J. BOOTE and L. H. ALLEN (1990): Global climate change and US agriculture. Nature 345(6272): 219-224.
- AKASHI, H. (1999): Within- and between-species DNA sequence variation and the ‘footprint’ of natural selection. Gene 238(1): 39-51.
- AL-RABAB’AH, M. A. and C. G. WILLIAMS (2002): Population dynamics of Pinus taeda L. based on nuclear microsatellites. Forest Ecol Manag 163(1-3): 263-271.
- AL-RABAB’AH, M. A. and C. G. WILLIAMS (2004): An ancient bottleneck in the Lost Pines of central Texas. Mol Ecol 13(5): 1075-1084.
- BROWN, G. R., D. L. BASSONI, G. P. GILL, J. R. FONTANA, N. C. WHEELER, R. A. MEGRAW, M. F. DAVIS, M. M. SEWELL, G. A. TUSKAN and D. B. NEALE (2003): Identification of quantitative trait loci influencing wood property traits in loblolly pine (Pinus taeda L.). III. QTL verification and candidate gene mapping. Genetics 164(4): 1537-1546.
- BROWN, G. R., G. P. GILL, R. J. KUNTZ, C. H. LANGLEY and D. B. NEALE (2004): Nucleotide diversity and linkage disequilibrium in loblolly pine. P Natl Acad Sci USA 101(42): 15255-15260.
- CARVALHO, A. B. and A. G. CLARK (1999): Intron size and natural selection. Nature 401(6751): 344-344.
- CASTILLO-DAVIS, C. I., S. L. MEKHEDOV, D. L. HARTL, E. V. KOONIN and F. A. KONDRASHOV (2002): Selection for short introns in highly expressed genes. Nat Genet 31(4): 415-418.
- CHANG, S. J., J. D. PURYEAR, M. A. D. L. DIAS, E. A. FUNKHOUSER, R. J. NEWTON and J. CAIRNEY (1996): Gene expression under water deficit in loblolly pine (Pinus taeda): Isolation and characterization of cDNA clones. Physiol Plantarum 97(1): 139-148.
- CHHATRE, V. E., T. D. BYRAM, D. B. NEALE, J. L. WEGRZYN and K. V. KRUTOVSKY (2013): Genetic structure and association mapping of adaptive and selective traits in the east Texas loblolly pine (Pinus taeda L.) breeding populations. Tree Genet Genomes 9(5): 1161-1178.
- COLLINS, R. A. (1988): Evidence of natural selection to maintain a functional domain outside of the ‘core’ in a large subclass of Group I introns. Nucleic Acids Res 16(6): 2705-2715.
- DESER, C., A. PHILLIPS, V. BOURDETTE and H. Y. TENG (2012): Uncertainty in climate change projections: the role of internal variability. Clim Dynam 38(3-4): 527-546.
- ECKERT, A. J., J. VAN HEERWAARDEN, J. L. WEGRZYN, C. D. NELSON, J. ROSS-IBARRA, S. C. GONZALEZ-MARTINEZ and D. B. NEALE (2010): Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185(3): 969-982.
- EDGAR, R. C. (2004): MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5): 1792-1797.
- ERSOZ, E. S., M. H. WRIGHT, S. C. GONZALEZ-MARTINEZ, C. H. LANGLEY and D. B. NEALE (2010): Evolution of disease response genes in loblolly pine: Insights from candidate genes. PLoS One 5(12): e14234.
- GALTIER, N., M. GOUY and C. GAUTIER (1996): SEAVIEW and PHYLO_WIN: Two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 12(6): 543-548.
- GERNANDT, D. S., S. MAGALLON, G. G. LOPEZ, O. Z. FLORES, A. WILLYARD and A. LISTON (2008): Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. Int J Plant Sci 169(8): 1086-1099.
- GONZALEZ-MARTINEZ, S. C., E. ERSOZ, G. R. BROWN, N. C. WHEELER and D. B. NEALE (2006): DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics 172(3): 1915-1926.
- GONZALEZ-MARTINEZ, S. C., D. HUBER, E. ERSOZ, J. M. DAVIS and D. B. NEALE (2008): Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101(1): 19-26.
- GONZALEZ-MARTINEZ, S. C., N. C. WHEELER, E. ERSOZ, C. D. NELSON and D. B. NEALE (2007): Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175(1): 399-409.
- GRAHAM, S. W., R. G. OLMSTEAD and S. C. H. BARRETT (2002): Rooting phylogenetic trees with distant outgroups: A case study from the commelinoid monocots. Mol Biol Evol 19(10): 1769-1781.
- HALL, T. A. (1999): BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
- HOEGH-GULDBERG, O. and J. F. BRUNO (2010): The impact of climate change on the world’s marine ecosystems. Science 328(5985): 1523-1528.
- HUANG, J., B. ABT, G. KINDERMANN and S. GHOSH (2011): Empirical analysis of climate change impact on loblolly pine plantations in the southern United States. Nat Resour Model 24(4): 445-476.
- HUDSON, R. R., M. KREITMAN and M. AGUADE (1987): A test of neutral molecular evolution based on nucleotide data. Genetics 116(1): 153-159.
- JACKSON, S. T., R. S. WEBB, K. H. ANDERSON, J. T. OVERPECK, T. WEBB, J. W. WILLIAMS and B. C. S. HANSEN (2000): Vegetation and environment in Eastern North America during the Last Glacial Maximum. Quaternary Sci Rev 19(6): 489-508.
- JUKES, T. H. and C. R. CANTOR (1969): Evolution of protein molecules, pp. 21-132. In: Mammalian protein metabolism, edited by M. N. MUNRO. Academic Press, New York.
- KIMURA, M. (1968): Evolutionary rate at molecular level. Nature 217(5129): 624-626.
- KREITMAN, M. (2000): Methods to detect selection in populations with applications to the human. Annu Rev Genom Hum G 1: 539-559.
- KRUTOVSKY, K., T. BYRAM, R. WHETTEN, N. WHEELER, D. NEALE, M. LU, T. KORALEWSKI and C. LOOPSTRA (2013): PINEMAP + PineRefSeq = Future Forests.
- PINEMAP (Pine Integrated Network: Education, Mitigation, and Adaptation Project) Year 2 Annual Report | March 2012-February 2013 “Mapping the future of southern pine management in a changing world” (http://www.pinemap.org/reports/annual-reports/PINEMAP_Year_2_Annual_Report_FINAL.pdf) 6-27.
- KRUTOVSKY, K. V., J. BURCZYK, I. CHYBICKI, R. FINKELDEY, T. PYHÄJÄRVI and J. J. ROBLEDO-ARNUNCIO (2012): Gene low, spatial structure, local adaptation, and assisted migration in trees, pp. 71-116. In: Genomics of Tree Crops, edited by R. J. SCHNELL and P. M. PRIYADARSHAN. Springer.
- LI, W. H., C. I. WU and C. C. LUO (1985): A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2(2): 150-174.
- LIBRADO, P. and J. ROZAS (2009): DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451-1452.
- LYONS-WEILER, J., G. A. HOELZER and R. J. TAUSCH (1998): Optimal outgroup analysis. Biol J Linn Soc 64(4): 493-511.
- MCDONALD, J. H. and M. KREITMAN (1991): Adaptive protein evolution at the Adh locus in Drosophila. Nature 351(6328): 652-654.
- NEI, M. and T. GOJOBORI (1986): Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3(5): 418-426.
- PETER, G. and D. NEALE (2004): Molecular basis for the evolution of xylem lignification. Curr Opin Plant Biol 7(6): 737-742.
- SCHMIDTLING, R. C. (2001): Southern pine seed sources. USDA, Forest Service, Southern Research Station. GTR SRS-44.
- SCHMIDTLING, R. C., E. CARROLL and T. LAFARGE (1999): Allozyme diversity of selected and natural loblolly pine populations. Silvae Genet 48(1): 35-45.
- SCHMIDTLING, R. C. and V. HIPKINS (1998): Genetic diversity in longleaf pine (Pinus palustris): influence of historical and prehistorical events. Can J Forest Res 28(8): 1135-1145.
- SEAGER, R., A. TZANOVA and J. NAKAMURA (2009): Drought in the southeastern United States: Causes, variability over the last millennium, and the potential for future hydroclimate change. J Climate 22(19): 5021-5045.
- SMITH, A. B. (1994): Rooting molecular trees: problems and strategies. Biol J Linn Soc 51(3): 279-292.
- SPERRY, J. S. (2003): Evolution of water transport and xylem structure. Int J Plant Sci 164(3): S115-S127.
- TAJIMA, F. (1989): Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3): 585-595.
- TAMURA, K., D. PETERSON, N. PETERSON, G. STECHER, M. NEI and S. KUMAR (2011): MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10): 2731-2739.
- THUILLER, W., S. LAVERGNE, C. ROQUET, I. BOULANGEAT, B. LAFOURCADE and M. B. ARAUJO (2011): Consequences of climate change on the tree of life in Europe. Nature 470(7335): 531-534.
- WELLS, O. O., G. L. SWITZER and R. C. SCHMIDTLING (1991): Geographic variation in Mississippi loblolly pine and sweetgum. Silvae Genet 40(3-4): 105-119.
- WILLIAMS, D. A., Y. Q. WANG, M. BORCHETTA and M. S. GAINES (2007): Genetic diversity and spatial structure of a keystone species in fragmented pine rockland habitat. Biol Conserv 138(1-2): 256-268.
- WILLYARD, A., J. SYRING, D. S. GERNANDT, A. LISTON and R. CRONN (2007): Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Mol Biol Evol 24(1): 90-101.
- WRAY, G. A., M. W. HAHN, E. ABOUHEIF, J. P. BALHOFF, M. PIZER, M. V. ROCKMAN and L. A. ROMANO (2003): The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20(9): 1377-1419.
- WRIGHT, S. I. and B. CHARLESWORTH (2004): The HKA test revisited: A maximum-likelihood-ratio test of the standard neutral model. Genetics 168(2): 1071-1076.
- XU, S. Q., C. G. TAUER and C. D. NELSON (2008): Genetic diversity within and among populations of shortleaf pine (Pinus echinata Mill.) and loblolly pine (Pinus taeda L.). Tree Genet Genomes 4(4): 859-868.