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C. L. Brubaker, Bourland, F. M., and Wendel, J. F., The origin and domestication of cotton, Cotton: Origin, history, technology, and production. John Wiley & Sons, New York, pp. 3-31, 1999.
J. F. Wendel, Brubaker, C. L., and Seelanan, T., The origin and evolution of Gossypium, in Physiology of cotton, Springer Netherlands, 2010, pp. 1-18.
J. Doebley, Wendel, J. F., Smith, J. S. C., Stuber, C. W., and Goodman, M. M., The origin of cornbelt maize: the isozyme evidence, Economic Botany, vol. 42, no. 1, pp. 120-131, 1988.
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R. Hovav, Chaudhary, B., Udall, J. A., Flagel, L., and Wendel, J. F., Parallel domestication, convergent evolution and duplicated gene recruitment in allopolyploid cotton, Genetics, vol. 179, no. 3, pp. 1725-1733, 2008.
B. Chaudhary, Hovav, R., Flagel, L., Mittler, R., and Wendel, J. F., Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium), Bmc Genomics, vol. 10, no. 1, p. 378, 2009.
Y. Bao, Hu, G., Flagel, L. E., Salmon, A., Bezanilla, M., Paterson, A. H., Wang, Z., and Wendel, J. F., Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium), Proceedings of the National Academy of Sciences, vol. 108, no. 52, pp. 21152-21157, 2011.
R. Hovav, Udall, J. A., Chaudhary, B., Rapp, R., Flagel, L., and Wendel, J. F., Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant, Proceedings of the National Academy of Sciences, vol. 105, no. 16, pp. 6191-6195, 2008.
R. Cronn, Cedroni, M., Haselkorn, T., Grover, C., and Wendel, J. F., PCR-mediated recombination in amplification products derived from polyploid cotton, Theoretical and Applied Genetics, vol. 104, no. 2-3, pp. 482-489, 2002.
S. Renny-Byfield, Gong, L., Gallagher, J. P., and Wendel, J. F., Persistence of Subgenomes in Paleopolyploid Cotton after 60 My of Evolution, Molecular biology and evolution, vol. 32, no. 4, pp. 1063-1071, 2015.
D. S. Senchina, Flagel, L. E., Wendel, J. F., and Kohut, M. L., Phenetic comparison of sevenEchinacea species based on immunomodulatory characteristics, Economic botany, vol. 60, no. 3, pp. 205-211, 2006.
C. E. Grover, Yu, Y., Wing, R. A., Paterson, A. H., and Wendel, J. F., A phylogenetic analysis of indel dynamics in the cotton genus, Molecular Biology and Evolution, vol. 25, no. 7, pp. 1415-1428, 2008.
T. Bureau, Hawkins, J. S., Hu, G., Rapp, R. A., Grafenberg, J. L., and Wendel, J. F., Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium, Genome, vol. 51, no. 1, pp. 11-18, 2007.
J. F. Wendel and Doyle, J. J., Phylogenetic incongruence: window into genome history and molecular evolution, in Molecular systematics of plants II, Springer US, 1998, pp. 265-296.
C. Grover, Hawkins, J., and Wendel, J. F., Phylogenetic insights into the pace and pattern of plant genome size evolution, 2008.
L. E. Flagel, Rapp, R. A., Grover, C. E., Widrlechner, M. P., Hawkins, J., Grafenberg, J. L., Álvarez, I., Chung, G. Young, and Wendel, J. F., Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea, American journal of botany, vol. 95, no. 6, pp. 756-765, 2008.
A. Schnabel, McDonel, P. E., and Wendel, J. F., Phylogenetic relationships in Gleditsia (Leguminosae) based on ITS sequences, American journal of botany, vol. 90, no. 2, pp. 310-320, 2003.
L. Betancur, Singh, B., Rapp, R. A., Wendel, J. F., M Marks, D., Roberts, A. W., and Haigler, C. H., Phylogenetically distinct cellulose synthase genes support secondary wall thickening in arabidopsis shoot trichomes and cotton fiber, Journal of integrative plant biology, vol. 52, no. 2, pp. 205-220, 2010.
J. F. Wendel and Albert, V. A., Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications, Systematic Botany, pp. 115-143, 1992.
R. L. Small and Wendel, J. F., Phylogeny, duplication, and intraspecific variation of Adh sequences in new world diploid cottons (Gossypium L., Malvaceae), Molecular Phylogenetics and Evolution, vol. 16, no. 1, pp. 73-84, 2000.
L. G. Clark, Zhang, W., and Wendel, J. F., A phylogeny of the grass family (Poaceae) based on ndhF sequence data, Systematic Botany, pp. 436-460, 1995.
I. Álvarez, Cronn, R., and Wendel, J. F., Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes, Plant Systematics and Evolution, vol. 252, no. 3-4, pp. 199-214, 2005.
E. H. Crane, Farrar, D. R., and Wendel, J. F., Phylogeny of the Vittariaceae: convergent simplification leads to a polyphyletic Vittaria, American Fern Journal, pp. 283-305, 1995.
J. Greilhuber, Dolezel, J., Leitch, I. J., and Wendel, J. F., Plant Genome Diversity: Vol. 1: Plant Genomes, Their Residents, and Their Evolutionary Dynamics. Springer, 2012.
I. J. Leitch, Greilhuber, J., Dolezel, J., and Wendel, J. F., Plant Genome Diversity Volume 2: Physical Structure, Behaviour and Evolution of Plant Genomes, vol. 2. Springer Science & Business Media, 2012.
L. H. Rieseberg and Wendel, J. F., Plant speciation–rise of the poor cousins, New Phytologist, vol. 161, no. 1, pp. 3-8, 2004.
B. Liu, Brubaker, C. L., Mergeai, G., Cronn, R. C., and Wendel, J. F., Polyploid formation in cotton is not accompanied by rapid genomic changes, Genome, vol. 44, no. 3, pp. 321-330, 2001.
M. L. Ainouche and Wendel, J. F., Polyploid speciation and genome evolution: Lessons from recent allopolyploids, in Evolutionary Biology: Genome Evolution, Speciation, Coevolution and Origin of Life, Springer International Publishing, 2014, pp. 87-113.
J. A. Udall and Wendel, J. F., Polyploidy and crop improvement, Crop Science, vol. 46, no. Supplement_1, p. S-3-S-14, 2006.
K. L. Adams and Wendel, J. F., Polyploidy and genome evolution in plants, Current opinion in plant biology, vol. 8, no. 2, pp. 135-141, 2005.
J. F. Wendel and Cronn, R. C., Polyploidy and the evolutionary history of cotton, Advances in agronomy, vol. 78, pp. 139-186, 2003.
M. Bohlke and Wendel, J. F., A possible hybrid in the genus Hieracium., 1976.
G. Hu, Koh, J., Yoo, M. ‐J., Grupp, K., Chen, S., and Wendel, J. F., Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense, New Phytologist, vol. 200, no. 2, pp. 570-582, 2013.
G. Hu, Koh, J., Yoo, M. - J., Pathak, D., Chen, S., and Wendel, J. F., Proteomics profiling of fiber development and domestication in upland cotton (Gossypium hirsutum L.), Planta, vol. 240, no. 6, pp. 1237-1251, 2014.
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R. C. Cronn, Small, R. L., Haselkorn, T., and Wendel, J. F., Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes, American Journal of Botany, vol. 89, no. 4, pp. 707-725, 2002.
J. S. Hawkins, Proulx, S. R., Rapp, R. A., and Wendel, J. F., Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants, Proceedings of the National Academy of Sciences, vol. 106, no. 42, pp. 17811-17816, 2009.
J. S. Hawkins, Rapp, R. A., and Wendel, J. F., Rapid DNA loss as a counterbalance to retrotransposon proliferation in plant genome size evolution, Transposable Elements and Genome Size Dynamics in Gossypium, p. 61, 2007.
A. H. Paterson, Brubaker, C. L., and Wendel, J. F., A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis, Plant Molecular Biology Reporter, vol. 11, no. 2, pp. 122-127, 1993.
D. S. Senchina, Álvarez, I., Cronn, R. C., Liu, B., Rong, J., Noyes, R. D., Paterson, A. H., Wing, R. A., Wilkins, T. A., and Wendel, J. F., Rate variation among nuclear genes and the age of polyploidy in Gossypium, Molecular biology and evolution, vol. 20, no. 4, pp. 633-643, 2003.
C. E. Grover and Wendel, J. F., Recent insights into mechanisms of genome size change in plants, Journal of Botany, vol. 2010, 2010.
B. Chaudhary, Flagel, L., Stupar, R. M., Udall, J. A., Verma, N., Springer, N. M., and Wendel, J. F., Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (Gossypium), Genetics, vol. 182, no. 2, pp. 503-517, 2009.
C. L. Brubaker and Wendel, J. F., Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs), American journal of botany, pp. 1309-1326, 1994.
C. E. Grover, Gallagher, J. P., Jareczek, J. J., Page, J. T., Udall, J. A., Gore, M. A., and Wendel, J. F., Re-evaluating the phylogeny of allopolyploid Gossypium L, Molecular Phylogenetics and Evolution, 2015.
C. E. Grover, Gallagher, J. P., Jareczek, J. J., Page, J. T., Udall, J. A., Gore, M. A., and Wendel, J. F., Re-evaluating the phylogeny of allopolyploid Gossypium L., Molecular phylogenetics and evolution, vol. 92, pp. 45-52, 2015.
J. S. Hawkins, Grover, C. E., and Wendel, J. F., Repeated big bangs and the expanding universe: Directionality in plant genome size evolution, Plant Science, vol. 174, no. 6, pp. 557-562, 2008.
A. H. Paterson, Wendel, J. F., Gundlach, H., Guo, H., Jenkins, J., Jin, D., Llewellyn, D., Showmaker, K. C., Shu, S., and Udall, J., Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres, Nature, vol. 492, no. 7429, pp. 423-427, 2012.
J. M. Pleasants and Wendel, J. F., Reproductive and Pollination Biology of the Endemic Hawaiian Cotton, Gossypium tomentosum (Malvaceae) 1, Pacific Science, vol. 64, no. 1, pp. 45-55, 2010.
K. L. Adams, Flagel, L., and Wendel, J. F., Responses of the cotton genome to polyploidy, in Genetics and Genomics of Cotton, Springer US, 2009, pp. 419-429.
L. Huang, Millet, E., Rong, J., Wendel, J. F., Anikster, Y., and Feldman, M., Restriction fragment length polymorphism in wild and cultivated tetraploid wheat, Israel Journal of Plant Sciences, vol. 47, no. 4, pp. 213-224, 1999.
B. Liu and Wendel, J. F., Retrotransposon activation followed by rapid repression in introgressed rice plants, Genome, vol. 43, no. 5, pp. 874-880, 2000.
J. F. Wendel and Wessler, S. R., Retrotransposon-mediated genome evolution on a local ecological scale, Proceedings of the National Academy of Sciences, vol. 97, no. 12, pp. 6250-6252, 2000.

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