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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.
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.
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.
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.
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.
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.
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.
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. 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.
C. Grover, Hawkins, J., and Wendel, J. F., Phylogenetic insights into the pace and pattern of plant genome size evolution, 2008.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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J. Dekker, Burmester, R., and Wendel, J. F., Mutant Weeds of Iowa: S-Triazine Resistant Pennsylvania Smartweed (Polygonum pensylvanicum), Weed Technology, pp. 211-213, 1991.
L. ‐F. Li, Liu, B., Olsen, K. M., and Wendel, J. F., Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops–Triticum complex, New Phytologist, 2015.
Y. Bao, Wendel, J. F., and Ge, S., Multiple patterns of rDNA evolution following polyploidy in Oryza, Molecular phylogenetics and evolution, vol. 55, no. 1, pp. 136-142, 2010.
J. F. Wendel, Edwards, M. D., and Stuber, C. W., MULTILOCUS GENETIC-CONTROL OF PREFERENTIAL FERTILIZATION IN ZEA-MAYS-L, AMERICAN JOURNAL OF BOTANY, vol. 74, no. 5. BOTANICAL SOC AMER INC OHIO STATE UNIV-DEPT BOTANY 1735 NEIL AVE, COLUMBUS, OH 43210, pp. 671-671, 1987.
M. A. Stanton, J Stewart, M. D., A Pervical, E., and Wendel, J. F., Morphological diversity and relationships in the A-genome cottons, Gossypium arboreum and G. herbaceum, Crop science, vol. 34, no. 2, pp. 519-527, 1994.
M. D. Edwards, Stuber, C. W., and Wendel, J. F., Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action, Genetics, vol. 116, no. 1, pp. 113-125, 1987.
T. Seelanan, Brubaker, C. L., McD, J., Craven, L. A., and Wendel, J. F., Molecular systematics of Australian Gossypium section grandicalyx (Malvaceae), Systematic Botany, pp. 183-208, 1999.
C. W. Stuber, Edwards, M. D., and Wendel, J. F., Molecular marker-facilitated investigations of quantitative trait loci in maize. II. Factors influencing yield and its component traits, Crop Science, vol. 27, no. 4, pp. 639-648, 1987.
J. F. Wendel, McD, J., and Rettig, J. H., Molecular evidence for homoploid reticulate evolution among Australian species of Gossypium, Evolution, pp. 694-711, 1991.
J. F. Wendel and Percival, A. E., Molecular divergence in the Galapagos Islands—Baja California species pair, Gossypium klotzschianum andG. davidsonii (Malvaceae), Plant Systematics and Evolution, vol. 171, no. 1-4, pp. 99-115, 1990.
C. R. Parks and Wendel, J. F., Molecular divergence between Asian and North American species of Liriodendron (Magnoliaceae) with implications for interpretation of fossil floras, American Journal of Botany, pp. 1243-1256, 1990.
R. A. Rapp, Álvarez, I., and Wendel, J. F., Molecular confirmation of the position of Gossypium trifurcatum Vollesen, Genetic Resources and Crop Evolution, vol. 52, no. 6, pp. 749-753, 2005.
C. E. Grover, Zhu, X., Grupp, K. K., Jareczek, J. J., Gallagher, J. P., Szadkowski, E., Seijo, J. G., and Wendel, J. F., Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum Wittmack, Genetic Resources and Crop Evolution, vol. 62, no. 1, pp. 103-114, 2014.
R. L. Small and Wendel, J. F., The mitochondrial genome of allotetraploid cotton (Gossypium L.)., The Journal of heredity, vol. 90, no. 1, pp. 251-253, 1998.
C. Grover, Kim, H., Wing, R. A., and Wendel, J. F., Microcolinearity in the Allotetraploid Gossypium hirsutum, Genome Exploitation: Data Mining the Genome, p. 231, 2007.
C. E. Grover, Kim, H. R., Wing, R. A., Paterson, A. H., and Wendel, J. F., Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium), The Plant Journal, vol. 50, no. 6, pp. 995-1006, 2007.
R. Hovav, Udall, J. A., Hovav, E., Rapp, R., Flagel, L., and Wendel, J. F., A majority of cotton genes are expressed in single-celled fiber, Planta, vol. 227, no. 2, pp. 319-329, 2008.

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