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K. L. Adams and Wendel, J. F., Exploring the genomic mysteries of polyploidy in cotton, Biological Journal of the Linnean Society, vol. 82, no. 4, pp. 573-581, 2004.
S. J. Snodgrass, Jareczek, J., and Wendel, J. F., An examination of nucleotypic effects in diploid and polyploid cotton, AoB Plants, p. plw082, 2016.
L. E. Flagel and Wendel, J. F., Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation, New Phytologist, vol. 186, no. 1, pp. 184-193, 2010.
J. J. Doyle, Flagel, L. E., Paterson, A. H., Rapp, R. A., Soltis, D. E., Soltis, P. S., and Wendel, J. F., Evolutionary genetics of genome merger and doubling in plants, Annual review of genetics, vol. 42, pp. 443-461, 2008.
P. M. Fortune, Schierenbeck, K. A., Ainouche, A. K., Jacquemin, J., Wendel, J. F., and Ainouche, M. L., Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae), Molecular phylogenetics and evolution, vol. 43, no. 3, pp. 1040-1055, 2007.
R. Hovav, Udall, J. A., Chaudhary, B., Hovav, E., Flagel, L., Hu, G., and Wendel, J. F., The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism, PLoS Genet, vol. 4, no. 2, p. e25, 2008.
J. F. Wendel, Brubaker, C., Álvarez, I., Cronn, R., and Stewart, J. McD., Evolution and natural history of the cotton genus, in Genetics and genomics of cotton, Springer US, 2009, pp. 3-22.
M. L. Cedroni, Cronn, R. C., Adams, K. L., Wilkins, T. A., and Wendel, J. F., Evolution and expression of MYB genes in diploid and polyploid cotton, Plant molecular biology, vol. 51, no. 3, pp. 313-325, 2003.
J. F. Wendel, Edwards, M. D., and Stuber, C. W., Evidence for multilocus genetic control of preferential fertilization in maize, Heredity, vol. 58, no. 2, pp. 297-301, 1987.
J. F. Wendel, Epigenetics and plant evolution., New Phytologist, vol. 168, no. 1, pp. 81-91, 2005.
R. A. Rapp and Wendel, J. F., Epigenetics and plant evolution, New Phytologist, vol. 168, no. 1, pp. 81-91, 2005.
B. Liu and Wendel, J. F., Epigenetic phenomena and the evolution of plant allopolyploids, Molecular phylogenetics and evolution, vol. 29, no. 3, pp. 365-379, 2003.
J. F. Wendel, Epigenetic phenomena and the evolution of plant allopolyploids, 中国生物学文摘, vol. 19, no. 4, pp. 8-22, 2005.
J. F. Wendel, Electrophoretic identification of polyploidCamellia japonica (Theaceae) cultivars and evidence for their sexual origin, Plant systematics and evolution, vol. 145, no. 3-4, pp. 223-226, 1984.
J. F. Wendel, Electrophoretic analysis of genetic variation in wild and cultivated Camellia japonica L., PhD Thesis, University of North Carolina, 1983.
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K. L. Adams and Wendel, J. F., Dynamics of duplicated gene expression in Polyploid Cotton, Polyploid and hybrid genomics, pp. 187-194, 2013.
J. F. Wendel, Stuber, C. W., Goodman, M. M., and Beckett, J. B., Duplicated plastid and triplicated cytosolic isozymes of triosephosphate isomerase in maize (Zea mays L.), Journal of Heredity, vol. 80, no. 3, pp. 218-228, 1989.
R. C. Cronn, Small, R. L., and Wendel, J. F., Duplicated genes evolve independently after polyploid formation in cotton, Proceedings of the National Academy of Sciences, vol. 96, no. 25, pp. 14406-14411, 1999.
J. F. Wendel, Stuber, C. W., Edwards, M. D., and Goodman, M. M., Duplicated chromosome segments in maize (Zea mays L.): further evidence from hexokinase isozymes, TAG Theoretical and Applied Genetics, vol. 72, no. 2, pp. 178-185, 1986.
L. Flagel, Udall, J., Nettleton, D., and Wendel, J. F., Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution, BMC biology, vol. 6, no. 1, p. 16, 2008.
L. E. Flagel, Wendel, J. F., and Udall, J. A., Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton, BMC genomics, vol. 13, no. 1, p. 302, 2012.
O. Panaud, Jackson, S. A., and Wendel, J. F., Drivers and dynamics of diversity in plant genomes, New Phytologist, vol. 202, no. 1, pp. 15-18, 2014.
S. Renny-Byfield and Wendel, J. F., Doubling down on genomes: polyploidy and crop plants, American journal of botany, vol. 101, no. 10, pp. 1711-1725, 2014.
R. Whitkus, Doebley, J., and Wendel, J. F., DNA-based markers in plants, Nuclear DNA markers in systematics and evolution. Kluwer, Amsterdam, pp. 116-141, 1994.
Q. Pan, Wendel, J. F., and Fluhr, R., Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes, Journal of molecular evolution, vol. 50, no. 3, pp. 203-213, 2000.
J. F. Wendel and Parks, C. R., Distorted segregation and linkage of alcohol dehydrogenase genes in Camellia japonica L.(Theacease), Biochemical genetics, vol. 22, no. 7-8, pp. 739-748, 1984.
D. M. Stelly, Wendel, J. F., and Paterson, A. H., Dispersed Repetitive DNA Has Spread to New Genomes Since Polyploid Formation in Cotton Xin-ping Zhao, Yang Si, Robert E. Hanson, 2 Charles F. Crane, 2 H. James Price, 2, Genome Research, vol. 8, pp. 479-492, 1998.
X. -ping Zhao, Si, Y., Hanson, R. E., Crane, C. F., H Price, J., Stelly, D. M., Wendel, J. F., and Paterson, A. H., Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton, Genome Research, vol. 8, no. 5, pp. 479-492, 1998.
X. P. Zhao, Si, Y., Hanson, R. E., Crane, C. F., Price, H. J., Stelly, D. M., Wendel, J. F., and Paterson, N. H., Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton (vol 8, pg 479, 1998), GENOME RESEARCH, vol. 8, no. 6, pp. 682-682, 1998.
J. S. Hawkins, Kim, H. R., Nason, J. D., Wing, R. A., and Wendel, J. F., Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium, Genome research, vol. 16, no. 10, pp. 1252-1261, 2006.
R. L. Small and Wendel, J. F., Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium), Molecular biology and evolution, vol. 19, no. 5, pp. 597-607, 2002.
A. J. Reinisch, Dong, J. - M., Brubaker, C. L., Stelly, D. M., Wendel, J. F., and Paterson, A. H., A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome., Genetics, vol. 138, no. 3, pp. 829-847, 1994.
J. I. Davis, Simmons, M. P., Stevenson, D. W., and Wendel, J. F., Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences, Systematic Biology, vol. 47, no. 2, pp. 282-310, 1998.
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L. Gong, Olson, M., and Wendel, J. F., Cytonuclear evolution of rubisco in four allopolyploid lineages, Molecular biology and evolution, vol. 31, no. 10, pp. 2624-2636, 2014.
L. Gong, Salmon, A., Yoo, M. - J., Grupp, K. K., Wang, Z., Paterson, A. H., and Wendel, J. F., The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco, Molecular biology and evolution, vol. 29, no. 10, pp. 3023-3036, 2012.
J. F. Wendel and Parks, C. R., Cultivar identification in Camellia japonica L. using allozyme polymorphisms., Journal American Society for Horticultural Science, 1983.
J. F. Wendel and Parks, C. R., Cultivar characterization and nomenclatural clarification by protein electrophoresis in Camellia japonica L, American Camellia Yearbook (USA), 1982.
R. Cronn and Wendel, J. F., Cryptic trysts, genomic mergers, and plant speciation, New Phytologist, vol. 161, no. 1, pp. 133-142, 2004.
R. Cronn, Small, R. L., Haselkorn, T., and Wendel, J. F., Cryptic repeated genomic recombination during speciation in Gossypium gossypioides, Evolution, vol. 57, no. 11, pp. 2475-2489, 2003.
I. Álvarez and Wendel, J. F., Cryptic interspecific introgression and genetic differentiation within Gossypium aridum (Malvaceae) and its relatives, Evolution, vol. 60, no. 3, pp. 505-517, 2006.
K. M. Olsen and Wendel, J. F., Crop plants as models for understanding plant adaptation and diversification, Frontiers in plant science, vol. 4, 2013.
R. L. Small and Wendel, J. F., Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium), Genetics, vol. 155, no. 4, pp. 1913-1926, 2000.
P. L. VanderWiel, Voytas, D. F., and Wendel, J. F., Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.), Journal of molecular evolution, vol. 36, no. 5, pp. 429-447, 1993.
L. E. Flagel, Chen, L., Chaudhary, B., and Wendel, J. F., Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton, Journal of heredity, p. esp003, 2009.
D. J. Crawford, Doyle, J. J., Soltis, D. E., Soltis, P. S., and Wendel, J. F., Contemporary and future studies in plant speciation, morphological/floral evolution and polyploidy: honouring the scientific contributions of Leslie D. Gottlieb to plant evolutionary biology, Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 369, no. 1648, p. 20130341, 2014.
D. J. Crawford, Doyle, J. J., Soltis, D. E., Soltis, P. S., and Wendel, J. F., Contemporary and future studies in plant speciation, 2014.
T. Seelanan, Schnabel, A., and Wendel, J. F., Congruence and consensus in the cotton tribe (Malvaceae), Systematic Botany, pp. 259-290, 1997.

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