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J. F. Wendel and Doyle, J., 7 Polyploidy and evolution in plants, Plant diversity and evolution: genotypic and phenotypic variation in higher plants, p. 97, 2005.
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K. L. Adams and Wendel, J. F., Allele-specific, bidirectional silencing of an alcohol dehydrogenase gene in different organs of interspecific diploid cotton hybrids, Genetics, vol. 171, no. 4, pp. 2139-2142, 2005.
J. F. Wendel and Percy, R. G., Allozyme diversity and introgression in the Galapagos Islands endemic Gossypium darwinii and its relationship to continental G. barbadense, Biochemical Systematics and Ecology, vol. 18, no. 7, pp. 517-528, 1990.
R. G. Percy and Wendel, J. F., Allozyme evidence for the origin and diversification of Gossypium barbadense L., Theoretical and Applied Genetics, vol. 79, no. 4, pp. 529-542, 1990.
R. Cronn, Brothers, M., Klier, K., Bretting, P. K., and Wendel, J. F., Allozyme variation in domesticated annual sunflower and its wild relatives, Theoretical and applied genetics, vol. 95, no. 4, pp. 532-545, 1997.
S. Renny-Byfield, Gallagher, J. P., Grover, C. E., Szadkowski, E., Page, J. T., Udall, J. A., Wang, X., Paterson, A. H., and Wendel, J. F., Ancient gene duplicates in Gossypium (Cotton) exhibit near-complete expression divergence, Genome biology and evolution, vol. 6, no. 3, pp. 559-571, 2014.
J. F. Wendel and Parks, C. R., Application of electrophoresis to taxonomic and breeding problems in Camellias, Camellia J, vol. 34, no. 4, pp. 39-41, 1979.
J. F. Doebley and Wendel, J. F., Application of RFLPs to plant systematics, Development and application of molecular markers to problems in plant genetics. New York, USA Cold Spring Harbor Laboratories, pp. 57-67, 1989.
C. E. Grover, Grupp, K. K., Wanzek, R. J., and Wendel, J. F., Assessing the monophyly of polyploid Gossypium species, Plant systematics and evolution, vol. 298, no. 6, pp. 1177-1183, 2012.
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C. E. Grover, Gallagher, J. P., and Wendel, J. F., Candidate Gene Identification of Flowering Time Genes in Cotton, The Plant Genome, 2015.
R. E. Masonbrink, Gallagher, J. P., Jareczek, J. J., Renny-Byfield, S., Grover, C. E., Gong, L., and Wendel, J. F., CenH3 evolution in diploids and polyploids of three angiosperm genera, BMC plant biology, vol. 14, no. 1, p. 383, 2014.
A. Schnabel and Wendel, J. F., Cladistic biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences, American Journal of Botany, vol. 85, no. 12, pp. 1753-1765, 1998.
L. Gong, Masonbrink, R. E., Grover, C. E., Renny-Byfield, S., and Wendel, J. F., A Cluster of Recently Inserted Transposable Elements Associated with siRNAs in, The Plant Genome, 2015.
W. L. Applequist, Cronn, R., and Wendel, J. F., Comparative development of fiber in wild and cultivated cotton, Evolution & development, vol. 3, no. 1, pp. 3-17, 2001.
M. - J. Yoo and Wendel, J. F., Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome, 2014.
C. L. Brubaker, Paterson, A. H., and Wendel, J. F., Comparative genetic mapping of allotetraploid cotton and its diploid progenitors, Genome, vol. 42, no. 2, pp. 184-203, 1999.
B. S. Gaut, Clark, L. G., Wendel, J. F., and Muse, S. V., Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae)., Molecular Biology and Evolution, vol. 14, no. 7, pp. 769-777, 1997.
L. Gong, Kakrana, A., Arikit, S., Meyers, B. C., and Wendel, J. F., Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species, Genome biology and evolution, vol. 5, no. 12, pp. 2449-2459, 2013.
T. Seelanan, Schnabel, A., and Wendel, J. F., Congruence and consensus in the cotton tribe (Malvaceae), Systematic Botany, pp. 259-290, 1997.
D. J. Crawford, Doyle, J. J., Soltis, D. E., Soltis, P. S., and Wendel, J. F., Contemporary and future studies in plant speciation, 2014.
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.
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.
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.
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.
K. M. Olsen and Wendel, J. F., Crop plants as models for understanding plant adaptation and diversification, Frontiers in plant science, vol. 4, 2013.
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.
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.
R. Cronn and Wendel, J. F., Cryptic trysts, genomic mergers, and plant speciation, New Phytologist, vol. 161, no. 1, pp. 133-142, 2004.
J. F. Wendel and Parks, C. R., Cultivar characterization and nomenclatural clarification by protein electrophoresis in Camellia japonica L, American Camellia Yearbook (USA), 1982.
J. F. Wendel and Parks, C. R., Cultivar identification in Camellia japonica L. using allozyme polymorphisms., Journal American Society for Horticultural Science, 1983.
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.
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.
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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.
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.
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.
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.
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.
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. 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. 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.
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.
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.
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.
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.

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