Selected Publications

Recent publication list – Wendel c.v. short

Watch Jeans, Genes, & Genomes: Exploring the Mysteries of Cotton - A Recent Lecture on Cotton Evolutionary Genomics

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Gong, L., M. Olson, and J. F. Wendel. 2014. Cytonuclear evolution of rubisco in four allopolyploid lineages. Molecular Biology and Evolution 31:2624–2636.

Renny-Byfield, S., J. P. Gallagher, C. E. Grover, E. Szadkowski, J. T. Page, J. A. Udall, X. Wang, A. H. Paterson and J. F. Wendel. 2014. Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence. Genome Biology and Evolution doi: 10.1093/gbe/evu037.

Xu, C., Y. B., X. Lin, N. Zhao, L. Hu, Z. Gong, J. F. Wendel, and B. Liu. 2104. Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Molecular Biology and Evolution 31:1066–1076.

Buggs, R. J. A., J. F. Wendel, J. J. Doyle, D. E. Soltis, P. S. Soltis and J. Coate. 2014. The legacy of diploid progenitors in allopolyploid gene expression patterns. Philosophical Transactions of the Royal Society B  doi:10.1098/rstb.2013.0354.

Crawford, D. J., J. J. Doyle, D. E. Soltis, P. S. Soltis, and J. F. Wendel. 2014. Introduction: 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 doi:10.1098/rstb.2013.0341.

Renny-Byfield, S., and J. F. Wendel. 2014. Doubling down on genomes: polyploidy and crop plants. American Journal of Botany 10.3732/ajb.1400119.

Grover C. E., X. Zhu, K.K. Grupp, J. Jareczek, J. P. Gallagher., E. Szadkowski and J. F. Wendel. 2014. Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum. Genetic Resources and Crop Evolution DOI 10.1007/s10722-014-0138-x.

Crawford, D. J., J. J. Doyle, D. E. Soltis, P. S. Soltis, and J. F. Wendel (Eds). 2014. 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, 369

Zhang, H., B. Zhu, B. Qi, X. Gou, Y. Dong, C. Xu, B. Zhang, W. Huang, C. Liu, X. Wang, C. Yang, H. Zhu, K. Kashkush, M. Feldman, J.F. Wendel, B. Liu. 2014. Evolution of the BBAA COmponent of Bread Wheat during Its History at the Allohexaploid Level. The Plant Cell, 26: 2761-2776.

Gong, L., A. Kakrana, S. Arikit, B. C. Meyers, and J. F. Wendel. 2013. Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome Biology and Evolution, 5 (12): 2449-2459.

Yoo, M. J. and J.F. Wendel. 2014. Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome. PLOS Genetics DOI: 10.1371/journal.pgen.1004073

Page, J. T., M. D. Huynh, Z. S. Liechty, K. Grupp, D. Stelly, A. Hulse, H. Ashrafi, A. van Deynze, J. F. Wendel, and J. A. Udall. 2013. Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencingG3: Genes, Genomes, Genetics 3:1809-1818.

Madlung, A. and J. F. Wendel. 2013. Genetic and epigenetic aspects polyploid evolution in plants. Cytogenetic and Genome Research 140 (2-4): 270-285.

Olsen, K. M. and J. F. Wendel. 2013. Crop plants as models for understanding plant adaptation and diversification. Frontiers in Plant Science, 4: 290.

Olsen K. M. Wendel J. F. 2013. A bountiful harvest: genomic insights into crop domestication phenotypes. Annu Rev Plant Biol 64: 47-70.

Hu G., Koh J., Yoo M. J., Grupp K., Chen S., Wendel J. F. 2013. Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbandense. New Phytologist 200: 570-582.

Madlung, A. and J.F. Wendel. 2013. Genetic and Epigenetic Aspects of Polyploid Evolution in Plants. Cytogenetic and Genome Research, DOI: 10.1159/000351430

Yoo, M-J, E. Szadkowski, J.F. Wendel. 2013. Homoelog expression bias and expression level dominance in allopolyploid cotton. Heredity, 110, 171-180.

Grover, C.E., J.P. Gallagher, E.P. Szadkowski, M.J. Yoo, L. E. Flagel, and J. F. Wendel. 2012. Homeolog expression bias and expression level dominance in allopolyploids. The New Phytologist, 196: 966-971.

Greilhuber, Johann, J. Dolezel, J. Wendel, and I. J. Leitch. 2012. Plant Genome Diversity, Volume 2: Phsyical Structure, Behaviour and Evolution of Plant Genomes. Springer, Vienna.

Paterson, Wendel, et al. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 492, 423-427.

Salmon, A., J.A. Udall, J. A. Jeddeloh, J. F. Wendel. 2012. Targeted Capture of Homoeologous Coding and Noncoding Sequence in Polyploid Cotton. G3, Vol. 2, No. 8, 921-930.

Grover, C.E., K.K. Grupp, R. J. Wanzek, J. F. Wendel. 2012. Assessing the monophyly of polyploid Gossypium species. Plant Systematics and Evolution. Springer, Vol. 298, No. 6, 1177-1183.

Wendel, J. F., J. Greilhuber, J. Dolozel, and I. J. Leitch.  2012.  Plant Genome Diversity, Volume 1 Plant Genomes, Their Residents, and Their Evolutionary Dynamics. Springer, Vienna.

Leitch, I. J., J. Greilhuber, J. Dolozel, and J. F. Wendel. 2012.  Plant Genome Diversity, Volume 2, Structure, Behavior and Evolution of Plant Genomes. Springer, Vienna (in press)

Gong, L., A. Salmon, M-J Yoo, K. K. Grupp, Z. Wang, A. H. Paterson and J. F. Wendel. 2012. The cytonuclear dimension of allopolyploid evolution: an example from cotton using rubisco. Molecular Biology and Evolution, 29(10):3023–3036.

Adams, K. L., and J. F. Wendel.  2012. Dynamics of duplicated gene expression in polyploid cotton.  In Polyploid and Hybrid Genomics (Z. J. Chen and J. Birchler, Eds.), Wiley Blackwell (in press).

Wendel, J. F., L. E. Flagel, and K. L. Adams. 2012. Jeans, genes, and genomes: cotton as a model for studying polyploidy. In Polyploidy and Genome Evolution (P. S. Soltis and D. E. Soltis, Eds). Springer, New York. (in press)

Grover, C. E., K. K. Grupp, R. J. Wanzek, and J. F. Wendel. 2012 Assessing the monophyly of polyploid Gossypium species. Plant Systematics and Evolution (in press)

Grover, C. E., A. Salmon, and J. F. Wendel. 2012. Targeted sequence capture as a powerful tool for evolutionary analysis. American Journal of Botany 99: 312–319.

Bao, Ying, Guanjing Hu, Lex E. Flagel, Armel Salmon, Magdalena Bezanilla, Andrew H. Paterson, Zining Wang, Jonathan F. Wendel. 2011. Parallel up-regulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium). PNAS, Vol. 108, No. 52, 21152-21157.

Hu, Guanjing, Norma L. Houston, Dharminder Pathak, Linnea Schmidt, Jay J. Thelen, Jonathan F. Wendel. 2011. Genomically Biased Accumulation of Seed Storage Proteins in Allopolyploid Cotton. Genetics, Vol. 189, 1103-1115.

Richards, Christina L. and Jonathan F. Wendel. 2011. The hairy problem of epigenetics in evolution. New Phytologist 191: 7-9.

Hu, Guanjing, Jennifers S. Hawkins, Corrine E. Grover, Jonathan Wendel. 2010. The history and disposition of transposable elements in polyploid Gossypium. Genome 53: 599-607.

Rapp, Ryan A., Candace H. Haigler, Lex Flagel, Ran H. Hovav, Joshua A. Udall, Jonathan F. Wendel. 2010. Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication. BMC Biology. 8:139.

Grover, C. E. and J. F. Wendel. 2010. Recent insights into mechanisms of genome size change in plants. Journal of Botany doi: 10.1155/2010/382732.

Salmon, Armel, Lex Flagel, Bao Ying, Joshua A. Udall, Jonathan F. Wendel. 2010. Homoeologous nonreciprocal recombination in polyploid cotton. New Phytologist. 186: 123-134.

Flagel, Lex E. and Jonathan F. Wendel. 2010. Evolutionary rate variatio, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation. New Phytologist. 186: 184-193.

Betancur, Lissete, Bir Singh, Ryan A. Rapp, Jonathan F. Wendel, M. David Marks, Alison W. Roberts, Candace H. Haigler. 2010. Phylogenetically Distinct Cellulose Synthase Genes Support Secondary Wall Thickening in Arabidopsis Shoot Trichomes and Cotton Fiber. Journal of Integrative Plant Biology. 2010, 52 (2): 205-220.

Wendel, Jonathan F., Curt Brubaker, and Tosak Seelanan. 2010. The Origin And Evolution of Gossypium. Physiology of Cotton. pp 1-18.

Pleasants, John M. and Jonathan F. Wendel. 2010. Reproductive and Pollination Biology of the Endemic Hawaiian Cotton, Gossypium tomentosum (Malvaceae). Pacific Science. January 2010. 45 - 55.

Hawkins, Jennifer S., Stephen R. Proulx, Ryan A. Rapp, Jonathan F. Wendel. 2009. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. PNAS. Published online before print October 7, 2009. doi: 10.1073/pnas.0904339106.

Chaudhary, Bhupendra, Ran Hovav, Lex Flagel, Ron Mittler, Jonathan F. Wendel. 2009. Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium). BMC Genomics 10: 378.

Flagel, Lex E., Jonathan F. Wendel. 2009. Gene duplication and evolutionary novelty in plants. New Phytologist 183: 557-564.

Flagel, Lex E., Liping Chen, Bhupendra Chaudhary, Jonathan F. Wendel. 2009. Coordinated and Fine-Scale Control of Homoeologous Gene Expression in Allotraploid Cotton. Journal of Heredity 100(4): 487-490.

Chaudhary, Bhupendra, Lex Flagel, Robert M. Stupar, Joshua A. Udall, Neetu Verma, Nathan M. Springer, Jonathan F. Wendel. 2009. Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium). Genetics 182: 503-517.

Rapp, Ryan A., Joshua A Udall, Jonathan F. Wendel. 2009. Genomic expression dominance in allopolyploids. BMC Biology 7:18.

Butterworh, Kara M., Dean C. Adams, Harry T. Horner, Jonathan F. Wendel. 2009. Initiation and Early Development of Fiber in Wild and Cultivated Cotton. International Journal of Plant Science 170(5): 561-574.

Doyle, Jeff J., Lex E. Flagel, Andrew H. Paterson, Ryan A. Rapp, Douglas E. Soltis, Pamela S. Soltis, Jonathan F. Wendel. 2008. Evolutionary Genetics of Genome Merger and Doubling in Plants. Annual Review of Genetics 42:443-61.

Chaudhary, Bhupendra, Ran Hovav, Ryan Rapp, Neetu Verma, Joshua Udall, Jonathan F. Wendel. 2008. Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evolution and Development 10:5, 567-582.

Flagel, Lex E., Ryan A. Rapp, Corrinne E.Grover, Mark P. Widrlechner, Jennifer Hawkins, Jessie L. Grafenberg, Inés Álvarez, Gyu Young Chung, and Jonathan F. Wendel. 2008. Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea. American Journal of Botany 95(6): 756-765.

Flagel, Lex E., J. Udall, D. Nettleton, J. F. Wendel. 2008. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology 6 (16).

Hovav, R., J.A. Udall, B. Chaudhary, L. Flagel, R. Rapp, J.F. Wendel. 2008. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. PNAS 105 (16) 6191-6195.

Hovav, R., J.A. Udall, E. Hovav, R. Rapp, L. Flagel, J.F. Wendel. 2008. A majority of cotton genes are expressed in single-celled fiber. Planta 227: 319-329.

Hovav, R., J.A. Udall, B. Chaudhary, E. Hovav, L. Flagel, G. Hu, J.F. Wendel. 2007. The Evolution of Spinnable Cotton Fiber Entailed Prolonged Development and a Novel Metabolism. PLoS Genet 4(2): e25.

Udall, J.A., L.E. Flagel, F. Cheung, A.W. Woodward, R. Havov, R.A. Rapp, J.M. Swanson, J.J. Lee, A. R. Gingle, D. Nettleton, C.D. Town, Z.J. Chen, and J.F. Wendel. 2007. Spotted cotton oligonucleotide microarrays for gene expression analysis. BMC Genomics 8: 81.

Grover, C.E., H. Kim, R.A. Wing, A.H. Paterson, and J.F. Wendel. 2007. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium). The Plant Journal 50: 995-1006.

Fortune, P.M., K.A. Schierenbeck, A.K. Ainouche, J. Jacquemin, J.F. Wendel, and M.L. Ainouche. 2007. Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae). Molecular Phylogenetics and Evolution 43: 1040-1055.

Udall, J. A., J. M. Swanson, D. Nettleton, R. J. Percifield, and J. F. Wendel.  2006.  A novel approach for characterizing expression levels of genes duplicated by polyploidy. Genetics 173: 1823-1827.

Keyte, A. L., R. Percifield, B. Liu, and J. F. Wendel. 2006.  Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.)Journal of Heredity 97: 444-450.

Hawkins, J. S., H. Kim, J. D. Nason, R. A. Wing, and J. F. Wendel.  2006.  Differential lineage-specific amplification of transposable elements is responsible for genome size variation in GossypiumGenome Research 16: 1252-1261. 

Udall, J. A. and J. F. Wendel.  2006.  Polyploidy and crop improvementThe Plant Genome, a Supplement to Crop Science 46: S3-14.

Alvarez, I. and J.F. Wendel.  2006. Cryptic Interspecific Introgression and Genetic Differentiation Within Gossypium aridum (Malvaceae) and Its Relatives. Evolution 60(3): 505-517.

Adams, K.L. and J.F. Wendel.  2005. Allele-Specific, Bidirectional Silencing of an Alcohol Dehydrogenase Gene in Different Organs of Interspecific Diploid Cotton Hybrids. Genetics. 171: 2139-2142.

Alvarez, I., Cronn, R., and J.F. Wendel. 2005. Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes. Pl. Syst. Evol. 252: 199–214.

Hawkins, J.S., Pleasants, J., and J.F. Wendel. 2005. Identification of AFLP markers that discriminate between cultivated cotton and the Hawaiian island endemic, Gossypium tomentosum Nuttall ex Seeman. Genetic Resources and Crop Evolution. 52: 1069–1078.

Rapp, R.A., Alvarez, I., and J.F. Wendel. 2005. Molecular confirmation of the position of Gossypium trifurcatum Vollesen. Genetic Resources and Crop Evolution. 52: 749–753.

Waghmare, V.N., Rong, J., Rogers, C.J., Pierce, G.J., Wendel, J.F., and A.H. Paterson. 2005. Genetic mapping of a cross between Gossypium hirsutum (cotton) and the Hawaiian endemic, Gossypium tomentosum. Theor Appl Genet. 111: 665–676.

Udall, Joshua A., Swanson, Jordan M., Haller, Karl, Rapp, Ryan A., Sparks, Michael E., Hatfield, Jamie, Yu, Yeisoo, Wu, Yingru, Dowd, Caitriona, Arpat, Aladdin B., Sickler, Brad A., Wilkins, Thea A., Guo, Jin Ying, Chen, Xiao Ya, Scheffler, Jodi, Taliercio, Earl, Turley, Ricky, McFadden, Helen, Payton, Paxton, Klueva, Natalya, Allen, Randell, Zhang, Deshui, Haigler, Candace, Wilkerson, Curtis, Suo, Jinfeng, Schulze, Stefan R., Pierce, Margaret L., Essenberg, Margaret, Kim, HyeRan, Llewellyn, Danny J., Dennis, Elizabeth S., Kudrna, David, Wing, Rod, Paterson, Andrew H., Soderlund, Cari, and , Jonathan F. Wendel. 2006. A global assembly of cotton ESTs. Genome Research 16:441-450.

Rapp, R.A. and J.F.Wendel. 2005. Epigenetics and plant evolution. New Phytologist. 168: 81-91.

Adams, K.L. and J.F. Wendel.  2005. Novel patterns of gene expression in polylploid plants.  Trends in Genetics 21(10): 539 - 543.

Salmon A. , Ainouche, M., and J.F. Wendel. 2005. Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Molecular Ecology. 14: 1163-1175.

Adams, K.L., and J.F. Wendel.  2005. Polyploidy and Genome Evolution in Plants. Current Opinions in Plant Biology 8: 135-141.

Adams, K.L., Percifield R., and J.F. Wendel.  2004. Organ-Specific Silencing of Duplicated Genes in a Newly Synthesized Cotton Allotetraploid. Genetics 168: 2217-2226.

Rudgers, J.A., Strauss, S.Y., and J.F. Wendel.  2004. Trade-offs among anti-herbivore resistance traits: insights from Gossypieae (Malvaceae). American Journal of Botany 91: 871-880.

Adams, K.L. and J.F. Wendel.  2004. Exploring the genomic mysteries of polyploidy in cotton.  Biological Journal of the Linnean Society 82: 573 - 581.

Grover, C.E., Kim, H-R, Wing, R.A., Paterson, A. H., and J.F. Wendel.  2004.  Incongruent patterns of local and global genome size evolution in cottonGenome Research 14: 1474-1482.

Small, R.S., Cronn, R.C., and J. F. Wendel.  2004.  Use of nuclear genes for phylogeny reconstruction in plants.  Australian Systematic Botany 17: 145-170.

Rong, J, et al. 2004. A 3347-Locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166: 389-417.

Cronn, R.C. and J.F. Wendel.  2004.  Cryptic trysts, genomic mergers, and plant speciationNew Phytologist 161:133-142.

Liu, B. and J.F. Wendel. 2003. Epigenetic phenomena and the evolution of plant allopolyploidsMolecular Phylogenetics and Evolution 29: 365-379.

Cronn, R.C., R.L. Small, T. Haselkorn, and J.F. Wendel. 2003. Cryptic repeated genomic recombination during speciation in Gossypium gossypioides. Evolution 57(11), 2003, pp 2475-2489.

Adams, K.L., R.C. Cronn, R. Percifield, and J.F. Wendel. 2003. Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing. Proceedings of the National Academy of Sciences USA 100: 4649–4654.

Cedroni, M.L., R.C. Cronn, K.L. Adams, T.A. Wilkins, and J.F. Wendel. 2003. Evolution and expression of MYB genes in diploid and polyploid cotton. Plant Molecular Biology 51: 313–325.

Senchina, D.S., I. Alvarez, R.C. Cronn, B. Liu, J. Rong, R.D. Noyes, A.H. Paterson, R.A. Wing, T.A. Wilkins, and J.F. Wendel. 2003. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol. Biol. Evol. 20(4):633–643.

Cronn, R.C. and K.L. Adams. 2003. Quantitative analysis of transcript accumulation from genes duplicated by polyploidy using cDNA-SSCP. Biotechniques 34: 726-734.

Wendel, J.F., R.C. Cronn, I. Alvarez, B. Liu, R.L. Small, and D.S. Senchina. 2002. Intron Size and Genome Size in Plants. Mol. Biol. Evol. 19(12):2346–2352.

Cronn, R. C., M. Cedroni, T. Haselkorn, C. Grover, and J. F. Wendel. 2002. PCR-mediated recombination in amplification products derived from polyploid cotton. Theoretical and Applied Genetics 104: 482-489.

Cronn, R. C., R. L. Small, T. Haselkorn, and J. F. Wendel. 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. American Journal of Botany 89(4): 707-725.

Small, R. L. and J. F. Wendel. 2002. Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Molecular Biology and Evolution 19(5): 597-607.

Liu, B. and J. F. Wendel. 2002. Non-Mendelian phenomena in allopolyploid genome evolution. Current Genomics Vol. 3, No. 6.

Wendel, J. F. and R. C. Cronn. 2002. Polyploidy and the evolutionary history of cotton. Advances in Agronomy.

Wendel, J. F., R. C. Cronn, J. S. Johnston and H. J. Price. 2002. Feast and famine in plant genomes. Genetica 115: 37-47.

Liu, B. and J.F.Wendel. 2001. Intersimple sequence repeat (ISSR) polymorphisms as a genetic marker system in cotton. Molecular Ecology Notes 1:205-208.

Liu, B., C. L. Brubaker, G. Mergeai, R. C. Cronn, and J. F. Wendel. 2001. Polyploid formation in cotton is not accompanied by rapid genomic changes. Genome 44: 321-330.

Applequist, W. L., R. C. Cronn, and J. F. Wendel. 2001. Comparative development of fiber in wild and cultivated cotton. Evol. Devel. 3: 1-15. Cover photo

Wendel, J.F. 2000. Genome evolution in polyploids. Plant Molecular Biology 42: 225-249.

Liu, B. and J. F. Wendel. 2000. Retroelement activation followed by rapid repression in interspecific hybrid plants. Genome 43: 874-880.

Wendel, J. F. and S. R. Wessler. 2000. Retrotransposon-mediated genome evolution on a local ecological scale. Proceedings of the National Academy of Sciences USA 97: 6250-6252.

Small, R. L. and J. F. Wendel. 2000. Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium L., Malvaceae). Molecular Phylogenetics and Evolution 16: 73-84.

Small, R. L. and J. F. Wendel. 2000. Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155: 1913-1926.

Cronn, R., R. L. Small, and J. F. Wendel. 1999. Duplicated genes evolve independently following polyploid formation in cotton. Proceedings of the National Academy of Sciences USA 96: 14406-14411.

Brubaker, C.L., A.H. Paterson, and J.F. Wendel. 1999. Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42:184-203.

Seelanan, T., C.L. Brubaker, J. McD. Stewart, L.A. Craven, and J.F. Wendel. 1999. Molecular Systematics of Australian Gossypium section Grandicalyx (Malvaceae). Systematic Botany 24:183-208.

Small, R.F., J.A. Ryburn, and J.F. Wendel. 1999. Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Molecular Biology and Evolution 16:491-501.

Schnabel, A. and J.F. Wendel. 1998. Cladistic Biogeography of Gleditsia (Leguminosae) based on ndhF and rpl16 chloroplast gene sequences. American Journal of Botany 85:1753-1765.

Wendel, J.F. and J.J. Doyle. 1998. Phylogenetic incongruence: Window into genome history and molecular evolution. Pp. 265-296 in: Molecular Systematics of Plants II (P. Soltis, and J. Doyle, eds.).

Chapman and Hall.Cronn, R.C. and J.F. Wendel. 1998. Simple methods for isolating homoeologous loci from allopolyploid genomes. Genome 41:756-762.

Small, R.L., J.A. Ryburn, R.C. Cronn, T. Seelanan, and J.F. Wendel. 1998. The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85:1301-1315.

Davis, J.I., M.P. Simmons, D.W. Stevenson and J.F. Wendel. 1998. Data decisiveness and data quality in phylogenetic analysis: an example from the monocots using mitochondrial atpA sequences. Systematic Biology 47:282-310.

Baum, D.A., R.L. Small, and J.F. Wendel. 1998. Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Systematic Biology 47:181-207.

Zhao, X.-P., Y. Si, R. E. Hanson, C. F. Crane, H. J. Price, D. M. Stelly, J. F. Wendel and A. H. Paterson. 1998. Dispersed repetitive DNA has colonized new genomes since polyploid formation in cotton. Genome Research 8: 479-492.

Seelanan, T., A. Schnabel and J.F. Wendel. 1997. Congruence and consensus in the cotton tribe. Systematic Botany 22:259-290.

Cronn, R. C., X. Zhao, A. H. Paterson, and J. F. Wendel. 1996. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. Journal of Molecular Evolution 42: 685-705.

Wendel, J.F., A. Schnabel, and T. Seelanan. 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences USA 92:280-284.

Wendel, J.F., A. Schnabel, and T. Seelanan. 1995. An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Molecular Phylogenetics and Evolution 4:298-313.

Wendel, J. F. 1995. Cotton. In: Evolution of Crop Plants (N. Simmonds and J. Smartt, eds.), pp. 358-366.

Longman, London.Brubaker, C. L. and J. F. Wendel. 1994. Reevaluating the origin of domesticated cotton (Gossypium hirsutum: Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). American Journal of Botany 81: 1309-1326.

Wendel, J. F. and V. A. Albert. 1992. Phylogenetics of the cotton genus (Gossypium L.): Character-state weighted parsimony analysis of chloroplast DNA restriction site data and its systematic and biogeographic implications. Systematic Botany 17: 115-143.

Wendel, J.F. 1989. New World tetraploid cottons contain Old World cytoplasm. Proceedings of the National Academy of Science USA 86: 4132-4136.