Recent Publications

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Selected works here

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

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Abbreviated Curriculum Vitae, Jonathan F. Wendel

Academic Training: B.S., University of Michigan (1976); M.S., University of North Carolina (1980); Ph.D., University of North Carolina (1983)

Academic Positions

5/83-7/86:               Geneticist, USDA, ARS, Genetics Dept., North Carolina State University

8/86-7/91:               Assistant Professor of Botany, Dept. of Botany, Iowa State University

8/91-7/96:               Associate Professor of Botany, Dept. of Botany, Iowa State University

12/97-6/98:             Jacob Meyerhoff Visiting Professor, Weizmann Institute, Rehovot, Israel

8/96-6/2002:           Professor of Botany, Dept. of Botany, Iowa State University

7/2002-6/2003:        Interim Chair, Department of Ecology, Evolution, & Organismal Biology, Iowa State University

7/2003-6/2017:        Chair, Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Iowa State University

7/2012-present:       Distinguished Professor, Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Iowa State University

Honors and Awards

Outstanding Achievement in Research, Iowa State University, 1999

Master Teacher, College of Liberal Arts and Sciences, Iowa State University, 2005

Outstanding Achievement in Departmental Leadership, Iowa State University, 2009

Fellow, American Association for the Advancement of Science, 2010

Outstanding Contributions to Cotton Genomics award, ICGI, 2012

Distinguished Professor, Iowa State University, 2012

Cotton Biotechnology Award, Cotton Incorporated, 2013

Distinguished Fellow, Botanical Society of America, 2015

Distinguised Scholar, Crop Science Society of America, 2015

Publications in chronological order (scroll to bottom for most recent)

Wendel, J.F. and C.R. Parks. 1979. The application of electrophoresis to taxonomic and breeding problems in Camellia. Camellia Journal 34: 39-4l.

Wendel, J.F. 1980. Enzyme extraction from a tannin-rich plant. Isozyme Bulletin l3:116.

Wendel, J.F. and C.R. Parks. 1982. Genetic control of isozyme variation in Camellia japonica L. (Theaceae). Journal of Heredity 73: l97-204.

Parks, C. R., N. G. Miller, J. F. Wendel and K. M. McDougal. 1983. Genetic divergence in the genus Liriodendron. Annals of the Missouri Botanical Garden 70: 658-666.

Wendel, J.F. and C.R. Parks. 1982. Cultivar characterization and nomenclatural clarification by protein electrophoresis in Camellia japonica L. American Camellia Society Yearbook 37: l9-32.

Wendel, J.F. 1983. Electrophoretic analysis of genetic variation in wild and cultivated Camellia japonica L. Ph.D. dissertation. University of North Carolina, Chapel Hill.

Cardy, B.J., C.W. Stuber, J.F. Wendel, and M.M. Goodman. 1983. Techniques for starch gel electrophoresis of enzymes from maize (Zea mays L.). 2nd revised edition. Institute of Statistics Mimeograph Series no. 1317R, North Carolina State University.

Suiter, K.A., J.F. Wendel and J.S. Case. 1983. LINKAGE-l, a computer program for the analysis of genetic segregation data. Journal of Heredity 74: 203-204.

Wendel, J.F. and C.R. Parks. 1983. Cultivar identification in Camellia japonica L. using allozyme polymorphisms. Journal of the American Society of Horticultural Science l08:290-295.

Wendel, J.F. 1984. Electrophoretic identification of polyploid Camellia japonica cultivars and evidence for their sexual origin. Plant Systematic and Evolution 145: 223-226.

Wendel, J.F. and C.R. Parks. 1984. Distorted segregation and linkage of alcohol dehydrogenase genes in Camellia japonica L. (Theaceae). Biochemical Genetics 22: 739-748.

Wendel, J.F. and C.W. Stuber. 1984. Plant Isozymes: Enzymes studied and buffer systems for their electrophoretic resolution in starch gels. Isozyme Bulletin 17:4-11.

Wendel, J.F. and C.R. Parks. 1985. Genetic diversity and population structure of Camellia japonica L. (Theaceae). American Journal of Botany 72: 52-65.

Wendel, J.F., C.W. Stuber, and M.M. Goodman. 1985. Twelve new isozyme loci in maize: Progress report on chromosomal locations, and the subunit composition and subcellular localization of their products. Maize Genetics Cooperation News Letter 59:87-88.

Wendel, J.F., C.W. Stuber, and M.M. Goodman. 1985. Linkage relationships between a hexokinase locus and previously assigned loci on chromosome six. Maize Genetics Cooperation News Letter 59: 89-90.

Wendel, J.F., C.W. Stuber, and M.M. Goodman. 1985. Localization of two new isozyme loci, Hex1 and Tpi4, to chromosome 3. Maize Genetics Cooperation News Letter 59:88.

Wendel, J.F., C.W. Stuber, and M.M. Goodman. 1985. Mapping data for 34 isozyme loci currently being studied. Maize Genetics Cooperation News Letter 59:90.

Wendel, J.F. and J.B. Beckett. 1986. Further localization of Tpi4 near the centromere on the long arm of chromosome 3. Maize Genetics Cooperation News Letter 60:119

Wendel, J.F., C.W. Stuber, and M.M. Goodman. 1986. Additional mapping experiments with maize isozyme loci. Maize Genetics Cooperation News Letter 60:120-122.

Wendel, J.F., C.W. Stuber, M.D. Edwards, and M.M. Goodman. 1986. Duplicated chromosome segments in Zea mays L.: Further evidence from hexokinase isozymes. Theoretical and Applied Genetics 72: 178-185.

Edwards, M.D., C.W. Stuber, and J.F. Wendel. 1987. Molecular marker facilitated investigations of quantitative trait loci in maize: I. Numbers, genomic distribution, and types of gene action. Genetics 116: 113-125.

Stuber, C.W., M.D. Edwards, and J.F. Wendel. 1987. Molecular marker facilitated investigations of quantitative trait loci in maize: II. Factors influencing yield and its component traits. Crop Science 27: 639-648.

Wendel, J.F., M.D. Edwards, and C.W. Stuber. 1987. Evidence for multilocus genetic control of preferential fertilization in maize. Heredity 58: 297-301.

Wendel, J. F. and J. B. Beckett. 1987. A new isozyme marker for the short arm of chromosome 6. Maize Genetics Cooperation News Letter 61:19.

Sisco, P.H., J.F. Wendel, and C.W. Stuber. 1987. Acp4 is the most distal marker on chromosome 1L. Maize Genetics Cooperation News Letter 61:86.

Doebley, J.F., J.F. Wendel, S.C. Smith, C.W. Stuber, and M.M. Goodman. 1988. The origin of cornbelt maize: the isozyme evidence. Economic Botany 42: 120-132.

Wendel, J.F., M.M. Goodman, C.W. Stuber, and J.B. Beckett. 1988. New isozyme systems for maize (Zea mays L.): Aconitate hydratase, adenylate kinase, NADH dehydrogenase, and shikimate dehydrogenase. Biochemical Genetics 26: 421-445.

Stuber, C.W., J.F. Wendel, M.M. Goodman, and J.S.C. Smith. 1988. Techniques and scoring procedures for starch gel electrophoresis of enzymes from maize (Zea mays L.). North Carolina State Experiment Station Technical Bulletin 286. North Carolina State University, Raleigh. 87pp.

Pleasants, J.P. and J.F. Wendel. 1989. Genetic diversity in a clonal narrow endemic, Erythronium propullans, and its widespread progenitor, E. albidum. American Journal of Botany 76: 1136-1151.

Weeden, N.F. and J.F. Wendel. 1989. Genetics of Plant Isozymes. In: D.E. Soltis and P.M. Soltis (eds.), Isozymes in Plant Biology, pp 46-72. Dioscorides Press, Portland, Oregon.

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

Wendel, J.F. and N.F. Weeden. 1989. Visualization and Interpretation of Plant Isozymes. In: D.E. Soltis and P.M. Soltis (eds.), Isozymes in Plant Biology, pp. 5-45. Dioscorides Press, Portland, Oregon.

Wendel, J.F., C.W. Stuber, M.M. Goodman, and J.B. Beckett. 1989. Duplicated plastid and triplicated cytosolic isozymes of triose phosphate isomerase in maize (Zea mays L.). Journal of Heredity 80: 218-228.

Wendel, J.F., P.D. Olson and J.M. Stewart. 1989. Genetic diversity, introgression and independent domestication of Old World cultivated cottons. American Journal of Botany 76: 1795-1806.

Doebley, J.F. and J. F. Wendel. 1989. Application of RFLPs to plant systematics. In: Current Communications in Molecular Biology - Development and Application of Molecular Markers to Problems in Plant Genetics (T. Helentjaris and B. Burr, Eds.). Cold Spring Harbor Laboratory.

Wendel, J. F. 1989. Chromosomal locations of isozyme loci in maize (Zea mays L.). Isozyme Bulletin 22:33-35.

Doebley, J. F., A. Stec, J. F. Wendel and M. Edwards. 1990. Genetic analysis of a maize-teosinte F2 population: Implications for the origin of maize. Proceedings of the National Academy of Science USA 87: 9888-9892.

Parks, C.R. and J.F. Wendel. 1990. Molecular divergence between Asian and North American species of Liriodendron (Magnoliaceae) with implications for interpretation of fossil geofloras. American Journal of Botany 77: 1243-1256.

Bretting, P. K. and J. F. Wendel. 1990. Utility of Tpi3 and Tpi4 variants in quality control of hybrid popcorn seed production. Maize Genetics Cooperation Newsletter 64:121-122.

Parks, C.R., J.F. Wendel, M.M. Sewell and L.Y. Qui. 1990. Genetic control of isozyme variation in the genus Liriodendron L. Journal of Heredity 81: 317-323.

Percy, R.G. and J.F. Wendel. 1990. Allozyme evidence for the origin and diversification of Gossypium barbadense L. Theoretical and Applied Genetics 79: 529-542.

Wendel, J. F. and A. E. Percival. 1990. Molecular divergence in the Galapagos Island-Baja California species pair, Gossypium klotzschianum and G. davidsonii (Malvaceae). Plant Systematics and Evolution 171: 99-115.

Wendel, J. F. and R. G. Percy. 1990. Allozyme diversity and introgression in the Galapagos endemic Gossypium darwinii and its relationship to continental G. barbadense. Biochemical Systematics and Ecology 18: 517-528.

Dekker, J., R. Burmester and J. Wendel. 1991. Mutant weeds of Iowa: S-triazine resistant Pennsylvania smartweed (Polygonum pensylvanicum). Weed technology 5: 211-213.

Klier, K., M. J. Leoschke and J. F. Wendel. 1991. Hybridization and introgression in white and yellow ladyslipper orchids (Cypripedium candidum and C. pubescens). Journal of Heredity 82:305-319.

Wendel, J. F., J. McD. Stewart and J. H. Rettig. 1991. Molecular evidence for homoploid reticulate evolution in Australian species of Gossypium. Evolution 45: 694-711.

DeJoode, D. R. and J. F. Wendel. 1992. Genetic diversity and origin of the Hawaiian Islands cotton, Gossypium tomentosum. American Journal of Botany 79: 1311-1319.

VanderWiel, P. L. and J. F. Wendel. 1992. Phylogenetic analysis of cotton retrotransposons. Plant Molecular Evolution Newsletter 1(2):34-37.

Bretting, P. K., S. M. Stack, J. F. Wendel, E. Meyerowitz, J. Colbert, L. Rieseberg, R. C. Jackson, V. Walbot and H. J. Price. 1992. BSA-Genetics section research agenda. Plant Genetics Newsletter 8:26-29.

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., C. L. Brubaker and A. E. Percival. 1992. Genetic diversity in Gossypium hirsutum and the origin of Upland cotton. American Journal of Botany 79: 1291-1310.

Brubaker, C. L. and J. F. Wendel. 1993. On the specific status of Gossypium lanceolatum Todaro. Genetic Resources and Crop Evolution 40: 165-170.

Brubaker, C. L., J. A. Koontz and J. F. Wendel. 1993. Bidirectional cytoplasmic and nuclear introgression in the New World cottons, Gossypium barbadense and G. hirsutum. American Journal of Botany 80: 222-227.

Paterson, A. H., C. L. Brubaker and J. F. Wendel. 1993. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP and PCR analysis. Plant Molecular Biology Reporter 11: 122-127.

Rieseberg, L. H. and J. F. Wendel. 1993. Introgression and its consequences in plants. In: Hybrid Zones and the Evolutionary Process, R. Harrison (ed.), pp. 70-109. Oxford University Press.

Wendel, J. F. and C. L. Brubaker. 1993. The gene pool of Gossypium hirsutum. Proceedings of the 1993 Beltwide Cotton Conference, National Cotton Council. 1556.

VanderWiel, P. S., D. F. Voytas and J. F. Wendel. 1993. Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.). Journal of Molecular Evolution 36: 429-447.

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.

Parks, C. R., J. F. Wendel, M. M. Sewell, and Y.-L. Qui. 1994. The significance of allozyme variation and introgression in the Liriodendron tulipifera complex (Magnoliaceae). American Journal of Botany 81: 878-889.

Reinisch, A. J. J. Dong, C. L. Brubaker, D. M. Stelly, J. F. Wendel, and A. H. Paterson. 1994. A detailed RFLP map of cotton, Gossypium hirsutum x G. barbadense: chromosome organization and evolution in a disomic polyploid genome. Genetics 138:829-847.

Stanton, M. A., J. McD. Stewart, A. E. Percival and J. F. Wendel. 1994. Morphological diversity and relationships in the A-genome cottons, Gossypium arboreum and G. herbaceum. Crop Science 34: 519-527.

Wendel, J. F., R. Rowley and J. Stewart. 1994. Genetic diversity in and phylogenetic relationships of the Brazilian endemic cotton, Gossypium mustelinum (Malvaceae). Plant Systematics and Evolution 192: 49-59.

Whitkus, R., J. Doebley, and J. F. Wendel. 1994. Nuclear DNA markers in systematics and evolution. In: DNA-based Markers in Plants (R. L. Phillips and I. K. Vasil, eds.), pp. 116-141. Kluwer Academic Publishers, Dordrecht, Holland.

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

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.

Wang, R.-L., J. F. Wendel, and J. H. Dekker. 1995. Weedy adaptation in Setaria spp.: I. Isozyme analysis of genetic diversity and population genetic structure in Setaria viridis. American Journal of Botany 82: 308-317.

Wang, R.-L., J. F. Wendel, and J. H. Dekker. 1995. Weedy adaptation in Setaria spp.: II. Genetic diversity and population genetic structure in S. glauca, S. geniculata, and S. faberii. American Journal of Botany 82: 1031-1039.

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

Paterson, A. H., J. F. Wendel, and R. J. Kohel. 1995. In Altenback, S. et al. (19 authors), USDA Plant genome research program. Advances in Agronomy 55: 113-166

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.

Clark, L. G., J. F. Wendel, and L. A. Craven. 1995. A New Species of Micraira (Poaceae: Micraireae) from northern Western Australia. The Beagle 12: 1-7.

Clark, L. G., W. Zhang, and J. F. Wendel. 1995. A phylogeny of the grass family based on ndhF sequence data. Systematic Botany 20: 436-460.

Crane, E. H., D. F. Farrar, and J. F. Wendel. 1995. Phylogeny of Vittariaceae: Convergent simplification leads to a polyphyletic Vittaria. American Fern Journal 85: 283-305.

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.

Kelchner, S. A. and J. F. Wendel. 1996. Hairpins create minute inversions in non-coding regions of chloroplast DNA. Current Genetics 30: 259-262.

Paterson, A. H., T.-H. Lan, K. P. Reischmann, C. Chang, Y.-R. Lin, S.-C. Liu, M. D. Burow, S. P. Kowalski, C. S. Katsar, T. A. DelMonte, K. A. Feldmann, K. F. Schertz, and J. F. Wendel. 1996. Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nature Genetics 14: 380-382.

Wendel, J. F. 1996. The evolution of cotton and its genome. Proceedings of the symposium “Biotechnology and Biodiversity”, University of Morelos, Mexico

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

Gaut, B. S., L. G. Clark, J. F. Wendel and S. V. Muse. 1997. Comparisons of the molecular evolutionary process at rbcL and ndhF in the grass family (Poaceae). Molecular Biology and Evolution 14: 769-777.

Zhang, W., J. F. Wendel, and L. G. Clark. 1997. Bamboozled again!: Inadvertent isolation of fungal rDNA sequences from bamboos (Poaceae: Bambusoideae). Molecular Phylogenetics and Evolution 8: 205-217.

Cronn, R., M. Brothers, K. Klier, P.K. Bretting, and J. F. Wendel. 1997. Allozyme variation in domesticated annual sunflower and its wild relatives. Theoretical and Applied Genetics 95:532-545.

Paterson, A. H., J. F. Wendel, D. M. Stelly, and X. Zhao. 1997. Status of genome mapping tools in the Malvaceae. In: Genome Mapping in Plants (A. H. Paterson, ed.), pp 229-239. Academic Press, NY.

Stewart, J. McD., L. A. Craven and J. F. Wendel. 1997. A new Australian species of Gossypium. Proc. Beltwide Cotton Conf. p. 448. National Cotton Council, Memphis, TN.

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.

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

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.

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.

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, D. Soltis, and J. Doyle, eds.). Kluwer Academic Publ., Dordrecht.

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.

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.

Small, R. L. and J. F. Wendel. 1999. The mitochondrial genome of allotetraploid cotton (Gossypium L.). Journal of Heredity 90: 251-253.

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.

Brubaker, C. L., F. M. Bourland and J. F. Wendel. 1999. The origin and domestication of cotton. In: Cotton; origin, history, technology and production (C. W. Smith and J. T. Cothren, eds.), pp. 3-31. John Wiley & Sons, New York.

Percival, A. E., J. McD. Stewart and J. F. Wendel. 1999. Taxonomy and germplasm resources. In: Cotton; origin, history, technology and production (C. W. Smith and J. T. Cothren, eds.), pp. 33-63. John Wiley & Sons, New York.

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.

Small, R. L., 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.

Huang, L., E. Millet, J.K. Rong, J. F. Wendel, and M. Feldman. 1999. Restriction fragment length polymorphism in wild and cultivated tetraploid wheat. Israeli Journal of Plant Science 47: 213-224.

Wendel, J. F, C. L. Brubaker and T. Seelanan. 1999. The origin and evolution of Gossypium. In: Cotton Physiology, Book II (J. Stewart, D. Oosterhuis, and J. Heitholt, eds.), The Cotton Foundation, Memphis, TN.

Wendel, J. F., R. L. Small, R. C. Cronn, and C. L. Brubaker. 1999. Genes, jeans, and genomes: Reconstructing the history of cotton. Pp. 133-161 in: Plant evolution in man-made habitats. Proceedings of the VIIth international symposium of the international organization of plant biosystematists (L.W.D. van Raamsdonk and J. C. M. den Nijs, eds.). Hugo de Vries Laboratory, Amsterdam, The Netherlands.

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.

Hanson, R. E., M. N. Islam-Faridi, C. F. Crane, M. S. Zwick, D. C. Czeschin, J. F. Wendel., T. D. McKnight, H. J. Price, and D. M. Stelly. 1999. Ty1-copia-retrotransposon behavior in a polyploid cotton. Chromosome Research 8: 73-76.

Wendel, J. F. 1999. Genes, jeans and genomes: cotton as a model of polyploid evolution. Focus; Proceedings of the MAPMBS Meetings, 1998, pp. 2-4.

Pan, Q., J. Wendel, D. Zamir and R. Fluhr. 2000. Divergent evolution of plant NBS-LRR homologues in dicot and cereal genomes. Journal of Molecular Evolution 50: 203-213.

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

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.

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.

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

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.

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

Brubaker, C. L. and J. F. Wendel. 2001. RFLP diversity in cotton. In: Genetic improvement of cotton: emerging technologies (J. N. Jenkins and S. Saha, eds.), pp. 81-102. Science Publishers Inc., Enfield, New Hampshire.

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

Cronn, R. C., M. Cedroni, T. Haselkorn, C. Osborne, 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: 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: 597-607.

Liu, B. and J. F. Wendel. 2002. Non-Mendelian phenomena in allopolyploid genome evolution. Current Genomics 3: 489-506.

Wendel, J. F., R. C. Cronn, I. Alvarez, B. Liu, R. L. Small, and D. Senchina. 2002. Intron size and genome size in plants. Molecular Biology and Evolution 19: 2346-2352.

Wendel, J. F. and R. C. Cronn. 2003. Polyploidy and the evolutionary history of cotton. Advances in Agronomy 78: 139-186.

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.

Schnabel, A., P. E. McDonel, and J. F. Wendel. 2003. Phylogenetic Relationships in Gleditsia (Leguminosae) based on ITS sequences. American Journal of Botany 90: 310-320.

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. Molecular Biology and Evolution 20:633-643.

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

Alvarez, I. and J. F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417-434.

Adams, K., R. 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.

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

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.

Rudgers, J. A., S. Y. Strauss, and J. F. Wendel. 2004. Trade-offs between anti-herbivore resistance traits: within- and among-species comparisons using Gossypium. American Journal of Botany 91: 871-880.

Small, R. A., R. C. Cronn, and J. F. Wendel. 2004. The use of nuclear genes for phylogeny reconstruction in plants. Australian Systematic Biology 17: 145-170.

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

Rieseberg, L. H. and J. F. Wendel. 2004. Commentary: Plant Speciation. New Phytologist 161: 3-6.

Rong, J., C. Abbey, J. E. Bowers, C. L. Brubaker, C. Chang, P. W. Chee, T. A. Delmonte, X. Ding, J. J. Garza, B. S. Marler, C. Park, G. J. Pierce, K. M. Rainey, V. K. Rastogi, S. R. Schulze, N. L. Trolinder, J. F. Wendel, T. A. Wilkins, T. D. Williams-Coplin, R. A. Wing, R. J. Wright, X. Zhao, L. Zhu, and A. H. Paterson. 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.

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

Adams, K.L., R. Percifield, and J. F. Wendel. 2004. Organ-specific silencing of duplicated genes in a newly synthesized cotton allotetraploid. Genetics 168:2217-2226.

Wendel, J. F. and K. L. Adams. 2005. Genome evolution and gene silencing in polyploid cotton. In: Plant species-level systematics: new perspectives on pattern and process (F. T. Bakker, L. W. Chatrou, B. Gravendeel, and P. Pelser (eds.), Gantner Verlag, Ruggell. Regnum Vegetabile 142: 271-290.

Wendel, J. F. and J. J. Doyle. 2005. Polyploidy and Evolution in plants. Pp 97-117 In: Plant Diversity and Evolution (R. J. Henry, Ed.). CABI Publishing, Wallingford, UK.

Adams, K. L. and J. F. Wendel. 2005. Polyploidy and genome evolution in plants. Current opinions in plant biology 8: 135-141.

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

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

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

Álvarez, I., R. Cronn, and J. F. Wendel. 2005. Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes. Plant Systematics and Evolution 252: 199-214.

Rong, J., G. J. Pierce, V. N. Waghmare, C. J. Rogers, A. Desai, P. W. Chee, O. L. May, J. R. Gannaway, J. F. Wendel, T. A. Wilkins, and A. H. Paterson. 2005. Genetic mapping and comparative analysis of seven mutants related to seed fiber development in cotton. Theor. Appl. Genet. 111:1137-1146.

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

Petrov, D. A. and J. F. Wendel. 2006. Genome evolution in eukaryotes: the genome size perspective. Pp 144-156, in: Evolutionary Genetics: Concepts and Case Studies (C. W. Fox and J. B. Wolf, Eds.). Oxford Univ. Press.

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

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

Adams, K. L. and J. F. Wendel. 2006. Allele-specific, bi-directional silencing of an alcohol dehydrogenase gene in different organs of interspecific cotton hybrids. Genetics 17: 2139-2142.

Udall, J. A., J. Swanson, K. Haller, R.A. Rapp, M. Sparks, J. Hatfield, Y. Yu, Y. Wu, A.B. Arpat, B.A. Sickler, T.A. Wilkins, J.-Y. Guo, X.-Y. Chen, E. Taliercio, R. Turley, C. Dowd, H. McFadden, N. Klueva, P. Payton, R. Allen, D. Zhang, C. Haigler, C. Wilkerson, J. Suo, S.R. Schulze, M.L. Pierce, M. Essenberg, H. Kim, D.J. Llewellyn, E.S. Dennis, D. Kudrna, R. Wing, A.H. Paterson, C. Soderlund, and J.F. Wendel. 2006. A global assembly of cotton ESTs. Genome Research 16: 441-450.

Álvarez, I. and J. F. Wendel. 2006. Ancient interspecific introgression and modern genetic differentiation within Gossypium aridum (Malvaceae) and its relatives. Evolution 60: 505-517.

Senchina, D. S., L. E. Flagel, J. F. Wendel, and M. L. Kohut. 2006. Phenetic comparison of seven Echinacea species based on immunomodulatory characteristics. Economic Botany 60: 205-211.

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 Gossypium. Genome Research 16: 1252-1261.

Udall, J. A. and J. F. Wendel. 2006. Polyploidy and crop improvement. The Plant Genome 46: 3-14.

Chen, Z. J., B. E. Scheffler, E. Dennis, B. Triplett, T. Zhang, X. Chen, D. M. Stelly, P. D. Rabinowicz, C. Town, T. Arioli, C. Brubaker, R. Cantrell, J.-M. Lacape, M. Ulloa, P. Chee, A. R. Gingle, C. Haigler, R. Percy, S. Saha, T. Wilkins, R. J. Wright, A. Van Deynze, Y. Zhu, S. Yu, W. Guo, I. Abdurakhmonov, I. Katageri, M. Rahman, Y. Zafar, J. Z. Yu, R. J. Kohel, J. Wendel, and A. H. Paterson. 2007. Towards sequencing cotton (Gossypium) genomes. Plant Physiology 145: 1303-1310.

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., F. Cheung, A. W. Woodward, J. M. Swanson, L. Flagel, R. Hovav, R. A. Rapp, D. Nettleton, J. J. Lee, A. R. Gingle, C. 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 size evolution in the AdhA region of diploid and polyploid cotton (Gossypium). The Plant Journal 50: 995-1006.

Rong, J., A. Feltus, V. N. Waghmare, G. J. Pierce, P. W. Chee, X. Draye, Y. Saranga, R. J. Wright, T. A. Wilkins, O. L. May, J. R. Gannaway, J. F. Wendel, A. H. Paterson. 2007. Meta-analysis of polyploid cotton QTLs shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development. Genetics 176: 2577-2588.

Grover, C.E., J.S. Hawkins, and J.F. Wendel. 2007. Tobacco genome quickly goes up in smoke. New Phytologist 175: 599-602.

Percifield, R., J. S. Hawkins, J. McCoy and J. F. Wendel. 2007. Genetic diversity in Hypericum and AFLP markers for species-specific identification of H. perforatum L. Planta Medica 73: 1614-1621.

Hovav, R., J. A. Udall, E. Hovav, R. Rapp, L. Flagel, and J. F. Wendel. 2008. Gene expression during cellular differentiation of the single-celled cotton trichome (fiber). Planta 227: 319-329.

Hawkins, J. S., G. Hu, R. A. Rapp, J. L. Grafenberg, and J. F. Wendel. 2008. Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium. Genome 51:11-18

Hovav, R., J. A. Udall, B. Chaudhary, E. Hovav, L. Flagel, G. Hu, and J. F. Wendel. 2008. The evolution of spinable cotton fiber entailed natural selection for prolonged development and a novel metabolism. PLOS Genetics 4, e25 doi:10.1371/journal.pgen.0040025.

Flagel, L., J. A. Udall, D. Nettleton, and J. F. Wendel. 2008. Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biology 6:16 doi:10.1186/1741-7007-6-16.

Grover, C. E., Y. Yu, R. A. Wing, A. H. Paterson, and J. F. Wendel. 2008. A phylogenetic analysis of indel dynamics in the cotton genus. Molecular Biology and Evolution 25: 1415–1428.

Hawkins, J. S., C. E. Grover, and J. F. Wendel. 2008. Repeated big bangs and the expanding universe: directionality in plant genome size evolution. Plant Science 174: 557-562.

Hovav, R., J. A. Udall, B. Chaudhary, R. Rapp, L. Flagel, and J. F. Wendel. 2008. Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proceedings of the National Academy of Sciences USA 105: 6191-6195.

Flagel, L., R. A Rapp, C. E. Grover, M. P. Widrlechner, J. H. Hawkins, J. L. Grafenberg, I. Alvarez, G. Y. Chung, and Jonathan F Wendel. 2008. Phylogenetic, morphological, and chemotaxonomic incongruence in the North American endemic genus Echinacea Moench. American Journal of Botany 95: 756-765.

Hovav, R., B. Chaudhary, J. A. Udall, L. Flagel, and J. F. Wendel. 2008. Parallel domestication, convergent evolution, and duplicate gene recruitment in allopolyploid cotton. Genetics 179: 1725-1733.

Doyle, J. J., L. A. Flagel, A. H. Paterson, R. Rapp, D. E. Soltis, P.S. Soltis, and J. F. Wendel. 2008. Evolutionary genetics of genome merger and doubling in plants.  Annual Review of Genetics 42: 443-461.

Grover, C.E., J.S. Hawkins, and J.F. Wendel. 2008. Phylogenetic insights into the pace and pattern of plant genome size evolution. Pp 57-68 in: Genome Dynamics, Volume 4, Genome Dynamics (J-N Volff, ed). Karger Publishers, Basel, Switzerland.

Chaudhary, B., R, Hovav, R, Rapp, N, Verma, J, A. Udall and J, F. Wendel. 2008. Global analysis of gene expression in cotton fibers from wild and domesticated Gossypium barbadense. Evolution and Development 10: 567-582.

Butterworth, K. M., D. C. Adams, H. T. Horner and J. F. Wendel. 2009. Initiation and early development of fiber in wild and cultivated cotton. International Journal of Plant Science 170: 561-574.

Rapp, R. A., J. A. Udall and Jonathan F. Wendel. 2009. Genomic expression dominance in allopolyploids. BMC Biology 7:18 doi:10.1186/1741-7007-7-18.

Stewart, J. MacD., L. A. Craven, C. Brubaker, and J. F. Wendel. 2009. Gossypium anapoides (Malvaceae), a New Species from Western Australia. Novon (in press).

Wendel, J. F., C. L. Brubaker, I. Alvarez, R. C. Cronn, and J. McD. Stewart. 2009. Evolution and natural history of the cotton genus. In: Genomics of cotton, Plant Genetics and Genomics; Crops and Models 3, pp. 3-22, A.H. Paterson (Ed.), Springer, New York.

Adams, K. L., L. Flagel, and J. F. Wendel. 2009. Responses of the cotton genome to polyploidy. In: Genomics of cotton, Plant Genetics and Genomics; Crops and Models 3, pp. 419-429. A.H. Paterson (Ed.), Springer, New York.

Chaudhary, B., L. Flagel, R. M. Stupar, J. A. Udall, N. Verma, N. M. Springer, and J. F. Wendel. 2009. Reciprocal silencing, transcriptional bias and functional divergence of homoeologs in polyploid cotton (Gossypium).  Genetics 182: 503–517.

Flagel L.F. and J.F. Wendel. 2009. Gene duplication and evolutionary novelty in plants.  New Phytologist 183: 557-564.

Flagel L.E., L. Chen, B. Chaudhary, and J.F. Wendel. 2009. Coordinated and fine-scale control of homoeologous gene expression in allotetraploid cotton.  Journal of Heredity 100: 487-490.

Chaudhary, B., R. Hovav, L. Flagel, R. Mittler and J. F. Wendel. 2009. Parallel expression evolution of oxidative stress-related genes in fiber from wild and domesticated diploid and polyploid cotton (Gossypium).  BMC Genomics 10:378doi:10.1186/1471-2164-10-378

Hawkins, J. S., R. A. Rapp, S. Proulx, and J. F. Wendel. 2009. Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proceedings of the National Academy of Sciences 106: 17811–17816.

Bao, Y., J. F. Wendel, and S. Ge. 2010. Multiple patterns of rDNA evolution following polyploidy in Oryza. Molecular Phylogenetics and Evolution 55: 136-142.

Betancur, L., B. Singh, R. A. Rapp, J. F. Wendel, M. D. Marks, A. W. Roberts and C. H. Haigler. 2010. Phylogenetically distinct cellulose synthase genes support secondary wall thickening in Arabidopsis shoot trichomes and cotton fiber. Journal of Integrative Plant Biology 52: 205-220.

Flagel, L. E. and J. F. Wendel. 2010. Evolutionary rate variation and scope of duplicate gene expression evolution in five allotetraploid cotton species. New Phytologist 186: 184–193.

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.

Paterson, A. H., J. Rong, A. R. Gingle, P. W. Chee, E. Dennis, D. Llewellyn, L. S. Dure III, C. Haigler, G. O. Meyers, D. G. Peterson, M. ur Rahman, Y. Zafar, U. Reddy, Y. Saranga, J. McD. Stewart, J. A. Udall, V. N. Waghmare, J. F. Wendel, T. A. Wilkins, R. J. Wright, E. Zaki; E.-S. Hafez and J. Zhu. 2010. Sequencing and utilization of the Gossypium genomes. Tropical Plant Biology 3: 71-74

Pleasants, J. M. and J. F. Wendel. 2010. Reproductive and pollination biology of the endemic Hawaiian cotton, Gossypium tomentosum (Malvaceae).  Pacific Science 64: 45–55.

Salmon, A., L. E. Flagel, B. Ying, J. A. Udall, and J. F. Wendel. 2010. Homoeologous gene conversion following allopolyploidy in cotton. New Phytologist 186: 123–134.

Wendel, J. F., C. L. Brubaker, and T. Seelanan. 2010.  The origin and evolution of Gossypium. Pp 1-18 in: Stewart, J.M.; Oosterhuis, D.; Heitholt, J.J.; Mauney, J.R. (Eds.), Physiology of cotton, Springer, Netherlands.

Lin, L., G. J. Pierce, J. E. Bowers, J. C. Estill, R. O. Compton, L. K Nelson, C. Kim, C. Lemke, J. Rong, H. Tang, X. Wang, M. Braidotti, A. H. Chen, K. Collura, E. Epps, W. Golser, C. Grover, K. Chicola, J. Ingles, S. Karunakaran, D. Kudrna, J. Olive, N. Tabassum, E. Um, M. Wissotski, Y. Yu, A. Zuccolo, M. Rahman, D. G. Peterson, R. A. Wing, J. F. Wendel, and A. H. Paterson. 2010. A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics, 11: 395.

Hu, G., J. S. Hawkins, C. E. Grover, and J. F. Wendel. 2010. The history and disposition of transposable elements in polyploid Gossypium. Genome 53: 1-9.

Rapp, R. A. C. H. Haigler, L. Flagel, R. H. Hovav, J. A. Udall and J. F. Wendel. 2010. Gene expression in developing fibers of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication. BMC Biology 8: 139.

Richards, C. L. and J. F. Wendel. 2011. The hairy problem of epigenetics in evolution.  New Phytologist 191: 7–9

Hu, G.,  N. L. Houston, D. Pathak, L. Schmidt, J. J. Thelen and J. F. Wendel. 2011. Genomically biased accumulation of seed storage proteins in allopolyploid cotton. Genetics 189: 1103–1115.

Wendel, J. F., and M. M. Goodman. 2011. Stanley George Stephens.  Biographical Memoirs of the National Academy of Sciences, 93: 1-22

Bao, Y., G. Hu, L. Flagel, A. Salmon, M. Bezanilla, A. Paterson, Z. Wang, and J. F. Wendel. 2011. Convergent upregulation of the profilin gene family following independent domestication of diploid and allopolyploid cotton (Gossypium). Proceedings of the National Academy of Sciences USA 108: 21152–21157.

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.

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 298: 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 (17 chapters). Springer, Vienna.

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).

Flagel, L. E., J. A. Udall, and J. F. Wendel. 2012. Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. BMC Genomics 13: 302; DOI: 10.1186/1471-2164-13-302

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. Pp 181-207.

Leitch, I. J., J. Greilhuber, J. Dolozel, and J. F. Wendel. 2012.  Plant Genome Diversity, Volume 2 (17 chapters). Springer, Vienna.

Gong, L., A. Salmon, M. J. Yoo, 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: 3023–3036

Salmon, A., J. A. Joshua, J. A. Jeddeloh, and J. F. Wendel. 2012. Targeted capture of homoeologous coding and non-coding sequence in polyploid cotton. G3: Genes, Genomes, Genetics 2: 921-930

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

Paterson, A. H., J. F. Wendel, H. Gundlach, H. Guo, J. Jenkins, D. Jin, D. Llewellyn, K. C. Showmaker, S. Shu, J. Udall, M. Yoo, R. Byers, W. Chen, A. Doron-Faigenboim, M. V. Duke, L. Gong, J. Grimwood, C. Grover, K. Grupp, G. Hu, T. Lee, J. Li, L. Lin, T. Liu, B. S. Marler, J. T. Page, A. W. Roberts, E. Romanel, W. S. Sanders, E. Szadkowski, X. Tan, H. Tang, C. Xu, J. Wang, Z. Wang, D. Zhang, L. Zhang, H. Ashrafi, F. Bedon, J. E. Bowers, C. L. Brubaker, P. W. Chee, S. Das, A. R. Gingle, C. H. Haigler, D. Harker, L. V. Hoffmann, R. Hovav, D. C. Jones, C. Lemke, S. Mansoor, M. ur Rahman, L. N. Rainville, A. Rambani, U. K. Reddy, J. Rong, Y. Saranga, B. E. Scheffler, J. A. Scheffler, D. M. Stelly, B. A. Triplett, A. Van Deynze, M. F. S. Vaslin, V. N. Waghmare, S. A. Walford, R. J. Wright, E. A. Zaki, T. Zhang, E. S. Dennis, K. F. X. Mayer, D. G. Peterson, D. S. Rokhsar, X. Wang, and J. Schmutz. 2012.  Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.  Nature 492: 423 – 428.

Olson, K. M. and J. F. Wendel. 2013. A bountiful harvest: genomic insights into crop domestication phenotypes. Annual Reviews of Plant Biology 64: 47-70.

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

Madlung, A. and J. F. Wendel. 2013. Genetic and epigenetic aspects polyploid evolution in plants. Cytogenetic and Genome Research 140:270-285 (DOI: 10.1159/000351430).

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

Olson, K. M. and J. F. Wendel. 2013. Crop plants as models for understanding plant adaptation and diversification. Frontiers in Plant Science, 4: article 290 (doi: 10.3389/fpls.2013.00290).

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-sequencing.  G3: Genes, Genomes, Genetics 3:1809-1818.

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: 2449-2459.

Panaud, O., S. A. Jackson, and J. F. Wendel. 2014. Drivers and dynamics of diversity in plant genomes.  The New Phytologist 202: 15–18

Yoo, M.-J. and J. F. Wendel. 2014. Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome. PLoS Genetics 10(1): e1004073.

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.

Ainouche, M. L. and J. F. Wendel. 2014. Polyploid speciation and genome evolution: Lessons from recent allopolyploids. In: P. Pontarotti (Ed.), Evolutionary Biology, 17th Meeting 2013. Springer-Verlag, Heidelberg 87-113.

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 101: 1711-1725.

Grover C. E., X. Zhu, K.K. Grupp, J. Jareczek, J. P. Gallagher., E. Szadkowski and J. F. Wendel. 2015. Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum. Genetic Resources and Crop Evolution 62: 103-114.

Gong, L., M. Olson, and J. F. Wendel. 2014. Cytonuclear evolution of rubisco in four allopolyploid lineages. Molecular Biology and Evolution doi: 10.1093/molbev/msu207.

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. Zhou, K. Kashkush, M. Feldman, J. F. Wendel and B. Liu. 2014. Evolution of the BBAA component of bread wheat during its history at the allohexaploid level. The Plant Cell 26: 2761–2776.

Shan, C.-M., X.-X. Shangguan, B. Zhao, X.-F. Zhang, L.-m. Chao, C.-Q. Yang, L-J Wang, H.-Y. Zhu, Y.-D. Zeng., W-Z Guo, B.-L. Zhou, G.-J. Hu, X.-Y. Guan, Z. J. Chen, J. F. Wendel,          T.-Z. Zhang and X.-Ya Chen. 2014. Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3. Nature Communications 5. doi:10.1038/ncomms6519.

Stewart, J. MacD., L. A. Craven, C. Brubaker, and J. F. Wendel. 2014. Gossypium anapoides (Malvaceae), a new species from Western Australia. Novon 23:447–451.

Hu, G., J. Koh, M.-J. Yoo, D. Pathak, S. Chen, and J. F. Wendel. 2014.  Cotton domestication and comparative evolutionary proteomics.  Planta. 240:1237–1251.

Masonbrink, E. R., J. P. Gallagher, J. J. Jareczek, S. Renny-Byfield, C. E. Grover, L. Gong, and J. F. Wendel. 2015. CenH3 evolution in diploids and polyploids of three angiosperm genera. BMC Plant Biology, 14:1588, DOI: 10.1186/s12870-014-0383-3.

Renny-Byfield, S., L. Gong, J. P. Gallagher and J. F. Wendel. 2015. Persistence of sub-genomes in paleopolyploid cotton after 60 million years of evolution.  Molecular Biology and Evolution 32: 1063-1071.

Grover C. E., X. Zhu, K.K. Grupp, J. Jareczek, J. P. Gallagher., E. Szadkowski and J. F. Wendel. 2015. Molecular confirmation of species status for the allopolyploid cotton species, Gossypium ekmanianum. Genetic Resources and Crop Evolution 62: 103-114.

Wendel, J. F. and C. E. Grover, 2015. Taxonomy and evolution of the cotton genus. In: D. Fang and R. Percy (Eds.), Cotton, Agronomy Monograph 24, pp. 25-44, ASA-CSSA-SSSA, Madison, WI.

Hovav, R., A. Faigenboim-Doron, N. Kadmon, G. Hu, X. Zhang, J. P. Gallagher, and J. F. Wendel. 2015. A transcriptome profile for developing seed of polyploid cotton (Gossypium hirsutum). The Plant Genome 8: doi: 10.3835/plantgenome2014.08.0041.

Gong, L., R. E. Masonbrink, C. E. Grover, S. Renny-Byfield, and J. F. Wendel. 2015. A cluster of recently inserted transposable elements associated with siRNAs in Gossypium raimondii. The Plant Genome doi:10.3835/plantgenome2014.11.0088.

Grover, C. E., J. P. Gallagher, and J. F Wendel. 2015. The flowering time network of cotton (Gossypium). The Plant Genome doi:10.3835/plantgenome2014.12.0098.

Hu, G., J. Koh, M.-J. Yoo, S. Chen, and J. F Wendel. 2015. Gene-expression novelty in allopolyploid cotton: a proteomic perspective. Genetics 200, 91–104.

Paterson, A. H., and J. F. Wendel. 2015. Unraveling the fabric of polyploidy.  Nature Biotechnology 33: 491 – 493.

Li, L.-F., B. Liu, K. Olsen, and J. F. Wendel. 2015. A re-evaluation of the homoploid hybrid origin of Aegilops tauschii, the donor of the wheat D-subgenome. The New Phytologist 208: 4-8.

Grover, C. E., J. P. Gallagher, J. J. Jareczek, J. T. Page, J. A. Udall, M. A. Gore, and J. F. Wendel. 2015. Re-evaluating the phylogeny of allopolyploid Gossypium L. Molecular Phylogenetics and Evolution 92: 45-52.

Li, L.-F., B. Liu, K. Olsen, and J. F. Wendel. 2015. Multiple rounds of ancient and recent hybridizations have occurred within the Aegilops-Triticum complex. The New Phytologist 208: 11-12.

Wendel, J. F. 2015. The wondrous cycles of polyploidy in plants.  American Journal of Botany 102: 1753 – 1756.

Wendel, J. F., S. A. Jackson, B. C. Meyers, and R. A. Wing. 2016. Evolution of plant genome architecture. Genome Biology 17:37, DOI: 10.1186/s13059-016-0908-1.

Casacuberta, J. M., S. Jackson, O. Panaud, M. Purugganan and J. F. Wendel. 2016. Evolution of plant phenotypes, from genomes to traits.  Genes, Genomes, and Genomics, doi:10.1534/g3.115.025502.

Gallagher, J. P., C. E. Grover, G. Hu, and J. F. Wendel. 2016. Insights into the ecology and evolution of polyploid plants through network analysis. Molecular Ecology 25: 2644–2660.

Renny-Byfield, S., J. T. Page, J. A. Udall, W. S. Sanders, D. G. Peterson, M. A. Arick, C. E. Grover and J. F. Wendel. 2016. Independent domestication of two Old World cotton species. Genome Biology and Evolution doi: 10.1093/gbe/evw129.

Chen, Z., K. Feng, C. E. Grover, P. Li, F. Liu, Y. Wang, Q. Xu, M. Shang, Z. Zhou, X. Cai, X. Wang, J. F. Wendel, K. Wang, and J. Hua. 2016. Chloroplast DNA structural variation, phylogeny, and age of divergence among diploid cotton species. PLoS ONE DOI:10.1371/journal.pone.0157183.

Chee, P. W., A. H. Paterson, J. A. Udall, and J. F. Wendel. 2016. Interspecific hybridization for upland cotton improvement. In Mason, A. (Ed.), Polyploidy and interspecific hybridisation for crop improvement.

Han, J., R. Masonbrink, W. Shan, F. Song, J. Zhang, W. Yu, K. Wang, Y. Wu, T. Yufeng, H. Tang, J. Wendel, and K. Wang. 2016. Rapid proliferation and nucleolar organizer targeting centromeric retrotransposons in cotton. The Plant Journal  doi: 10.1111/tpj.13309.

Snodgrass, S.J., J. Jareczek, and J.F.Wendel. 2017. An examination of nucleotypic effects in diploid and polyploid cotton. Annals of Botany Plants ) 9: DOI: https://doi.org/10.1093/aobpla/plw082.

Hu, G., R. Hovav, C. E. Grover, A. Faigenboim-Doron, N. Kadmon, J.T. Page, J. A. Udall and J. F. Wendel. 2017. Evolutionary conservation and divergence of gene co-expression networks in Gossypium (cotton) seeds. Genome Biology and Evolution 8: 3765-3783.

Hinze, L. L., A. M. Hulse-Kemp, I. W. Wilson, Q.-H. Zhu, D. J. Llewellyn, J. M. Taylor, A. Spriggs, D. D. Fang, M. Ulloa, J. J. Burke, M. Giband, J.-M. Lacape, A. Van Deynze, J. A. Udall, J. A. Scheffler, S. Hague, J. Wendel1, A. E. Pepper, J. Frelichowski, C. T. Lawley, D. C. Jones, R. G. Percy, and D. M. Stelly. 2017. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biology 17: 37, DOI 10.1186/s12870-017-0981-y

Chen, Z., H. Nie, C. E. Grover, Y. Wang, P. Li, M. Wang, H. Pei, Y. Zhao, S. Li, J. F. Wendel, and J. Hua. 2017. Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A-genome species as cytoplasmic donor of the allotetraploid species. Plant Biology 19: 484-493.

Gallagher, J.P., C. E. Grover, K. Rex, M. Moran, and J. F. Wendel. 2017. A new species of cotton from the Wake Atoll, Gossypium stephensii (Malvaceae). Systematic Botany 42:115-123.

Grover, C. E., J. P. Gallagher, E. P. Szadkowski, J. T. Page, M. A. Gore, J. A. Udall and J. F. Wendel. 2017. Nucleotide diversity in the two co-resident genomes of allopolyploid cotton. Plant Systematics and Evolution DOI 10.1007/s00606-017-1411-1.

Chen, Z., P. Li, C. E. Grover, Y. Wang, C. Hu, M. Wang, H. Nie, H. Pei, Y. Su, Y. Zhao, F. Liu, Z. Zhou, X. Cai, X. Wang, K. Wang, J. F. Wendel, and J. Hua. 2017. Molecular evolution of the plastid genome during diversification of the cotton genus. Molecular Phylogenetics and Evolution 112: 268–276.

Wang, X., Z. Zhang, T. Fu  L. Hu, C. Xu , L.Gong, J. F. Wendel and B. Liu. 2017.  Gene-body CG methylation and divergent expression of duplicate genes in rice. Scientific Reports 7: 2675. DOI:10.1038/s41598-017-02860-4.

Chen, Z., N. Zhao, S. Li, C. E. Grover, H. Nie, J. F. Wendel and J. Hua. Plant mitochondrial genome evolution and cytoplasmic male sterility. 2017. Critical Reviews in Plant Sciences (doi.org/10.1080/07352689.2017.1327762).

Lewis, D. Q., and Wendel, J. F. 2017. Lynn G. Clark—Recipient of the 2016 Peter Raven Award. Systematic Botany 42: 4-5.

Rousseau, H., M. Rousseau-Gueutin, X. dauvergne, J. Boutte, G. Simon, N. Marnet, A. Bouchereau, S. Vacher-Guiheneuf, J. Bazureau, J. Morice, S. Ravanel, F. Cabello-Hurtado, A. Ainouche, A. Salmon, and J Wendel. 2017. Evolution of DMSP (dimethylsulfoniopropionate) biosynthesis pathway: Origin and phylogenetic distribution in polyploid Spartina (Poaceae, Chloridoideae). Molecular Phylogenetics and Evolution 114: 401–414.

Sun, Y., Y. Wu, C. Yang, S. Sun, X. Lin, L. Liu, C. Xu, J. Wendel, L. Gong, and B. Liu. 2017. Segmental allotetraploidy generates extensive homeologous expression rewiring and phenotypic diversity at the population level in rice. Molecular Ecology  DOI: 10.1111/mec.14297.

Sharbrough, J, J. L. Conover, J. A. Tate, J. F. Wendel and D. B. Sloan. 2017. Cytonuclear responses to genome doubling. American Journal of Botany 104: 1277 – 128.

Wendel, J. F., D. Lisch, G. Hu,  and A. S. Mason. 2018. The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation. Current Opinion in Genetics and Development 49:1–7.

Zhao, B., J.-F. Cao, G. Hu, Z. W. Chen, L.-Y. Wang, X.-X. Shangguan, L.-J. Wang, Y.-B. Mao, T. Zhang, J. F. Wendel, and X.-Y. Chen. 2018. Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation. New Phytologist 18: 1061-1075.

Bottani, S.,  N. Radu Zabet, J. F. Wendel and R. A. Veitia. 2018. Gene expression dominance in allopolyploids: hypotheses and models. Trends in Plant Science https://doi.org/10.1016/j.tplants.2018.01.002.

Wang, K., J. F. Wendel, and J. Hua. 2018. Designations for individual genomes and chromosomes in Gossypium. Journal of Cotton Research 1:3-7, https://doi.org/10.1186/s42397-018-0002-1.

Hu, G. and J. F. Wendel. 2018. Cis-trans controls and regulatory novelty accompanying allopolyploidization. New Phytologist doi.org/10.1111/nph.15515.

Li, C., X. Sun, J. L. Conover, Z. Zhang, J. Wang, X. Wang, X. Deng, H. Wang, B. Liu, J. F. Wendel and L. Gong. 2018. Cytonuclear coevolution following homoploid hybrid speciation in Aegilops tauschii. Molecular Biology and Evolution https://doi.org/10.1093/molbev/msy215.

Grover, C. E., M. A. Arick, A. Thrash, J. L. Conover, W. S. Sanders, D. G. Peterson, J. E. Frelichowski, J. A. Scheffler, B. E. Scheffler, and J. F. Wendel. 2019. Insights into the evolution of the New World diploid cottons (Gossypium, subgenus Houzingenia) based on genome sequencing. Genome Biology and Evolution (in press).

Conover, J. L., N. Karimi, N. Stenz, C. Ané, C. E. Grover, C. Skema, J. A. Tate, K. Wolff, S. Logan, J. F. Wendel, and D. A. Baum. 2019. A Malvaceae mystery: a mallow maelstrom of genome multiplications and maybe misleading methods? Journal of Integrative Plant Biology (in press).