Publications

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1994
C. L. Brubaker and Wendel, J. F., “Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs)”, American journal of botany, pp. 1309-1326, 1994.
C. R. Parks, Wendel, J. F., Sewell, M. M., and Qiu, Y. - L., “The significance of allozyme variation and introgression in the Liriodendron tulipifera complex (Magnoliaceae)”, American Journal of Botany, pp. 878-889, 1994.
1995
J. F. Wendel, Schnabel, A., and Seelanan, T., “Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium)”, Proceedings of the National Academy of Sciences, vol. 92, no. 1, pp. 280-284, 1995.
L. G. Clark, Wendel, J. F., and Ven, L. A. Cra, “A new species of Micraira (Poaceae: Micraireae) from northern Western Australia”, 1995.
L. G. Clark, Zhang, W., and Wendel, J. F., “A phylogeny of the grass family (Poaceae) based on ndhF sequence data”, Systematic Botany, pp. 436-460, 1995.
E. H. Crane, Farrar, D. R., and Wendel, J. F., “Phylogeny of the Vittariaceae: convergent simplification leads to a polyphyletic Vittaria”, American Fern Journal, pp. 283-305, 1995.
J. F. Wendel, Schnabel, A., and Seelanan, T., “An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression”, Molecular phylogenetics and evolution, vol. 4, no. 3, pp. 298-313, 1995.
R. -lin Wang, Wendel, J. F., and Dekker, J. H., “Weedy adaptation in Setaria spp. I. Isozyme analysis of genetic diversity and population genetic structure in Setaria viridis”, American Journal of Botany, pp. 308-317, 1995.
R. -lin Wang, Wendel, J. F., and Dekker, J. H., “Weedy adaptation in Setaria spp. II. Genetic diversity and population genetic structure in S. glauca, S. geniculata, and S. faberii (Poaceae)”, American Journal of Botany, pp. 1031-1039, 1995.
1996
S. A. Kelchner and Wendel, J. F., “Hairpins create minute inversions in non-coding regions of chloroplast DNA”, Current genetics, vol. 30, no. 3, pp. 259-262, 1996.
1997
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.
W. Zhang, Wendel, J. F., and Clark, L. G., “Bamboozled again! Inadvertent isolation of fungal rDNA sequences from bamboos (Poaceae: Bambusoideae)”, Molecular phylogenetics and evolution, vol. 8, no. 2, pp. 205-217, 1997.
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.
T. Seelanan, Schnabel, A., and Wendel, J. F., “Congruence and consensus in the cotton tribe (Malvaceae)”, Systematic Botany, pp. 259-290, 1997.
1998
D. A. Baum, Small, R. L., and Wendel, J. F., “Biogeography and floral evolution of Baobabs Adansonia, Bombacaceae as inferred from multiple data sets”, Systematic Biology, vol. 47, no. 2, pp. 181-207, 1998.
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.
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.
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.
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.
R. L. Small and Wendel, J. F., “The mitochondrial genome of allotetraploid cotton (Gossypium L.).”, The Journal of heredity, vol. 90, no. 1, pp. 251-253, 1998.
J. F. Wendel and Doyle, J. J., “Phylogenetic incongruence: window into genome history and molecular evolution”, in Molecular systematics of plants II, Springer US, 1998, pp. 265-296.
R. Cronn and Wendel, J. F., “Simple methods for isolating homoeologous loci from allopolyploid genomes”, Genome, vol. 41, no. 6, pp. 756-762, 1998.
R. L. Small, Ryburn, J. A., Cronn, R. C., Seelanan, T., and Wendel, J. F., “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, vol. 85, no. 9, pp. 1301-1315, 1998.
1999
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.
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.
L. Huang, Millet, E., Rong, J., Wendel, J. F., Anikster, Y., Feldman, M., Sotirova, V., Shtereva, L., Zagorska, N., and Dimitrov, B., “ISRAEL JOURNAL OF LIBRARY PLANT SCIENCES jul o 7 2000 Vol. 47, NO. 4, 1^^ RB^ YUBRAH#. ISSN 0792-9978™***”, Israel Journal of Plant Sciences, vol. 47, p. 211, 1999.
R. L. Small, Ryburn, J. A., and Wendel, J. F., “Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.).”, Molecular biology and evolution, vol. 16, no. 4, pp. 491-501, 1999.
T. Seelanan, Brubaker, C. L., McD, J., Craven, L. A., and Wendel, J. F., “Molecular systematics of Australian Gossypium section grandicalyx (Malvaceae)”, Systematic Botany, pp. 183-208, 1999.
C. L. Brubaker, Bourland, F. M., and Wendel, J. F., “The origin and domestication of cotton”, Cotton: Origin, history, technology, and production. John Wiley & Sons, New York, pp. 3-31, 1999.
L. Huang, Millet, E., Rong, J., Wendel, J. F., Anikster, Y., and Feldman, M., “Restriction fragment length polymorphism in wild and cultivated tetraploid wheat”, Israel Journal of Plant Sciences, vol. 47, no. 4, pp. 213-224, 1999.
A. E. Percival, Wendel, J. F., and Stewart, J. M., “Taxonomy and germplasm resources”, Cotton: Origin, History, Technology, and Production. WC Smith and JT Cothren eds. John Wiley and Sons, Inc., New York, NY, 1999.
2000
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.
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, “Genome evolution in polyploids”, in Plant molecular evolution, Springer Netherlands, 2000, pp. 225-249.
R. L. Small and Wendel, J. F., “Phylogeny, duplication, and intraspecific variation of Adh sequences in new world diploid cottons (Gossypium L., Malvaceae)”, Molecular Phylogenetics and Evolution, vol. 16, no. 1, pp. 73-84, 2000.
B. Liu and Wendel, J. F., “Retrotransposon activation followed by rapid repression in introgressed rice plants”, Genome, vol. 43, no. 5, pp. 874-880, 2000.
J. F. Wendel and Wessler, S. R., “Retrotransposon-mediated genome evolution on a local ecological scale”, Proceedings of the National Academy of Sciences, vol. 97, no. 12, pp. 6250-6252, 2000.
R. E. Hanson, M Islam-Faridi, N., Crane, C. F., Zwick, M. S., Czeschin, D. G., Wendel, J. F., McKnight, T. D., H Price, J., and Stelly, D. M., “Ty1-copia-retrotransposon behavior in a polyploid cotton”, Chromosome Research, vol. 8, no. 1, pp. 73-76, 2000.
2001
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.
B. Liu and Wendel, J. F., “Intersimple sequence repeat (ISSR) polymorphisms as a genetic marker system in cotton”, Molecular Ecology Notes, vol. 1, no. 3, pp. 205-208, 2001.
B. Liu, Brubaker, C. L., Mergeai, G., Cronn, R. C., and Wendel, J. F., “Polyploid formation in cotton is not accompanied by rapid genomic changes”, Genome, vol. 44, no. 3, pp. 321-330, 2001.
C. L. Brubaker and Wendel, J. F., “RFLP diversity in cotton”, Genetic improvement of cotton, emerging technologies. Science Publisher, Inc, Enfield, NH, pp. 81-101, 2001.
2002
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. F. Wendel, Cronn, R. C., J Johnston, S., and H Price, J., “Feast and famine in plant genomes”, Genetica, vol. 115, no. 1, pp. 37-47, 2002.
J. F. Wendel, Cronn, R. C., Álvarez, I., Liu, B., Small, R. L., and Senchina, D. S., “Intron size and genome size in plants”, Molecular biology and evolution, vol. 19, no. 12, pp. 2346-2352, 2002.
B. Liu and Wendel, J. F., “Non-Mendelian phenomena in allopolyploid genome evolution”, Current Genomics, vol. 3, no. 6, pp. 489-505, 2002.
R. Cronn, Cedroni, M., Haselkorn, T., Grover, C., and Wendel, J. F., “PCR-mediated recombination in amplification products derived from polyploid cotton”, Theoretical and Applied Genetics, vol. 104, no. 2-3, pp. 482-489, 2002.
R. C. Cronn, Small, R. L., Haselkorn, T., and Wendel, J. F., “Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes”, American Journal of Botany, vol. 89, no. 4, pp. 707-725, 2002.
2003
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.

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