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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.
D. M. Stelly, Wendel, J. F., and Paterson, A. H., Dispersed Repetitive DNA Has Spread to New Genomes Since Polyploid Formation in Cotton Xin-ping Zhao, Yang Si, Robert E. Hanson, 2 Charles F. Crane, 2 H. James Price, 2, Genome Research, vol. 8, pp. 479-492, 1998.
X. P. Zhao, Si, Y., Hanson, R. E., Crane, C. F., Price, H. J., Stelly, D. M., Wendel, J. F., and Paterson, N. H., Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton (vol 8, pg 479, 1998), GENOME RESEARCH, vol. 8, no. 6, pp. 682-682, 1998.
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.
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.
1994
A. J. Reinisch, Dong, J. - M., Brubaker, C. L., Stelly, D. M., Wendel, J. F., and Paterson, A. H., A detailed RFLP map of cotton, Gossypium hirsutum x Gossypium barbadense: chromosome organization and evolution in a disomic polyploid genome., Genetics, vol. 138, no. 3, pp. 829-847, 1994.
R. Whitkus, Doebley, J., and Wendel, J. F., DNA-based markers in plants, Nuclear DNA markers in systematics and evolution. Kluwer, Amsterdam, pp. 116-141, 1994.
J. F. Wendel, Rowley, R., and Stewart, J. McD., Genetic diversity in and phylogenetic relationships of the Brazilian endemic cotton, Gossypium mustelinum (Malvaceae), Plant Systematics and Evolution, vol. 192, no. 1-2, pp. 49-59, 1994.
M. A. Stanton, J Stewart, M. D., A Pervical, E., and Wendel, J. F., Morphological diversity and relationships in the A-genome cottons, Gossypium arboreum and G. herbaceum, Crop science, vol. 34, no. 2, pp. 519-527, 1994.
R. Whitkus, Doebley, J., and Wendel, J. F., Nuclear DNA markers in systematics and evolution, in DNA-based markers in plants, Springer Netherlands, 1994, pp. 116-141.
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.
1990
J. F. Wendel and Percy, R. G., Allozyme diversity and introgression in the Galapagos Islands endemic Gossypium darwinii and its relationship to continental G. barbadense, Biochemical Systematics and Ecology, vol. 18, no. 7, pp. 517-528, 1990.
R. G. Percy and Wendel, J. F., Allozyme evidence for the origin and diversification of Gossypium barbadense L., Theoretical and Applied Genetics, vol. 79, no. 4, pp. 529-542, 1990.
J. Doebley, Stec, A., Wendel, J. F., and Edwards, M., Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize, Proceedings of the National Academy of Sciences, vol. 87, no. 24, pp. 9888-9892, 1990.
C. R. Parks, Wendel, J. F., Sewell, M. M., and Qui, Y. L., Genetic control of isozyme variation in the genus Liriodendron L.(Magnoliaceae)., Journal of Heredity, vol. 81, no. 4, pp. 317-323, 1990.
C. R. Parks and Wendel, J. F., Molecular divergence between Asian and North American species of Liriodendron (Magnoliaceae) with implications for interpretation of fossil floras, American Journal of Botany, pp. 1243-1256, 1990.
J. F. Wendel and Percival, A. E., Molecular divergence in the Galapagos Islands—Baja California species pair, Gossypium klotzschianum andG. davidsonii (Malvaceae), Plant Systematics and Evolution, vol. 171, no. 1-4, pp. 99-115, 1990.
P. K. Bretting and Wendel, J. F., Utility of Tpi3 and Tpi4 variants in quality control of hybrid popcorn seed production., Maize Genetics Cooperation News Letter, no. 64, pp. 121-122, 1990.

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