In our lab we work on the fascinating connections between molecular evolutionary processes and genotypic/phenotypic diversity.  Our many research projects explore various aspects of  molecular and genome evolution, phylogenetics, and phenotypic evolution of higher plants.  We use a diverse set of technologies and approaches to explore the manner in which genomes change over evolutionary time, as well as the relationship between these events and morphological change. We have a particular interest in the mysterious and common phenomenon of genome doubling, or polyploidy, with a special focus on the cotton genus (Gossypium).   Read more about


Polyploid speciation is exceptionally common in plants, often operating sympatrically to saltationally generate new lineages.

Comparative evolutionary genomics and domestication genomics are among the most active areas of research in the lab. Please check back here often for updates on our massive genomic resequencing effort, our comparative molecular evolutionary analyses, and our work on domestication genomics.

Somewhat remarkably, given its importance in human commence, new species of cotton continue to be discovered.  Our lab is among the few worldwide that maintains an active interest in fundamental plant exploration and discovery in the cotton genus.

One of the important realizations to emerge from numerous studies of polyploid plants is that polyploid creates massive alterations in gene expression. 

Recent Publications

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

Wang, K., J. F. Wendel, and J. Hua. 2018. Designations for individual genomes and chromosomes in Gossypium. Journal of Cotton Research 1:3-7,

Hu, G. and J. F. Wendel. 2018. Cis-trans controls and regulatory novelty accompanying allopolyploidization. New Phytologist

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

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). Read more about