Publications

The Amborella Genome and the Evolution of Flowering Plants (2013)

Amborella Genome Project.  2013.  The Amborella Genome and the Evolution of Flowering Plants.   Science 342: DOI: 10.1126/science.1241089

Monocot Systematics and Evolution

(See Google ScholarResearchGate or PubMed for expanded publiction list)

Selected Publications

Phylogenomic Investigations of Green Plant (Viridiplantae) Diversification

A phylotranscriptomic analysis of the origin and early diversification of land plants (2014)

Wickett, N.J., S. Mirarab, N. Nguyen, T. Warnow, E. Carpenter, N. Matasci, S. Ayyampalayam, M. Barker, G. J. Burleigh, M. A. Gitzendanner, B. Ruhfel, E. Wafula, J.P. Der, S. W. Graham, S. Mathews, M. Melkonian, D. E. Soltis, P. S. Soltis, C. Rothfels, L. Pokorny, J. Shaw, L. DeGironimo, D. Stevenson, B. Surek, J.C. Villarreal, B. Roure, H. Philippe, C. W. dePamphilis, T. Chen, M. Deyholos, J. Wang, Y. Zhang, Z. Tian, Z. Yan, X. Wu, X. Sun, G. K-S. Wong, and J. Leebens-Mack.  2014.  A phylotranscriptomic analysis of the origin and early diversification of land plants.  Proceedings of the National Academy of Sciences, U.S.A. 111 (45):E4859–E4868. doi: 10.1073/pnas.1323926111

Ancestral polyploidy in seed plants and angiosperms (2011)

Jiao, Y., Wickett, N.J., Ayyampalayam, S., Chanderbali, A.S., Landherr, L., Ralph, P.E., Tomsho, L.P., Hu, Y., Liang, H., Soltis, P.S., Soltis, D.E., Clifton, S.W., Schlarbaum, S.E., Schuster, S.C., Leebens-Mack, J., Depamphilis, C.W. 2011. Ancestral polyploidy in seed plants and angiosperms. Nature. 473(7345), 97-100. doi:10.1038/nature09916

Origin and Early Diversification of Flowering Plants

The Amborella Genome and the Evolution of Flowering Plants (2013)

Amborella Genome Project.  2013.  The Amborella Genome and the Evolution of Flowering Plants.   Science 342: DOI: 10.1126/science.1241089

A genome triplication associated with early diversification of the core eudicots (2012)

Jiao, Y., J. Leebens-Mack, S, Ayyampalayam, J. E. Bowers, M. R McKain, J. McNeal, M. Rolf, D. R Ruzicka, E. Wafula, N. J Wickett, X. Wu, Y. Zhang, J. Wang, Y. Zhang, E. Carpenter, M. K Deyholos, T. M Kutchan, A. S. Chanderbali, P. S. Soltis, D. W. Stevenson, R. McCombie, J. C. Pires, G. Ka-Shu Wong, D. E. Soltis and C. W. dePamphilis. 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biology 13(1):R3. doi:10.1186/gb-2012-13-1-r3.

Monocot Systematics and Evolution

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales

McKain, M.R., Tang, J.R., Ayyampalayam, S., Davis, J.I., dePamphilis, C.W., Givnish, T.J., Pires, J.C., Stevenson, D.W., Leebens-Mack, J.H. 2016.  A phylogenomic assessment of ancient polyploidy and genome evolution across the poales.  Genome Biology and Evolution. 8 (4): 1150–1164.  https://doi.org/10.1093/gbe/evw060

Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots

Givnish, T.J., Zuluaga, A., Spalink, D., Soto Gomez, M,, Lam, V.K.Y., Saarela, J.M., Sass, C., Iles, W.J.D., de Sousa, D.J.L., Leebens-Mack, J., Pires, J.C., Zomlefer, W.B., Gandolfo, M.A., Davis, J.I., Stevenson, D.W., dePamphilis, C., Specht, C.D., Graham S.W., Barrett, C.F., Ané, C. 2018.  Monocot plastid phylogenomics, timeline, net rates of species diversification, the power of multi-gene analyses, and a functional model for the origin of monocots.  American Journal of Botany, Epub ahead of print https://doi.org/10.1002/ajb2.1178

Evolution of Dioecy and Sex Determination in Asparagus

The asparagus genome sheds light on the origin and evolution of a young Y chromosome 

Harkess, A., Zhou, J., Xu, C., Bowers, JE., Hulst, R., Ayyampalayam, S., Mercati, F., Riccardi, P., McKain, MR., Kakrana, A., Tang, H., Ray, J., Groenendijk J., Arikit, S., Mathioni, SM., Nakano, M., Shan, H., Telgmann-Rauber, A., Kanno, A., Yue, Z., Chen, H., Li, Y., Chen, Y., Xu, X., Zhang, Y., Luo, S., Chen, H., Gao, J., Mao, Z., Pires, JC., Luo, M., Kudrna, D., Wing, RA., Meyers, BC., Yi, K., Kong, H., Lavrijsen, P., Sunseri, F., Falavigna, A., Ye, Y., Leebens-Mack, JH., Chen, G.  2017. The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nature Communications. 8(1):1279. doi:10.1038/s41467-017-01064-8

Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis) 

Harkess, A., Mercati, F., Shan, H.-Y., Sunseri, F., Falavigna, A., Leebens-Mack, J. 2015. Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis). New Phytologist. 207, 883–892. 

Plant-Pollinator Coevolution

Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae) 

Mckain, M.R., Mcneal, J.R., Kellar, P.R., Eguiarte, L.E., Pires, J.C., Leebens-Mack, J. 2016. Timing of rapid diversification and convergent origins of active pollination within Agavoideae (Asparagaceae). American Journal of Botany. 103, 1717–1729. https://doi.org/10.3732/ajb.1600198

Yucca aloifolia (Asparagaceae) opts out of an obligate pollination mutualism

Rentsch, J.D., and J. Leebens-Mack. 2014.  Yucca aloifolia (Asparagaceae) opts out of an obligate pollination mutualism. American Journal of Botany. 101(12):2062-2067. https://doi.org/10.3732/ajb.1400351

Crassulecean Acid Metabolism and its Impact on Biodiversity

Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism 

Heyduk, K., Ray, J.N., Ayyampalayam, S., Leebens-Mack, J. 2018. Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism. American Journal of Botany. 105, 587–601. https://doi.org/10.1002/ajb2.1017

Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (2016)

Heyduk, K., Mckain, M.R., Lalani, F., Leebens-Mack, J. 2016. Evolution of a CAM anatomy predates the origins of Crassulacean acid metabolism in the Agavoideae (Asparagaceae). Molecular Phylogenetics and Evolution. 105, 102–113. https://doi.org/10.1016/j.ympev.2016.08.018

The pineapple genome and the evolution of CAM photosynthesis

Ming, R., Vanburen, R., Wai, C.M., Tang, H., Schatz, M.C., Bowers, J.E., Lyons, E., Wang, M.-L., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H., Yim, W.C., Priest, H.D., Zheng, C., Woodhouse, M., Edger, P.P., Guyot, R., Guo, H.-B., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F.J., Harkess, A., Mckain, M.R., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L.-Y., Shirley, N., Lin, Y.-R., Liu, L.-Y., Hernandez, A.G., Wright, C.L., Bulone, V., Tuskan, G.A., Heath, K., Zee, F., Moore, P.H., Sunkar, R., Leebens-Mack, J.H., Mockler, T., Bennetzen, J.L., Freeling, M., Sankoff, D., Paterson, A.H., Zhu, X., Yang, X., Smith, J.A.C., Cushman, J.C., Paull, R.E., Yu, Q. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47, 1435–1442. doi: 10.1038/ng.3435