James H. Leebens-Mack
Associate Professor
Office: 
Plant Sciences, Rm 4504
Phone Number:  706-583-5573
Fax: 
706-542-1805
Office/Lab:  Plant Sciences, Rm 4501
Phone Number: 
706-583-5572
Education: 

Ph.D Plant Systematics and Evolutionary Biology, University of Texas 1995

Research Projects: 

My research employs genomic, phylogenetic and experimental analyses to investigate the genetic and ecology processes that influence diversification. Specific interests include the molecular genetics of diversification including speciation; the molecular basis of adaptation; the evolution of genome structure; genomic processes influencing gene family evolution; the evolutionary consequences of species interactions; and the coevolution of genes interacting in regulatory and developmental pathways.

Phylogenomics employs genome scale sequence data to resolve organismal relationships and investigate gene family evolution within the context of organismal relationships. Our lab uses phylogenomic approaches to explore the ecological, genetic and developmental processes that contribute to phenotypic diversification and speciation. We focus most of our attention on the evolution of reproductive characters in flowering plants. Much of our research involves phylogenetically based analyses, and we are working with collaborators to develop new empirical and analytical tools to extend the use of phylogenetic methods in comparative genomics. These tools form the foundation for comparative studies aimed at testing the degree to which characterizations of gene function and regulatory networks in model systems are applicable to other plant species.

Grant Support: 

National Science Foundation (Systematic Biology and Biodiversity Inventories) “Doctoral Dissertation Research: The genomic basis of dioecy in Asparagus (Asparagaceae)” (PI with student Alex Harkess),

 

National Science Foundation (IOS Plant Genome Research Program).  “ABR-PG: Developing Flowering Dogwood as a Focal Genomic Resource for Woody Ornamentals” (PI), CJ Tsai and Magdy Alabady (UGA), Jenny Xiang (North Carolina State University) and Phil Wadl (University of Tennessee), Co-PIs.

 

National Science Foundation (DEB Dimensions of Biodiversity) “Dimensions: Collaborative Proposal: Molecular, ecological and evolutionary dynamics of carbon fixation and diversification in Agavoideae (Asparagaceae) and Oncidiinae (Orchidaceae)” (PI) Erin Dolan (UGA), Katia Silvera UC Riverside and Vic Albert (University of Buffalo), Co-PIs. 

 

National Science Foundation (IOS), 2014-2017, “RUI: Collaborative: unPAK: undergraduates Phenotyping Arabidopsis Knockouts: A distributed genomic approach to examine evolutionarily important traits” (Co-PI), Matthew Rutter (PI), Courtney Murren and Allan Strand (College of Charleston), Hilary Callahan (Barnard College), Michael Wolyniak (Hampden-Sydney College), and Erin Dolan and Jennifer Jo Thompson (UGA) 

 

National Science Foundation (Plant Genome Research Program), 2009-2015, “The Amborella Genome Project” (Co-PI with Claude dePamphilis [PI] and Hong Ma (Penn State), Doug Soltis, Pam Soltis, and Brad Barbazuk (Florida), Sue Wessler (UC Riverside) and Vic Albert (Buffalo)) 

Of Note: 

Faculty Director, Georgia Genomics Facility (http://dna.uga.edu/)

Editorial Board, BMC Plant Biology, Plant Systematics and Evolution. 

Analysis team leader, OneKP project - http://www.onekp.com/ 2009-Present

Velux Visiting Professor, University of Copenhagen (Fall, 2015)

Recent Publications: 

Augustin, M.M., D. Ruzicka, A.K. Shukla, J.M. Augustin, M.R. McKain, CM. Starks, M. O’Neil-Johnson, P.P. Edger, J.C. Pires, J.H. Leebens-Mack, and T.M. Kutchan, 2015. Accelerating biochemical pathway elucidation in non-model systems : Formation of the antineoplastic cyclopamine in Veratrum californicum. The Plant Journal.  In Press DOI: 10.1111/tpj.12871

 

Harkess, A.,  F. Mercati, H-Y. Shan, F.  Sunseri, A. Falavigna and J. Leebens-Mack.   2015.  Sex-biased gene expression in dioecious garden asparagus (Asparagus officinalis L.) New Phytologist. Early Access DOI: 10.1111/nph.13389

 

Mercati, F., P. Riccardi, A. Harkess, T. Sala, M. R. Abenavoli, J. H. Leebens-Mack, A. Falavigna, F. Sunseri.  2015.  SNP-based parentage analysis and population structure in garden asparagus, a worldwide genetic stock classification.  Molecular Breeding, 35:59.  doi: 10.1007/s11032-015-0217-5

 

Cannon, S.  M. R. McKain, A. Harkess, M. Deyholos, M. Chase, C. N. 

Stewart, Y. Peng, B. Joyce, P. Soltis, D. Soltis, M. N. Nelson, N. Miles, T. Kutchan,  X. Tan, C. Chen,  E. Carpenter, Y. Zhang, G. Ka-Shu Wong, J. J. Doyle and J. H. Leebens-Mack. 2015.  Independent genome duplication events and the evolution of nodulation in the legumes.  Molecular Biology and Evolution, 32 (1): 193-210 doi:10.1093/molbev/msu296

 

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

 

Rentsch, J.D., and J. Leebens-Mack. 2014.  Yucca aloifolia (Agavoidea, Asparabaceae) opts out of an obligate pollination mutualism? Evidence for diurnal, non-moth pollination of a Yucca species. American Journal of Botany. 101(12): 2062-2067.  doi: 10.3732/ajb.1400351

 

Eserman L.A., G. P. Tiley, R. L. Jarret, J. H. Leebens-Mack, R. E. Miller.  2014.  Phylogenetics and diversification of morning glories based on whole plastome sequences.  American Journal of Botany 101(1):92-103. doi: 10.3732/ajb.1300207

Barrett, C.F., C. D. Specht, J. Leebens-Mack, D. W. Stevenson, W. B. Zomlefer, and J. I. Davis.  2014.  Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales Griseb.)? Annals of Botany 113(1):119-33. doi: 10.1093/aob/mct264

 

The Amborella Genome Project (J. J. Acosta, V. A. Albert, N. S. Altman, J. S. S. Ammiraju, S. Arikit, M. J. Axtell, S. Ayyampalayam, W. B. Barbazuk, R. A. Bruenn, J. M. Burnette, L. Carretero-Paulet, S. Chamala, A. S. Chanderbali, T-H. Chang, F. Chen, J-Q. Chen, V. Chiang, A. de Kochko, C. W. dePamphilis, J. P. Der, R. Determann, J. C. Estill, N. P. Farrell, B. Fogliani, C. Guo, J. Harholt, A. Harkess, L. R. Herrera-Estrella, E. Ibarra-Laclette, Y. Jiao, C. Job, D. Job, S. Kim, M. Kirst, H. Kong, T. Lan, J. H. Leebens-Mack, G. Li, L. Li, J. Liu, K. Liu, E. Lyons, H. Ma, W. Mei, B. C. Meyers, J. D. Palmer, E. De Paoli, J. Park, S. P. Pissis, V. Poncet, X. Qi, L. Rajjou, P. Ralph, S. Rounsley, D. Sankoff, V. Sarramegna, S. C. Schuster, R. Sederoff, S. Shahid, D. E. Soltis, P. S. Soltis, Y-H. Sun, J. Talag, H. Tang, L. Tomsho, P. Ulvskov, M. Villegente, E. Wafula, B. Walts, S. Wanke, S. R. Wessler, R. A. Wing, J-Y. Xue, T-F. Yeh, X. Yu, J. Zhai, X. Zhang, C. Zheng).  2013.  The Amborella Genome and the Evolution of Flowering Plants.  Science 342(6165):1241089. doi: 10.1126/science.1241089

 

Chamala S, A.S. Chanderbali, J.P. Der, T. Lan, B. Walts, V.A. Albert, C.W. dePamphilis, J. Leebens-Mack, S. Rounsley, S.C. Schuster, R.A. Wing, N. Xiao, R. Moore, P.S. Soltis, D.E. Soltis, W.B. Barbazuk.  2013. Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella.  Science 342(6165):1516-7. doi: 10.1126/science.1241130

 

Vitte, C., M. Estep, J. Leebens-Mack and J. L. Bennetzen. 2013. Young, intact and nested retrotransposons in the onion and asparagus genomes.  Annals of Botany 112(5):881-9 10.1093/aob/mct155

 

Davis,J.I., J.R. McNeal, C.F. Barrett, M.W. Chase, J.I . Cohen, M.R. Duvall, T.J. Givnish, S.W. Graham, G. Petersen, J.C.  Pires, O. Seberg, D.W. Stevenson, and J. Leebens-Mack.  2012.  Contrasting Patterns of Support among Plastid Genes and Genomes for Major Clades of the Monocotyledons. In Early Events in Monocot Evolution, P. Wilkin and S.J. Mayo, eds. Cambridge University Press. pp. 315-349

 

Rentsch JD, Leebens-Mack J. 2012. Homoploid hybrid origin of Yucca gloriosa: intersectional hybrid speciation in Yucca (Agavoideae, Asparagaceae). Ecol Evol. 2(9):2213-22. doi: 10.1002/ece3.328.

 

D’Hont, A., F. Denoeud, J-M. Aury, F-C. Baurens, F. Carreel, O. Garsmeur, B. Noel, S. Bocs, G. Droc,  M. Rouard, C. Da Silva, K. Jabbari,, C. Cardi, J. Poulain, M. Souquet, K. Labadie, C. Jourda, J. Lengelle, M. Rodier-Goud, A. Alberti, M. Bernard,  M. Correa,  S. Ayyampalayam, M. R. Mckain, J. Leebens-Mack, D. Burgess, M. Freeling, D. Mbéguié, A. Mbéguié, R. Habas, R. Rivallan,  T. Wicker, O. Panaud, J. Barbosa, E. Hribova, P. Heslop-Harrison, M. Chabannes, P. Francois, C. Poiron, A. Kilian, D. Burthia, C. Jenny, F. Bakry, S. Brown, V. Guignon, G. Kema, M. Dita, C. Waalwijk, S. Joseph, A. Dievart, O. Jaillon,, J. Leclercq, X. Argout, E. Lyons, A. Almeida, M. Jeridi, J. Dolezel, N. Roux, A-M Risterucci, J. Weissenbach,, M. Ruiz, J-C. Glaszmann, F. Quétier, N. Yahiaoui, P. Wincker. 2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213-7.  doi:10.1038/nature11241

 

McKain, M.R., N. Wickett, Y. Zhang, S. Ayyampalayam, W. R. McCombie, M. W. Chase, J. C.Pires, C. W. dePamphilis and J. Leebens-Mack 2012. Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).  American Journal of Botany 99:397-406, doi:10.3732/ajb.1100537

 

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

 

Althoff D.M., K.A. Segraves, C.I. Smith, J. Leebens-Mack, O. Pellmyr. 2012. Geographic isolation trumps coevolution as a driver of yucca and yucca moth diversification. Mol Phylogenet Evol. 62(3):898-906. http://dx.doi.org/10.1016/j.ympev.2011.11.024

 

Zuccolo, A. J.E. Bowers, J. C. Estill, Z. Xiong, M. Luo,, A. Sebastian, J. L. Goicoechea, K.Collura, Y. Yu, Y. Jiao, J. Duarte, H. Tang, S. Ayyampalayam, S. Rounsley, D. Kudrna, A. H. Paterson,, J. C. Pires, D. E. Soltis, S. Chamala, B. Barbazuk, P.S. Soltis, V. A. Albert, H. Ma, D. Mandoli, J. Banks, J. E. Carlson, J. Tomkins, C. W. dePamphilis, R. A. Wing. J. Leebens-Mack. 2011. A Physical Map for the Amborella Genome Sheds Light on the Evolution of Angiosperm Genome Structure. Genome Biology 12(5):R48.  doi:10.1186/gb-2011-12-5-r48

 

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

 

Givnish, T.J., M.A. Sevillano, J.R. McNeal, M. R. McKain, P.R. Steele, C.W. dePamphilis, S. W. Graham, J. C. Pires, D. W. Stevenson, W. B. Zomlefer, B. G. Briggs, M. R. Duvall, M. J. Moore, D. E. Soltis, P. S. Soltis, K. Thiele, and J. H. Leebens-Mack. 2010. Assembling the tree of the monocotyledons: Plastome sequence phylogeny and evolution of Poales. Annals of the Missouri Botanical Gardens 97(4):584-616.  doi: http://dx.doi.org/10.3417/2010023​ 

BioOne Online Journals - Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales

Thomas J. Givnish, Mercedes Ames, Joel R. McNeal, Michael R. McKain, P. Roxanne Steele, Claude W. dePamphilis, Sean W. Graham, J. Chris Pires, Dennis W. Stevenson, Wendy B. Zomlefer, Barbara G. Briggs, Melvin R. Duvall, Michael J. Moore, J. Michael Heaney, Douglas E. Soltis, Pamela S. Soltis, Kevin Thiele, and James H. Leebens-Mack (2010) Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales. Annals of the Missouri Botanical Garden: Vol. 97, No. 4, pp. 584-616. doi: http://dx.doi.org/10.3417/2010023

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