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

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 (Major Research Instrumentation Program), Pending, “MRI: Acquisition of a CPU/GPU high performance computing system for research and training at the interface of the Biological and Physical Sciences” (PI with coPIs, Jonathan Arnold, Jessica Kissinger, Heinz-Bernd Schuttler and Thiab Taha) - $ 1,332,637
  • National Science Foundation (Systematic Biology and Biodiversity Inventories) “Doctoral Dissertation Research: Effects Of Paleopolploidy On Genome Composition And Evolution In Agavaceae” (PI with Student, Michael McKain).
  • National Science Foundation (Plant Genome Research Program), 2009-2013, “TheAmborella 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)) - $809,476 to Leebens-Mack.
  • National Science Foundation (Cyberinfrastructure Program, subcontract from University of Arizona, iPlant Collaborative) 2009-2011 - $ 131,861
  • National Institutes of Health, 2009-2011, “Evolution of Pathways to Pharmaceuticals in the Poppy Family”.
  • National Science Foundation, 2009-2010, “Collaborative Research: Comparative Investigation of Incipient Sex Chromosome Evolution in the genus Asparagus”.
  • Roche, 2009, “Plant Reproductive Genomics at the Plant and Animal Genome Conference”.
  • National Science Foundation, 2008-2013, “Collaborative Research: From Acorus to Zingiber: Assembling the Phylogeny of the Monocots”.
  • National Science Foundation, 2007-2012, “Collaborative Research: Large-scale Simultaneous Multiple Alignment and Phylogeny Estimation”.
  • National Science Foundation (Plant Genome Comparative Sequencing Program), 2007-2010, “The Ancestral Angiosperm Genome Project”.
Of Note: 
  • Working Group Leader: Plant Evolutionary Genomics Working Group, National Evolutionary Synthesis Center (NESCent), 2006-2009.
  • Workshop organizer: Plant Reproductive Genomics session at the Plant and Animal Genome Conference, January 2003, 2005 – 2009.
  • Advisory Panel Member: Genomic Standards Consortium; 1000 Plant Transcriptomes Project.
  • Participant: iPlant Collaborative Tree of Life Working Group Meeting (November 2008); iPlant Tree of Life (iPToL) Tree Reconciliation Working Group.
  • Plant Biology teaching assistantship planning committee (2006-present).
  • Laboratory for Genomics and Bioinformatics Advisory Committee (2006-present).
  • Taskforce on Diversity and Inclusion (2007-present).
  • Laboratory for Genomics and Bioinformatics Faculty Advisor for Bioinformatics (2006 present).
  • Chair, Institute of Bioinformatics Computational Resources Committee (2009-present).
  • UGA Research Computing Advisory Committee (2009-present).
Selected Publications: 
  • 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 Published on-line ahead of print 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 Published on-line ahead of print 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). 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
  • Panahiazar M, A Ranabahu, R.Vos, A Stoltzfus, AP Sheth, and J. Leebens-Mack. 2013. 
Advancing the Reusability of Resources in Phyloinformatics with an Ontology-Driven Semantic Web Approach. BMC Medical Genomics 6(Suppl 3):S5 doi:10.1186/1755- 8794-6-S3-S5
  • 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
  • Khera, P., H. D. Upadhyaya, M. K. Pandey, M. Roorkiwal, M. Sriswathi, P. Janila, Y, Guo, M, R. McKain, E. D. Nagy, S. J. Knapp, J. Leebens-Mack, J. A. Conner, P. Ozias- Akins, and R. K. Varshney. 2013. Single Nucleotide Polymorphism–based Genetic Diversity in the Reference Set of Peanut (Arachis spp.) by Developing and Applying Cost-Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays. The Plant Genome 6: 1-11 doi: 10.3835/plantgenome2013.06.0019
  • Mercati, F., P. Riccardi, J. Leebens-Mack, M. R. Abenavoli, A. Falavigna, F. Sunseri. 2013. Single nucleotide polymorphism isolated from a novel EST dataset in garden asparagus (Asparagus officinalis L.). Plant Science 203-204:115–123.
  • Bliss BJ, Wanke S, Barakat A, Ayyampalayam S, Wickett N, Wall PK, Jiao Y, Landherr 
L, Ralph PE, Hu Y, Neinhuis C, Leebens-Mack J, Arumuganathan K, Clifton SW, Maximova SN, Ma H, Depamphilis CW. 2013. Characterization of the basal angiosperm Aristolochia fimbriata: a potential experimental system for genetic studies. BMC Plant Biol. 13(1):13.
  • 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
  • Barrett, CF, JI Davis, J Leebens‐ Mack, JG Conran, DW Stevenson. 2012. Plastid genomes and deep relationships among the commelinid monocot angiosperms. Cladistics 29 (1): 65–87.
  • Panahiazar M, A Ranabahu, V Taslimi, H Yalamanchili, A Stoltzfus, J Leebens-Mack, AP Sheth. 2012. PhylOnt: A domain-specific ontology for phylogeny analysis. BIBM/IEEE Conference Proceedings: 1-6.
  • Riccardi, P, J Leebens-Mack, R Cifarelli, A Falavigna, F Sunseri. 2012. EST Libraries Development in Asparagus officinalis for SNPs Discovery. Acta Horticulturae 950:127- 132.
  • 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.
  • Johnson MT, Carpenter EJ, Tian Z, Bruskiewich R, Burris JN, Carrigan CT, Chase MW, Clarke ND, Covshoff S, Depamphilis CW, Edger PP, Goh F, Graham S, Greiner S, Hibberd JM, Jordon-Thaden I, Kutchan TM, Leebens-Mack J, Melkonian M, Miles N, Myburg H, Patterson J, Pires JC, Ralph P, Rolf M, Sage RF, Soltis D, Soltis P, Stevenson D, Stewart CN Jr, Surek B, Thomsen CJ, Villarreal JC, Wu X, Zhang Y, Deyholos MK, Wong GK. 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 7(11):e50226.
  • Bagal UR, Leebens-Mack JH, Lorenz WW, Dean JF. 2012. The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage. BMC Genomics 13 Suppl 3:S1.
  • 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.
  • 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
  • Steele, P. R., K. L. Hertweck, D. Mayfield, M. R. McKain, J. Leebens-Mack, and J. C. Pires. 2012. Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae. American Journal of Botany 99:330-348, doi:10.3732/ajb.1100491
  • 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. [Epub ahead of print], 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 Biology12: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 473:97-100
  • Liang, H., S. Ayyampalayam, N. Wickett, A. Barakat,Y. Xu, L. Landherr, P. E. Ralph, Y. Jiao, Tao Xu, S. E. Schlarbaum, H. Ma, J. H. Leebens-Mack, C.W. dePamphilis. 2011. Generation of a large-scale genomic resource for functional and comparative genomics in Liriodendron tulipifera L. Tree Genetics & Genomes advance access
  • 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.
  • Yellina, Y.L., S. Lange, S. Orashakova, J.H. Leebens-Mack, and A. Becker. 2010. Functional analysis of floral homeotic C function genes in the basal eudicot California poppy. Evodevo 1:13
  • Zahn, L.M., X. Ma, N. S. Altman, Q. Zhang, P K. Wall, D. Tian, C. J Gibas, R. Gharaibeh, J. H Leebens-Mack, C. W dePamphilis, H. Ma. 2010. Comparative transcriptomics among floral organs of the basal eudicot Eschscholzia californica as reference for floral evolutionary developmental studies. Genome Biology 11:R101
  • Duarte. J.M., P. K. Wall, P. P. Edger, L.L. Landherr, H. Ma, J.C. Pires, J. Leebens-Mack and C.W. dePamphilis. 2010. Identification of shared single copy nuclear genes inArabidopsisPopulusVitis and Oryza and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology 10:61
  • Chanderbali A.S., M.J. Yoo, L.M. Zahn, S.F. Brockington, P.K. Wall, M.A. Gitzendanner, V.A. Albert, J. H. Leebens-Mack, A.S. Altman, H. Ma, C.W. dePamphilis, D.E. Soltis, P.S. Soltis. 2010. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proc Natl Acad Sci U S A 107:22570-22575
  • Sankoff, D., C. Zheng, P.K. Wall, C. dePamphilis, J. Leebens-Mack, and V.A. Albert. 2009. Towards improved reconstruction of ancestral gene order in angiosperm phylogeny. J Comput Biol. 16(10):1353-67
  • McNeal, J.R., J.H. Leebens-Mack, J.V. Kuehl, J.L. Boore, and C.W. dePamphilis. 2009. Parallel loss of plastid introns and their maturase in the genus Cuscuta. PLoS ONE. 4(6):e5982.
  • Shan, H., L. Zahn, S. Guindon, P. K. Wall, H. Kong, H. Ma, C.W. dePamphilis and J. H. Leebens-Mack. 2009. Evolution of plant MADS box transcription factors: evidence for relaxed selection in association with early angiosperm diversification. Molecular Biology and Evolution 26(10):2229-44.
  • Wall, P.K., J. Leebens-Mack, A. Chanderbali, A. Barakat, H. Liang, L. Landherr, L. P. Tomsho, Y. Hu, H. Ma, J.E. Carlson, S. Schuster, D. E. Soltis, P.S. Soltis, N. Altman, and C.W. dePamphilis. 2009. Comparison of next generation sequencing technologies for de novo transcriptome characterization. BMC Genomics. 10:347.
  • Wang, L-S., J. Leebens-Mack, P.K. Wall, K. Beckmann, C.W. dePamphilis, and T. Warnow. 2009. The impact of protein multiple sequence alignment on phylogenetic estimation. Transactions on Computational Biology and Bioinformatics In Press.
  • Chanderbali, A.S., V.A. Albert, J. Leebens-Mack, N. S. Altman, D.E. Soltis, and P. S. Soltis. 2009. Transcriptional signatures of ancient floral developmental genetics in avocado (Persea americana; Lauraceae). Proceedings of the National Academy of Sciences. 106(22):8929-34
  • Soltis, D.E., V.A. Albert, J.H. Leebens-Mack, C.D. Bell, A. Paterson, C. Zheng, D. Sankoff, and P.S. Soltis. 2009. Polyploidy and angiosperm diversification. Amer. J. Bot. 96:336-348.
  • Baucom, R.S., J.C. Estill, J.H. Leebens-Mack, J.L. Bennetzen. 2009. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Research 19(2):243-254.
  • Zheng, C., P.K. Wall, J. Leebens-Mack, C.W. dePamphilis, V.A. Albert, and D. Sankoff. 2009. Gene loss under neighbourhood selection following whole genome duplication and the reconstruction of the ancestral Populus genome. Journal of Bioinformatics and Computational Biology. 7(3):499-520.
  • Zheng, C., P.K. Wall, J. Leebens-Mack, C.W. dePamphilis, V.A. Albert, and D. Sankoff. 2009. The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral Populus diploid. In: Markstein P, Xu Y (eds.) Computational Systems Bioinformatics: Proceedings of the CSB 2008 Conference (World Scientific Publishing Co.).