Michael McKain

Michael  McKain

Assistant Professor | Curator of the University of Alabama Herbarium


  • Ph.D., Plant Biology, University of Georgia, 2012
  • Postdoctoral research: University of Missouri-St. Louis and the Donald Danforth Plant Science Center

Research Interests

  • Plant systematics with emphasis on monocots, especially grasses and agaves
  • Phylogenomics
  • Comparative genomics
  • Polyploidy
  • Software development
  • Herbarium genomics


Teisher, J. K., M. R. McKain, B. A. Schaal, and E. A. Kellogg. 2017. Polyphyly of Arundinoideae (Poaceae) and Evolution of the Twisted Geniculate Lemma Awn. Annals of Botany.  In press.

Harrington, A. W., M. R. McKain, D. Michalski, K. M. Bauer, J. M. Daugherty, and M. Steiniger.  2017. Drosophila melanogaster retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations. BMC Genomics 18(1): 304.

McKain, M. R., J. R. McNeal, P. R. Kellar, L. E. Eguiarte, J. C. Pires, and J. H. Leebens-Mack. 2016. Timing of rapid diversification and parallel origins of active pollination within Agavoideae (Asparagaceae). AmE.an Journal of Botany 103(10): 1-13.

Studer, A. J., J.  C. Schnable, A. R. Kolbe, M. R. McKain, Y.  Shao, A. B. Cousins, E.  A. Kellogg, and T.  P. Brutnell. 2016. The draft genome of Dichanthelium oligosanthes: A C3 panicoid grass species. Genome Biology 17: 223.

McKain, M. R.*, R. H. Hartsock*, M.  M. Wohl, and E.  A. Kellogg. 201X. Verdant: automated annotation, alignment, and phylogenetic anlaysis of whole chloroplast genomes. Bioinformatics. First published online September 14, 2016. doi: 10.1093/bioinformatics/btw583. *Co-first author

Hackenberg, D.*, M. R. McKain*, S. Lee, T. McCann, S. Schreier,  S. Roy Choudhury, A. Harkess, J. C. Pires, G. W.g, J.  Jez, E.  A. Kellogg, and S. Pandey. 2016. Gα:RGS protein pairs maintain functional compatibility and conserved interaction interfaces throughout evolution despite frequent loss of RGS proteins in plants. New Phytologist. First published online September 16, 2016. doi: 10.1111/nph.14180. *Co-first author 

Heyduk, K., M. R. McKain, F. Lalani, and J. H. Leebens-Mack. 2016. Evolution of CAM anatomy predates the origin of Crassulacean acid metabolism in the Agavoideae (Asparagaceae). Molecular Phylogenetics and Evolution 105: 102-113.

Harkess, A., F. Mercati, L. Abbate, M. R. McKain, J. C. Pires, T. Sala, F. Sunseri, A. Falavigna, and J. Leebens-Mack. 2016. Retrotransposon proliferation coincident with the evolution of dioecy in Asparagus. G3: Genes, Genomes, and Genetics 6(9): 2679-2685.

Welker, C. A. D., Tatiana T. Souza-Chies, H. M. Longhi-Wagner, M. C. Peichoto, M. R. McKain, E.  A. Kellogg. 2016. Multilocus phylogeny and phylogenomics of Eriochrysis P. Beauv. (Poaceae-Andropogoneae): taxonomic implications and evidence of interspecific hybridization. Molecular Phylogenetics and Evolution 99: 155-167. 

Vallejo-Marin, M., A. M. Cooley, M. Y. Lee, M. R. McKain, and J. R. Puzey. 2016. Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor. AmE.an Journal of Botany 103(7): 1272-1288.

McKain, M. R., H. Tang, J. R. McNeal, S. Ayyampalayam, J. I. Davis, Claude W. dePamphilis, T.  J. Givnish, J. C. Pires, D. Wm. Stevenson, and J. H. Leebens-Mack. 2016. A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales. Genome Biology and Evolution 8(4): 1150-1164.

Schröder, S., S. Mamidi, R. Lee, M. R. McKain, P. E. McClean, and J. M. Osorno. 2015. Optimization of Genotyping by Sequencing (GBS) Data in Common Bean (Phaseolus vulgaris L.).  Molecular Breeding 36(1): 1-9.

Ming, R., R. Van Buren, C. M. Wai, H. Tang, M. Schatz, J. E. Bowers, E. Lyons, M-L. Wang, N. Chen, X. Yang, E. Biggers, J. Zhang, L. Huang, L. Zhang, W. Miao, J. Zhang, Z. Ye, C. Miao, H. D. Priest, W. C. Yim, P. P. Edger, C. Zheng, M. Woodhouse, H. Wang, G. Zheng, R. Guyot, X. Min, Y. Zhang, R. Singh, H. Lee, J.  Gurtowski, F. Sedlazeck, H. Guo, H. Guo, A. Harkess, M. R. McKain, et al. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics 47(12): 1435-1442.

Frank, M. H., M.  B. Edwards, E. R. Schultz, M. R. McKain, Z. Fei, I. Sørensen, J. K. C. Rose, and M. J. Scanlon. 2015. Dissecting the molecular signatures of apical cell-type shoot meristems from two ancient land plant lineages. New Phytologist 207(3): 893-904.

Augustin, M. M., D. Ruzicka, Ashutosh K. Shukla , J, M. Augustin, M. R.  McKain, C. M. Starks, M. O’Neil-Johnson, M. D. Barrett, A. Smithson, G. Ka-Shu Wong, M. K. Deyholos, P. P. Edger, J. C. Pires, J. H. Leebens-Mack, D. A. Mann, and T. M. Kutchan. 2015.  Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells. The Plant Journal 82(6): 991-1003.

Welker, C. A. D., T. T. Souza-Chies, H. M. Longhi-Wagner, M. Carolina Peichoto, M. R. McKain, and E.  A. Kellogg. 2015. Phylogenetic analysis of Saccharum s. l. (Poaceae—Andropogoneae), with emphasis on the circumscription of the South AmE.an Species.  AmE.an Journal of Botany 102(2): 248-263.

Cannon, S. B.*, M. R. McKain*, A. E. Harkess*,  N. Nelson, S. Dash, M. K. Deyholos, Y. Peng, B. Joyce, C. N. Steward Jr., M. Rolf, T. Kutchan, X. Tan, C. Chen, Y. Zhang, E. Carpenter, G. Ka-Shu W.g, J. J. Doyle, J. Leebens-Mack. 2015. Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes. Molecular Biology and Evolution 32(1): 193-210. *Co-first author

Estep, M.*, M. R. McKain*, D. Vela Diaz*, J, Zhong*, J. G. Hodge, T. R. Hodkinson, D. J. Layton, S. Malcomber, R/ Pasquet, and E.  A. Kellogg. 2014. Allopolyploidy, diversification, and the Miocene grass expansion. PNAS 111(42): 15149-15154.  *Co-first author

Zomlefer, W. B., M. R. McKain, J. Rentsch. 2014. Documentation of the chromosome number for Zigadenus glaberrimus (Liliales: Melanthiaceae) and its significance in the taxonomy of tribe Melanthieae. Systematic Botany 39(2): 411-414.

Arias, T., M. Belstein, M. Tang, M. R. McKain, J. C. Pires. 2014. Diversification times among Brassica crops suggest hybrid formation after twenty million years of divergence.  AmE.an Journal of Botany 10(1): 86-91.

Pawan, K., 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, R. K. Varshney. 2013.  Single Nucleotide Polymorphism–based Genetic Diversity in the Reference Set of Peanut (spp.) by Developing and ApplY.  Cost-Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays. The Plant Genome. 6(3): 10.3835/plantgenome2013.06.001.

D’hont, A., F. Denoeud, JM. Aury, FC. Baurens, F. Carreel, O. Garsmeur, B. Noel, S. Bocs, Gaëtan Droc, M. Rouard, C. Da Silva, K. Jabbari, C. Cardi, J. Poulain, M. Souquet, K. Labadie, C. Jourda, J. Lengellé, M. Rodier-Goud, A. Alberti, M. Bernard, M.  Correa, S. Ayyampalayam, M. R. McKain, et al.  2012. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.  Nature 488: 213-217.

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

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.  AmE.an Journal of Botany 99: 320-329.

Jiao, Y., J. Leebens-Mack, R. 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. Chanerbali, P. S. Soltis, D. W. Stevenson, R. McCombie, C. J. Pires, G. K-S. W.g, D. E. Soltis, and C. W. dePamphilis.  2012.  A genome triplication associated with early diversification of the core eudicots.  Genome Biology 13:  R3.

Givinish, T. J., M. Ames Sevillano, J. R. McNeal, M. R. McKain, P. R. Steele, C. W. dePamphilis, S. W. Graham, J. C. Pires, D. W. Stevenson, W. Zomlefer, B. C. 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: 584-616. 

McKain, M. R., M. A. Chapman and A. L. Ingram.  2010.  Confirmation of the hybrid origin of Eupatorium x truncatum (Asteraceae) using nuclear and plastid markers.  Castanea 75(3): 381-387.