Michelle McMahon

Associate Research Professor - School of Plant Sciences, Ecology and Evolutionary Biology, Bio5
mcmahonm@email.arizona.edu, Marley 441G, Herring 105

Research Interests

  • Research in Dr. McMahon's lab focuses on the analysis of biological diversity, particularly through phylogenetic systematics of plants. Lab-based work includes comparative molecular sequencing, aimed at inferring evolutionary relationships among lineages in the legume family (Fabaceae), and using the resulting phylogenies to infer historical rates and modes of floral morphological evolution. Computational research includes testing data from public molecular sequence databases for the ability to construct large-scale phylogenetic trees for all 1.7 million known species, investigating theoretical limits to phylogenetic inference, and developing software for analyzing the effects of fragmentation in phylogenetic and phylogenomic data sets.

Selected Publications

Copetti D, Búrquez A, Bustamante E, Charboneau J, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing R, Wojciechowski MF, Sanderson MJ. 2017. Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. Proceedings of the National Academy of Sciences 114:12003-12008
Sanderson MJ, Nicolae M, McMahon MM. 2017. Homology-aware phylogenomics at gigabase scales. Systematic Biology doi:10.1093/sysbio/syw104
McMahon MM, Deepak A, Fernández-Baca D, Boss D, Sanderson MJ. 2015. STBase: One Million Species Trees for Comparative Biology. PLoS ONE 10(2): e0117987. doi:10.1371/journal.pone.0117987
Sanderson MJ, McMahon MM, Stamatakis A, Zwickl DJ, Steel M. 2015. Impacts of terraces on phylogenetic inference. Systematic Biology 64:709-726. doi:10.1093/sysbio/syv024
Sanderson MJ, Copetti D, Búrquez A, Bustamante E, Charboneau J, Eguiarte L, Kumar S, Lee HO, Lee J, McMahon M, Steele K, Wing R, Yang T-J, Zwickl D, Wojciechowski MF. 2015. Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea, Cactaceae): loss of the ndh gene suite and inverted repeat. American Journal of Botany 102:1115-1127. doi:10.3732/ajb.1500184.
Marazzi, B., E. Conti, M. J. Sanderson, M. M. McMahon, J. L. Bronstein. 2013. Diversity and evolution of a trait mediating ant-plant interactions: Insights from extrafloral nectaries in Senna (Leguminosae). Annals of Botany 111:1263–1275.
Deepak, A., D. Fernández-Baca, S. Tirthapura, M. J. Sanderson, M. M. McMahon. 2014. EvoMiner: Frequent subtree mining in phylogenetic databases. Knowledge and Information Systems 41:559-590. doi:10.1007/s10115-013-0676-0
Deepak A., D. Fernández-Baca, M. M. McMahon. 2013. Extracting conflict-free information from multi-labeled trees. Algorithms for Molecular Biology 8:18
The Legume Phylogeny Working Group. (37 authors, including M. M. McMahon). 2013. Legume phylogeny and classification in the 21st century: progress, prospects and lessons. Taxon 62:217-248.
Sanderson, M. J., M. M. McMahon, and M. Steel. 2011. Terraces in phylogenetic tree space. Science 333: 448-450.
Chang, P. L., B. P. Dilkes, M. McMahon, L. Comai and S. V. Nuzhdin. 2010. Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biology 11:R125.
Sanderson, M. J., M. M. McMahon, and M. Steel. 2010. Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evolutionary Biology 10:155.

Teaching Responsibilities

  • PLS 472/572: Plant Systematics

Research Areas

  • Biodiversity and Evolutionary Biology
  • Genomics, Bioinformatics, and Systems Biology