Michelle M Mcmahon

Michelle M Mcmahon

Associate Professor, Ecology and Evolutionary Biology
Associate Research Professor
Curator, Herbarium
Associate Director, Academic Programs
Primary Department
Department Affiliations
(520) 621-7243

Research Interest

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


Marazzi, B., Conti, E., Sanderson, M. J., McMahon, M. M., & Bronstein, J. -. (2013). Diversity and evolution of a trait mediating ant-plant interactions: Insights from extrafloral nectaries in Senna (Leguminosae). Annals of Botany, 111, 1263–1275.
BIO5 Collaborators
Judith Bronstein, Michelle M Mcmahon
Sanderson, M. J., McMahon, M. M., Stamatakis, A., Zwickl, D. J., & Steel, M. (2015). Impacts of terraces on phylogenetic inference. Systematic Biology, 64(5), 709-726.
Hufford, L., & McMahon, M. (2004). Morphological evolution and systematics of Synthyris and Besseya (Veronicaceae): A phylogenetic analysis. Systematic Botany, 29(3), 716-736.


Phylogenetic analyses are used to examine the morphological diversity and systematics of Synthyris and Besseya. The placement of Synthyris and Besseya in Veronicaceae is strongly supported in parsimony analyses of nuclear ribosomal ITS DNA sequences. Parsimony and maximum likelihood (ML) criteria provide consistent hypotheses of clades of Synthyris and Besseya based on the ITS data. The combination of morphological characters and ITS data resolve additional clades of Synthyris and Besseya. The results show that Synthyris is paraphyletic to Besseya. In the monophyletic Synthyris clade, Besseya forms part of a Northwest clade that also includes the alpine S. canbyi, S. dissecta, and S. lanuginosa and mesic forest S. cordate, S. reniformis, S. platycarpa, and S. schizantha. The Northwest clade is the sister of S. borealis. An Intermountain clade, comprising S. ranunculina, S. laciniata, S. pinnatifida, and S. missurka, is the sister to the rest of the Synthyris clade. Constraint topologies are used to test prior hypotheses of relationships and morphological similarities. Parametric bootstrapping is used to compare the likelihood values of the best trees obtained in searches under constraints to that of the best tree found without constraints. These results indicate that topologies in which a monophyletic Synthyris is the sister of Besseya are significantly worse than the best ML tree in which Synthyris is paraphyletic to Besseya. Similarly, forcing either the monophyly of all taxa that have deeply incised leaf margins or those that have reniform laminas and broadly rounded apices results in trees that are significantly worse than the best ML tree, in which leaf margin incision and reniform laminas are homoplastic. We propose a new classification for Synthyris that emphasizes monophyletic groups. The new combination Synthyris oblongifolia is proposed.

Hufford, L., McMahon, M. M., O'Quinn, R., & Poston, M. E. (2005). A phylogenetic analysis of loasaceae subfamily loasoideae based on plastid DNA sequences. International Journal of Plant Sciences, 166(2), 289-300.


Questions of tribal and generic circumscriptions and relationships in Loasaceae subfamily Loasoideae are addressed in phylogenetic analyses that apply four plastid regions in parsimony and maximum likelihood analyses. As circumscribed in the influential monograph of Urban and Gilg, Loaseae are paraphyletic to the sister clades Klaprothieae (Klaprothia, Plakothira, and Xylopodia) and Kissenieae (Kissenia). This problem centers on the paraphyly of Huidobria: Huidobria chilensis is sister to Klaprothieae + Kissenieae, and Huidobria fruticosa is sister to all other Loasoideae. Parametric bootstrapping finds topologies that force the monophyly of Huidobria to be significantly different from the optimal topologies in which the genus is paraphyletic; however, Templeton and Shimodaira-Hasegawa tests did not distinguish between these phylogenetic alternatives. We recognize a strongly supported Loaseae sensu stricto (s.str.) as a clade consisting of Nasa, Aosa, Chichicaste, Presliophytum, Blumenbachia, Cajophora, Loasa sect. Loasa, and Scyphanthus. In Loaseae s.str., the monophyly of each of the following has strong support: (1) Nasa, (2) Aosa + Chichicaste, (3) Presliophytum + Loasa malesherbioides, and (4) a higher Loaseae clade that consists of Blumenbachia, Cajophora, Scyphanthus, and the Loasa complex (=sect. Loasa, excluding L. malesherbioides). Blumenbachia, Cajophora (including exemplars from sections Bialatae and Bicallosae), and Scyphanthus are independently monophyletic, and clades of the Loasa complex are mixed among them. The paraphyletic Loasa complex includes the following clades: (1) ser. Pinnatae, (2) ser. Acaules + Volubile, (3) ser. Macrospermae, placed as the sister of Blumenbachia, and (4) ser. Acanthifolia + Floribundae + Deserticolae, which includes the type for Loasa and is the group we recommend as the basis for a revised circumscription of Loasa. © 2005 by The University of Chicago. All rights reserved.

Bruneau, A., Doyle, J. J., Herendeen, P., Hughes, C., ..., .. .., McMahon, M. M., & ..., .. .. (2013). Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades. Taxon, 62(2), 217-248.

Group Author: Legume Phylogeny Working Group. Thirty-seven authors in total; McMahon is 24th.