Michelle M Mcmahon
Associate Professor, Ecology and Evolutionary Biology
Associate Research Professor
Curator, Herbarium
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., Copetti, D., Burquez, A., Bustamante, E., Charboneau, J. L., Eguiarte, L. E., Kumar, S., Lee, H. O., Lee, J., McMahon, M., Steele, K., Wing, R., Yang, T., Zwickl, D., & Wojciechowski, M. F. (2015). Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): Loss of the ndh gene suite and inverted repeat. AMERICAN JOURNAL OF BOTANY, 102(7), 1115-1127.

PREMISE OF THE STUDY: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.

McMahon, M., & Hufford, L. (2005). Evolution and development in the amorphoid clade (Amorpheae: Papilionoideae: Leguminosae): Petal loss and dedifferentiation. International Journal of Plant Sciences, 166(3), 383-396.


We used comparative developmental morphology to study the evolution of nonpapilionaceous corollas in the amorphoid clade of the tribe Amorpheae (Papilionoideae). This clade consists of five genera in which there are no papilionaceous corollas (five petals differentiated into one banner, two wing, and two keel petals). We studied the ontogenies of three nonpapilionaceous forms: corollas consisting of one petal (exemplified by Amorpha canescens), no petals (Parryella filifolia), and five petals in two types (Errazurizia megacarpa). We compared these to the ontogeny of a papilionaceous corolla (exemplified by the closely related Psorothamnus scoparius). In A. canescens, all petals initiated, but four did not grow beyond the primordial stage. In P. filifolia, no distinct petal primordia were visible. The corolla of E. megacarpa, which has only two types of petals, exhibits nonpapilionaceous characteristics at an early ontogenetic stage. Aside from the earliest primordial mounds, the petals of Psorothamnus and Errazurizia do not resemble each other, indicating that paedomorphosis is not responsible for the nonpapilionaceousness of Errazurizia. Comparing the morphological results to a phylogeny, we infer a single origin of the characteristics that differentiate Errazurizia petals from Psorothamnus petals, and we infer at least two evolutionary events leading to the reduced corolla in Parryella, Amorpha, and Errazurizia rotundata. When considered in the context of the remaining Amorpheae, in which additional floral diversification has occurred, and in the context of the entire papilionoid group, in which floral form is relatively conserved, our results indicate a relaxation of selective or developmental constraint within the clade Amorpheae. © 2005 by The University of Chicago. All rights reserved.

Deepak, A., Fernandez-Baca, D., & McMahon, M. M. (2013). Extracting conflict-free information from multi-labeled trees. Algorithms for Molecular Biology, 8:18, 1-11.
Copetti, D., Búrquez, A., Bustamante, E., Charboneau, J. L., Childs, K. L., Eguiarte, L. E., Lee, S., Liu, T. L., McMahon, M. M., Whiteman, N. K., Wing, R. A., Wojciechowski, M. F., & Sanderson, M. J. (2017). Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. Proceedings of the National Academy of Sciences of the United States of America, 114(45), 12003-12008. doi:10.1073/pnas.1706367114

Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.