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 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
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.

Maddison, W., & McMahon, M. (2000). Divergence and reticulation among Montane populations of a jumping spider (Habronattus pugillis Griswold). Systematic Biology, 49(3), 400-421.

PMID: 12116419;Abstract:

Populations of the jumping spider Habronattus pugillis Griswold isolated on nearby mountain ranges in southern Arizona are differentiated in many features of the males (color, shape, and orientation of setae on face; shape of carapace; markings of palpi and legs; motions during courtship behavior). These features are (mostly) consistent within a range and different between ranges. The concentration of differences in male courtship behavior and body parts exposed to the female during courtship and correlations between form and courtship behavior suggest sexual selection was involved in the differentiation. A phylogenetic analysis of the populations yields a tree that for the most part groups geographic neighbors, but the history of H. pugillis populations may not be adequately described by a tree. Geographic proximity of apparent convergences suggests that populations from at least some of the mountain ranges acquired characteristics through introgression. Lowering of the woodland habitat during the last glacial period probably brought some populations into contact, but it is not clear whether the interrange woodlands would have provided corridors for extensive mixing.

McMahon, M., & Hufford, L. (2004). Phylogeny of Amorpheae (Fabaceae: Papilionoideae). American Journal of Botany, 91(8), 1219-1230.

PMID: 21653479;Abstract:

The legume tribe Amorpheae comprises eight genera and 240 species with variable floral form. In this study, we inferred a phylogeny for Amorpheae using DNA sequence data from the plastid trnK intron, including matK, and the nuclear ribosomal ITS1, 5.8S, and ITS2. Our data resulted in a well-resolved phylogeny in which the tribe is divided into the daleoids (Dalea, Marina, and Psorothamnus), characterized by generally papilionaceous corollas, and the amorphoids (Amorpha, Apoplanesia, Errazurizia, Eysenhardtia, and Parryella), characterized by non-papilionaceous flowers. We found evidence for the paraphyly of Psorothamnus and for the monophyly of Dalea once D. filiciformis is transferred to monophyletic Marina. Errazurizia rotundata is more closely related to Amorpha than to the other errazurizias, and Eysenhardtia is supported to be monophyletic. The monotypic Parryella and Apoplanesia are placed within the amorphoids. Among Papilionoideae, trnK/matK sequence data provide strong evidence for the monophyly of Amorpheae and place Amorpheae as sister to the recently discovered dalbergioid clade.