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
McMahon, M. M., Deepak, A., Fernandez-Baca, D., Boss, D., & Sanderson, M. J. (2015). STBase: One million species trees for comparative biology. PLoS ONE, 10(2), e0117987.
Sanderson, M. J., Nicolae, M., & Mcmahon, M. M. (2017). Homology-aware phylogenomics at gigabase scales. Systematic Biology, 66, 590-603. doi:10.1093/sysbio/syw104
Chang, P. L., Dilkes, B. P., McMahon, M., Comai, L., & Nuzhdin, S. V. (2010). Homoeolog-specific retention and use in allotetraploid Arabidopsis suecica depends on parent of origin and network partners. Genome Biology, 11(12).

PMID: 21182768;PMCID: PMC3046485;Abstract:

Background: Allotetraploids carry pairs of diverged homoeologs for most genes. With the genome doubled in size, the number of putative interactions is enormous. This poses challenges on how to coordinate the two disparate genomes, and creates opportunities by enhancing the phenotypic variation. New combinations of alleles co-adapt and respond to new environmental pressures. Three stages of the allopolyploidization process - parental species divergence, hybridization, and genome duplication - have been well analyzed. The last stage of evolutionary adjustments remains mysterious.Results: Homoeolog-specific retention and use were analyzed in Arabidopsis suecica (As), a species derived from A. thaliana (At) and A. arenosa (Aa) in a single event 12,000 to 300,000 years ago. We used 405,466 diagnostic features on tiling microarrays to recognize At and Aa contributions to the As genome and transcriptome: 324 genes lacked Aa contributions and 614 genes lacked At contributions within As. In leaf tissues, 3,458 genes preferentially expressed At homoeologs while 4,150 favored Aa homoeologs. These patterns were validated with resequencing. Genes with preferential use of Aa homoeologs were enriched for expression functions, consistent with the dominance of Aa transcription. Heterologous networks - mixed from At and Aa transcripts - were underrepresented.Conclusions: Thousands of deleted and silenced homoeologs in the genome of As were identified. Since heterologous networks may be compromised by interspecies incompatibilities, these networks evolve co-biases, expressing either only Aa or only At homoeologs. This progressive change towards predominantly pure parental networks might contribute to phenotypic variability and plasticity, and enable the species to exploit a larger range of environments. © 2010 Chang et al.; licensee BioMed Central Ltd.

McMahon, M. M. (2005). Phylogenetic relationships and floral evolution in the papilionoid legume clade Amorpheae. Brittonia, 57(4), 397-411.


Amorpheae (Fabaceae: Papilionoideae) was first considered a natural group by Rupert Barneby in his illustrated monograph Daleae Imagines. Amorpheae currently comprise eight genera, ca. 250 spp., and extensive floral diversity, including loss of corolla and addition of a stemonozone. The Amorpheae and many of Barneby's subtribal groups are supported as monophyletic by previous phylogenetic analysis of nuclear ribosomal and chloroplast sequence data. However, some relationships remain unclear. A nuclear marker derived from a genomic study in Medicago, CNGC4, was sequenced in selected Amorpheae. This is one of the first applications of this marker for phylogenetic study. The new data confirm some relationships inferred using trnK and ITS, but also provide evidence for new arrangements. Combined data were used to explore several aspects of Barneby's taxonomic framework. The phylogeny, in concert with data on floral morphology, implies that simplification of the complex papilionoid flower has occurred several times in the history of the Amorpheae. © 2005, by The New York Botanical Garden Press.