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
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.

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.