Michelle M Mcmahon

Interests

No activities entered.

Courses

Scholarly Contributions

Journals/Publications

• Monihan, S. M., Magness, C. A., Ryu, C., Mcmahon, M. M., Beilstein, M. A., & Schumaker, K. S. (2020). Duplication and functional divergence of a calcium sensor in the Brassicaceae. Journal of Experimental Botany. doi:10.1093/jxb/eraa031
• 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
  More info

  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.
• 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
• 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., 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.
  More info

  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.
• 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.
• Deepak, A., Fernandez-Baca, D., Tirthapura, S., Sanderson, M. J., & McMahon, M. M. (2014). EvoMiner: frequent subtree mining in phylogenetic databases. KNOWLEDGE AND INFORMATION SYSTEMS, 41(3), 559-590.
  More info

  The problem of mining collections of trees to identify common patterns, called frequent subtrees (FSTs), arises often when trying to interpret the results of phylogenetic analysis. FST mining generalizes the well-known maximum agreement subtree problem. Here we present EvoMiner, a new algorithm for mining frequent subtrees in collections of phylogenetic trees. EvoMiner is an Apriori-like levelwise method, which uses a novel phylogeny-specific constant-time candidate generation scheme, an efficient fingerprinting-based technique for downward closure, and a lowest-common-ancestor-based support counting step that requires neither costly subtree operations nor database traversal. Our algorithm achieves speedups of up to 100 times or more over Phylominer, the current state-of-the-art algorithm for mining phylogenetic trees. EvoMiner can also work in depth-first enumeration mode to use less memory at the expense of speed. We demonstrate the utility of FST mining as a way to extract meaningful phylogenetic information from collections of trees when compared to maximum agreement subtrees and majority-rule trees-two commonly used approaches in phylogenetic analysis for extracting consensus information from a collection of trees over a common leaf set.
• 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.
  More info

  Group Author: Legume Phylogeny Working Group. Thirty-seven authors in total; McMahon is 24th.
• 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.
• 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.
• Sanderson, M., McMahon, M., & Steel, M. (2011). Terraces in Phylogenetic Tree Space. Science, 448-450.
• 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).
  More info

  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.
• 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.
  More info

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

  Abstract: 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.
• 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.
  More info

  Abstract: 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.
• Hufford, L., & McMahon, M. (2004). Morphological evolution and systematics of Synthyris and Besseya (Veronicaceae): A phylogenetic analysis. Systematic Botany, 29(3), 716-736.
  More info

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

  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.
• Hufford, L., McMahon, M. M., Sherwood, A. M., Reeves, G., & Chase, M. W. (2003). The major clades of Loasaceae: Phylogenetic analysis using the plastid matK and trnL-trnF regions. American Journal of Botany, 90(8), 1215-1228.
  More info

  PMID: 21659222;Abstract: Phylogenetic analyses of Loasaceae that apply DNA sequence data from the plastid trnL-trnF region and matK gene in both maximum-parsimony and maximum-likelihood searches are presented. The results place subfamily Loasoideae as the sister of a subfamily Gronovioideae-Mentzelia clade. Schismocarpus is the sister of the Loasoideae-Gronovioideae-Mentzelia clade. The Schismocarpus-Loasoideae-Gronovioideae-Mentzelia clade is the sister of Eucnide. Several clades in Loasoideae receive strong support, providing insights on generic circumscription problems. Within Mentzelia, several major clades receive strong support, which clarifies relationships among previously circumscribed sections. Prior taxonomic and phylogenetic hypotheses are modeled using topology constraints in parsimony and likelihood analyses; tree lengths and likelihoods, respectively, are compared from constrained and unconstrained analyses to evaluate the relative support for various hypotheses. We use the Shimodaira-Hasegawa (SH) test to establish the significance of the differences between constrained and unconstrained topologies. The SH test rejects topologies based on hypotheses for (1) the placement of gronovioids as the sister of the rest of Loasaceae, (2) the monophyly of subfamily Mentzelioideae as well as Gronovioideae and Loasoideae, (3) the monophyly of Loasa sensu lato as circumscribed by Urban and Gilg, and (4) the monophyly of Mentzelia torreyi and Mentzelia sect. Bartonia.
• McMahon, M., & Hufford, L. (2002). Developmental morphology and structural homology of corolla-androecium synorganization in the tribe Amorpheae (Fabaceae: Papilionoideae). American Journal of Botany, 89(12), 1884-1898.
  More info

  PMID: 21665617;Abstract: Comparative developmental morphology was used to assess structural homology of flowers in Dalea, Marina, and Psorothamnus of the tribe Amorpheae (Fabaceae: Papilionoideae). Dalea, Marina, and some species of Psorothamnus have an unusual petal-stamen synorganization (stemonozone) in which free petals are inserted on a region that is continuous with fused stamen filaments. Developmental studies of these three genera demonstrated similarity during organogenesis. Zonal growth results in several synorganized regions, including the stemonozone of Dalea, Marina, and some Psorothamnus. Psorothamnus species that lack a stemonozone have fused stamens and free petals inserted on the hypanthium, as in most other papilionoid legumes. We concluded that the stemonozone is not strictly homologous to either androecium or receptacle, but that it is the product of a modified androecial developmental program. In the prairie clover daleas, petaloid structures positioned between the stamens have been variously interpreted as petals or as staminodes; we infer that they have an extreme form of the daleoid stemonozone, on which five petals (no staminodes) and five stamens are inserted. Assessing structural homology of these flowers allows us to characterize accurately daleoid morphology for evolutionary studies in the tribe Amorpheae.
• Maddison, W., & McMahon, M. (2000). Divergence and reticulation among Montane populations of a jumping spider (Habronattus pugillis Griswold). Systematic Biology, 49(3), 400-421.
  More info

  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.

Presentations

• Mcmahon, M. M. (2017, January). Genomic phylogeography of saguaro cactus. International Biogeography Society Conference. Tucson, AZ: International Biogeography Society.
  More info

  Research reported in this presentation was conducted by a myself and a team of collaborators at UNAM, ASU, and UA.
• Mcmahon, M. M. (2011). Phylogenetic Systematics in the School of Plant Sciences. Recruitment presentation summarizing my research program for ABBS recruits..
• Mcmahon, M. M. (2011). Specimen Digitization at The University of Arizona Herbarium. Annual Meetings of TORCH (Texas Oklahoma Regional Consortia of Herbaria).. Junction, TX.

Poster Presentations

• Mcmahon, M. M. (2017, October). Homology-aware Phylogenomics at Gigabase Scales (fast and furious phylogenomics). Plant Genome Evolution Conference. Sitges, Spain.
• Marazzi, B., Bronstein, J. L., & Mcmahon, M. M. (2014, June). Disentangling the evolutionary histories of extrafloral nectaries in deserts. Angiosperm Radiations Conference. Zurich, Switzerland.
• Marazzi, B., McMahon, M., Lanan, M., & Bronstein, J. (2011, July). Diversity and evolution of extrafloral nectaries in Sonoran desert plants. International Botanical Congress. Melbourne, Australia.

Others

• Mcmahon, M. M. (2021, 12). New website for Desert Legume Program. https://cals.arizona.edu/desertlegumeprogram/
  More info

  Research-enriched searchable database of germplasm repository at DELEP. Some aspects still under construction.
• Mcmahon, M. M. (2011, Fall). UA Herbarium website and specimen search engine.