Mark Simmons

Mark SimmonsProfessor and Curator of the Charles Maurer Herbarium
Office: Biology 418
Phone: 970-491-2154
Education: Ph.D., Cornell University
Curriculum Vitae: Click to View

My research program consists of two interrelated components: phylogeny and taxonomy of the flowering-plant family Celastraceae (the spindle-tree family), and conceptual aspects of molecular phylogenetics (using genomic data to reconstruct evolutionary relationships among species). The Celastraceae are a large family, primarily of lianas, shrubs, and trees with a sub-cosmopolitan distribution. Within the family, the aril has undergone tremendous diversification and ranges in form from a mucilaginous pulp to a broad wing. I am working to assess overall relationships within the family and track the pattern of aril diversification. For my conceptual research, I am working on problems such as: how alignment changes with increasing genetic distance, the trade-offs of using either nucleotide or amino acid characters, the incorporation of duplicate genes into phylogenetic analyses, the measurement of phylogenetic signal, and the use of morphological characters when entire genomes are sequenced. Molecular phylogenetics is playing an increasingly central role in biology, from inferring the diversification of multigene families, to tracking invasive species, conservation of protected species, as evidence in criminal investigations, and fighting bioterrorism.

Selected Publications

Simmons, M.P., D.B. Sloan, M.S. Springer, and J.G. Gatesy. 2019. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Molecular Phylogenetics and Evolution 131: 80-92.

Polato, N.R., B.A Gill, A.A. Shah, M.M. Gray, KL. Casner, A. Barthelet, P.W. Messer, M.P. Simmons, J.M. Guayasamin, A.C. Encalada, B.C. Kondratieff, A.S. Flecker, S.A. Thomas, C.K. Ghalambor, N.L. Poff, W.C. Funk, and K.R. Zamudio. 2018. Narrow thermal tolerance and low dispersal drive diversification in tropical mountains. Proceedings of the National Academy of Sciences of the U.S.A. 115: 12471-12476.

Wang, J., J.J. Cappa, J. Harris, P.P. Edger, W. Zhou, J.C. Pires, M. Adair, S.A. Unruh, M.P. Simmons, M. Schiavon, and E.A.H. Pilon-Smits. 2018. Transcriptome-wide comparison of selenium hyperaccumulator and non-accumulator Stanleya species provides new insight into key processes mediating the hyperaccumulation syndrome. Plant Biotechnology Journal 16: 1582-1594.

Simmons, M.P. 2018.  Ten rules for associate editors. Botanical Review 84: 99-107.

Biral, L., M.P. Simmons, E.C. Smidt, M. Bolson, L.R. Tembrock, R.H. Archer, and J.A. Lombardi. 2017. Systematics of New World Maytenus (Celastraceae) and a new delimitation of the genus. Systematic Botany 42: 680-693.

Simmons, M.P. 2017. Mutually exclusive phylogenetic inferences from both nuclear and plastid genomic datasets at the root of the angiosperms: Amborella is supported as sister and Observed Variability is biased. Cladistics 33: 488-512.

Tembrock, L.R., C.D. Broeckling, A.L. Heuberger, M.P. Simmons, F.R. Stermitz, and J. Uvarov. 2017. Employing GC-MS and two-stage derivatization to assay for cathine and related stimulant alkaloids across the Celastraceae. Phytochemical Analysis 28: 257-266.

Gatesy, J., R.W. Meredith, J.E. Janecka, M.P. Simmons, W.J. Murphy, and M.S. Springer. 2017. Resolution of a concatenation/coalescence kerfuffle: partititioned coalescence support and a robust family-level tree for Mammalia. Cladistics 33: 295-332.

Tembrock, L.R., M.P. Simmons, C.M. Richards, P.A. Reeves, A. Reilley, M.A. Curto, H. Meimberg, G. Ngugi, S. Demissew, A.W. Al Khulaidi, M. Althobhani, S. Simpson, and D.M. Varisco. 2017. Phylogeography of the wild and cultivated stimulant plant qat (Catha edulis, Celastraceae) in areas of historic cultivation. American Journal of Botany 104: 538-549.

Simmons, M.P. 2017. Relative benefits of amino-acid, codon, degeneracy, DNA, and purine-pyrimidine character coding for phylogenetic analyses of exons. Journal of Systematics and Evolution 55: 85-109.

Darbyshire, I., M.P. Simmons, J.J. Cappa, F.J. Breteler, and S. Buerki. 2016. A questionable African species of Pleurostylia is actually a member of the New World Crossopetalum (Celastraceae). Systematic Botany 41: 851-864.

Gill, B.A., B.C. Kondratieff, K.L. Casner, A.C. Encalada, A.S. Flecker, D.G. Gannon, C.K. Ghalambor, J.M. Guayasamin, N.L. Poff, M.P. Simmons, S.A. Thomas, K.R. Zamudio, and W.C. Funk. 2016. Cryptic species diversity reveals biogeographic support for the ‘mountain passes are higher in the tropics’ hypothesis. Proceedings of the Royal Society B: Biological Sciences 283: 20160553.

Simmons, M.P. and J. Gatesy. 2016. Biases of tree-independent-character-subsampling methods. Molecular Phylogenetics and Evolution 100: 424-443.

Simmons, M.P., D.B. Sloan, and J. Gatesy. 2016. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Molecular Phylogenetics and Evolution 97: 76-89.

Warren, J.M., M.P. Simmons, Z. Wu, and D.B. Sloan. 2016. Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes. Genome Biology and Evolution 8: 364-374.

Gu, C., L.R. Tembrock, N.G. Johnson, M.P. Simmons, and Z. Wu. 2016. The complete plastid genome of Lagerstroemia fauriei and loss of an rpl2 intron from Lagerstroemia (Lythraceae). PLOS One 11: e0150752.

Judd, C.R., A. Koyama, M.P. Simmons, P. Brewer, J.C. von Fischer. 2016. Co-variation in methanotroph community composition and activity in three temperate grassland soils. Soil Biology & Biochemistry 95: 78 – 86.

Bacon, C.D., M.P. Simmons, R.H. Archer, L. Zhao, and J. Andriantiana. 2016. Biogeography of the Malagasy Celastraceae: multiple independent origins followed by widespread dispersal of genera from Madagascar. Molecular Phylogenetics and Evolution 94: 365-382.

Simmons, M.P. 2015. Ten simple rules for writing a reply paper. PLoS Computational Biology 11: e1004536.

Simmons, M.P. and J. Gatesy. 2015. Coalescence vs. concatenation: sophisticated analyses vs. first principles applied to rooting the angiosperms. Molecular Phylogenetics and Evolution 91: 98-122.

Cappa, J.J., C. Yetter, S. Fakra, P.J. Cappa, R. DeTar, C. Landes, E.A.H. Pilon-Smits, and M.P. Simmons. 2015. Evolution of selenium hyperaccumulation in Stanleya (Brassicaceae) as inferred from phylogeny, physiology and X-ray microprobe analysis. New Phytologist 205: 583-595.

Goloboff, P.A. and M.P. Simmons. 2014. Bias in tree searches, and its consequences for measuring group supports. Systematic Biology 63: 851-861.

Simmons, M.P. 2014. A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses. Molecular Phylogenetics and Evolution 80: 267-280.

Simmons, M.P. and P.A. Goloboff. 2014. Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches. Molecular Phylogenetics and Evolution 78: 334-348.

Simmons, M.P. and C.P. Randle. 2014. Disparate parametric branch-support values from ambiguous characters. Molecular Phylogenetics and Evolution 78: 66-86.

Groppo, M., M.P. Simmons, J.J. Cappa, L. Biral, and J.A. Lombardi. 2014. A new species of Maytenus (Celastraceae) with fleshy fruits from eastern Brazil with notes on the delimitation of Maytenus. Systematic Botany 39: 478-484.

Cappa, J.J., P.J. Cappa, A.F. El Mehdawi, J.M. McAleer, M.P. Simmons and E.A.H. Pilon-Smits. 2014. Characterization of selenium and sulfur accumulation in Stanleya (Brassicaceae): a field survey and common-garden experiment. American Journal of Botany 101: 830-839.

Simmons, M.P. 2014. Limitations of locally sampled characters in phylogenetic analyses of sparse supermatrices. Molecular Phylogenetics and Evolution 74: 1-14.

Simmons, M.P. and A.P. Norton. 2014. Divergent maximum-likelihood-branch-support values for polytomies. Molecular Phylogenetics and Evolution 73: 87-96.

Gilligan, T.M., D.J. Wright, J. Munz, K. Yakobson, and M.P. Simmons. 2014. Molecular phylogeny and revised classification of Eucosma Hübner and related genera (Lepidoptera: Tortricidae: Eucosmini). Systematic Entomology 39: 49-67.

Bacon, C.D., F. Michonneau, A.J. Henderson, M.J. McKenna, A.M. Milroy, and M.P. Simmons. 2013. Geographic and taxonomic disparities in species diversity: dispersal and diversification across Wallace's Line. Evolution 67: 2058-2071.

Simmons, M.P. and P.A. Goloboff. 2013. An artifact of undersampling optimal trees in supermatrix analyses of locally sampled characters. Molecular Phylogenetics and Evolution 69: 265-275.

Curto, M.A., L. Tembrock, P. Puppo, M. Nogueira, M.P. Simmons and H. Meimberg. 2013. Evaluation of microsatellites of Catha edulis (qat; Celastraceae) identified using pyrosequencing. Biochemical Systematics and Ecology 49: 1-9.

Simmons, M.P. and A.P. Norton. 2013. Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example. Molecular Phylogenetics and Evolution 67: 277-296.

Simmons, M.P. and J.J. Cappa. 2013. Wilczekra, a new genus of Celastraceae for a disjunct lineage of Euonymus. Systematic Botany 38: 148-153.

Guo, X., R.-J. Wang, M.P. Simmons, P.P.-H. But and J. Yu. 2013. Phylogeny of the Asian Hedyotis-Oldenlandia complex (Spermacoceae, Rubiaceae): Evidence for high levels of polyphyly and parallel evolution of diplophragmous capsules. Molecular Phylogenetics and Evolution 67: 110-122.

Simmons, M.P. and J.V. Freudenstein. 2011. Spurious 99% bootstrap and jackknife support for unsupported clades. Molecular Phylogenetics and Evolution 61: 177-191.

Simmons, M.P., K.F. Müller and C.T. Webb. 2011. The deterministic effects of alignment bias in phylogenetic inference. Cladistics 27: 402-416.

Simmons, M.P., L.-B. Zhang and K.F. Müller. 2011. Phylogenetic inference using non-redundant coding of dependent characters vs. alternative approaches when applied to protein-coding genes. Cladistics 27: 186-196.

Law, S.K.-Y., M.P. Simmons, N. Techen, I.A. Khan, M.-F. He, P.-C. Shaw, and P.P.-H. But. 2011. Molecular analyses of the Chinese herb leigongteng (Tripterygium wilfordii Hook.f.). Phytochemistry 72: 21-26.

Coughenour, J.M., M.P. Simmons, J.A. Lombardi, K. Yakobson and R.H. Archer. 2011. Phylogeny of Celastraceae subfamily Hippocrateoideae inferred from morphological characters and nuclear and plastid loci. Molecular Phylogenetics and Evolution 59: 320-330.

Guo, X., M.P. Simmons, P.P.-H. But, P.-C. Shaw and R.-J Wang. 2011. Application of DNA barcodes in Hedyotis L. (Spermacoceae, Rubiaceae). Journal of Systematics and Evolution 49: 203-212.

Bacon, C.D., G.P. Johnson, H. Meimberg, P. Puppo, M.P. Simmons, and W.L. Wagner. 2011. Development of microsatellites in the Hawaiian endemic palm Pritchardia martii (Arecaceae) and their utility in congeners. American Journal of Botany Primer Notes & Protocols in the Plant Sciences 98: E139-140.

McKenna, M.J., M.P. Simmons, C.D. Bacon and J.A. Lombardi. 2011. Delimitation of the segregate genera of Maytenus sensu lato (Celastraceae) based on morphological and molecular characters. Systematic Botany 36: 922-932.

Simmons, M.P., C.D. Bacon, J.J. Cappa and M.J. McKenna. 2012. Phylogeny of Celastraceae subfamilies Cassinoideae and Tripterygioideae inferred from morphological characters and nuclear and plastid loci. Systematic Botany 37: 456-467.

Simmons, M.P., M.J. McKenna, C.D. Bacon, J.J. Cappa, R.H. Archer and A.J. Ford. 2012. Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid loci.  Molecular Phylogenetics and Evolution 62: 9-20.

Bernhardt, S.A., M.P. Simmons, K.E. Olson, B.J. Beaty, C.D. Blair, and W.C. Black. 2012. Intraspecific evolution of miRNA and siRNA genes in the mosquito Aedes aegypti. PLoS One 7: e44198.

Bacon, C.D., M.J. McKenna, M.P. Simmons and W.L. Wagner. 2012. Evaluating multiple criteria for species delimitation: an empirical example using Hawaiian palms (Arecaceae: Pritchardia). BMC Evolutionary Biology 12: 23.

Bacon, C.D., W.J. Baker and M.P. Simmons. 2012. Miocene dispersal drives island radiations in the palm tribe Trachycarpeae (Arecaceae). Systematic Biology 61: 426-442.

Simmons, M.P. 2012. Misleading results of likelihood-based phylogenetic analyses in the presence of missing data. Cladistics 28: 208-222.

Simmons, M.P. 2012. Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data. Molecular Phylogenetics and Evolution 62: 472-484.