Mark Simmons

Associate Professor and Herbarium Curator
Office: Anatomy/Zoology Building E212B
Phone: 970-491-2154
Website: http://lamar.colostate.edu/~psimmons
Education: Ph.D., Cornell University
Email: psimmons@lamar.colostate.edu

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. 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.