Description Of Research
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.
Representative Publications
Zhang, L.-B., M.P. Simmons and S.S. Renner. 2007. A phylogeny of Anisophyllaceae based on six nuclear and plastid loci: ancient disjunctions and recent dispersal between South America, Africa, and Asia. Molecular Phylogenetics and Evolution 44: 1057-1067.
Simmons, M.P., L.-B. Zhang, C.T. Webb and K. Müller. 2007. A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference. Molecular Phylogenetics and Evolution 42: 528-542.
Simmons, M.P., K. M�ller and A.P. Norton. 2007. The relative performance of indel-coding methods in simulations. Molecular Phylogenetics and Evolution 44: 724-740.
Zhang, L.-B., M.P. Simmons, A. Kocyan, and S.S. Renner. 2006. Phylogeny of the Cucurbitales based on DNA sequences of nine loci from three genomes: implications for morphological and sexual system evolution. Molecular Phylogenetics and Evolution 39: 305-322.
Zhang, L.-B. and M.P. Simmons. 2006. Phylogeny and delimitation of the Celastrales inferred from nuclear and plastid genes. Systematic Botany 31: 122-137.
Richardson, D., M.P. Simmons and A.S.N. Reddy. 2006. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. BMC Genomics 7: 18.
Poff, N.L., J.D. Olden, N.K.M. Vieira, D.S. Finn, M.P. Simmons and B.C. Kondratieff. 2006. Functional trait niches of North American lotic insects: evolutionary constraints on trait-based ecological applications. Journal of the North American Benthological Society 25: 730-755.
Petersen, G., O. Seberg, J.I. Davis, D.H. Goldman, D.W. Stevenson, L.M. Campbell, F.A. Michelangeli, C.D. Specht, M.W. Chase, M.F. Fay, J.C. Pires, J.V. Freudenstein, C.R. Hardy and M.P. Simmons. 2006. Mitochondrial DNA in monocot phylogenetics. Aliso 22: 52-62.
Islam, M.B., M.P. Simmons and R.H. Archer. 2006. Phylogeny of the Elaeodendron group (Celastraceae) inferred from morphological characters and nuclear and plastid genes. Systematic Botany 31: 512-524.
Islam, M.B. and M.P. Simmons. 2006. A thorny dilemma: testing alternative intrageneric classifications within Ziziphus (Rhamnaceae). Systematic Botany 31: 826-842.
Davis, J.I., G. Petersen, O. Seberg, D.W. Stevenson, C.R. Hardy, M.P. Simmons, F.A. Michelangeli, D.H. Goldman, L.M. Campbell, C.D. Specht and J.I. Cohen. 2006. Are mitochondrial genes useful for the analysis of monocot relationships? Taxon 55: 857-870.
Simmons, M.P., L.-B. Zhang, C.T. Webb, A. Reeves and J.A. Miller. 2006. The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters. Cladistics 22: 171-185.
Simmons, M.P., L.-B. Zhang, C.T. Webb and A. Reeves. 2006. How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants. Systematic Biology 55: 245-258.
Simmons, M.P. and C.T. Webb. 2006. Quantification of the success of phylogenetic inference in simulations. Cladistics 22: 249-255.
