Select Research from the Department of Biology
Students and faculty in our department are engaged in a wide variety of investigations, and an increasing number are taking advantage of the Internet and other new technologies. The Department of Biology is pleased to house the results of some of these efforts on our web site, and to make them available to the global research community.
Papers and Supplementary Data
  • Simmons, M. P. Submitted. Supplementary data for "Potential use of host-derived genome signatures to root virus phylogenies."
  • Simmons, M. P., K. F. Müller, and C. T. Webb, Submitted. Supplementary data for "The relative sensitivity of different alignment methods and character codings in sensitivity analysis."
  • Zhang, L.-B., M. P. Simmons, and S. S. Renner, 2006. Supplementary data for "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., K. Müller, and A. P. Norton, 2007. Supplementary data for "The relative performance of indel-coding methods in simulations." (Molecular Phylogenetics and Evolution 44: 724-740.)
  • Simmons, M. P., D. Richardson and A. S. N. Reddy. 2008 Supplementary data for "Submitted. Incorporation of gap characters and lineage-specific regions into phylogenetic analyses of gene families from divergent clades: An example from the kinesin superfamily across eukaryotes." (Cladistics 24: 372-384.)
  • Simmons, M.P., L.-B. Zhang, C.T. Webb and K. Müller, 2007. Supplementary data for "A penalty of using anonymous dominant markers (AFLPs, ISSRs, and RAPDs) for phylogenetic inference." (Molecular Phylogenetics and Evolution 42: 528-542.)
  • Islam, M. B. and M. P. Simmons, 2006. Supplementary data for "A thorny dilemma: Testing alternative intrageneric classifications within Ziziphus (Rhamnaceae)."(Systematic Botany 31: 826-842.)
  • Poon, W.-S., P.-C. Shaw, M. P. Simmons and P. P.-H. But, 2007. Supplementary data for "The congruence of molecular, morphological and biochemical profiles in Rutaceae: a cladistic analysis of the subfamilies Rutoideae and Toddalioideae." (Systematic Botany 32: 837-846.)
  • Poff, N. L., J. D. Olden, N. M. Vieira, D. S. Finn, M. P. Simmons and B. C. Kondratieff, 2006. Supplementary data for "Functional trait niches of North American lotic insects: traits-based ecological applications in light of phylogenetic relationships" (Journal of the North American Benthological Society 25: 730-755)
  • Islam, M. B, M. P. Simmons, R. H. Archer, 2006. Supplementary data for "Phylogeny of the Elaeodendron Group (Celastraceae) Inferred from Morphological Characters and Nuclear and Plastid Genes." (Systematic Botany 31: 512-524)
  • Zhang, L.-B., M. P. Simmons, A. Kocyan, and S. S. Renner, 2006. Supplementary data for "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)
  • Simmons, M. P. and C. T. Webb 2006. Supplementary data for "Quantification of the success of phylogenetic inference in simulations." (Cladistics 22: 249-255.)
  • Simmons, M. P., L.-B. Zhang, C. T. Webb and A. Reeves, 2006. Supplementary data for "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)
  • Zhang, L.-B. and M. P. Simmons, 2006. Supplementary data for "Phylogeny and Delimitation of the Celastrales Inferred from Nuclear and Plastid Genes." (Systematic Botany 31: 122-137.)
  • Simmons, M. P., T. G. Carr and K. O'Neill, 2004. Supplementary data for "Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters." (Molecular Phylogenetics and Evolution 32: 913-926.)
  • Simmons, M. P., A. Reeves, and J. I. Davis, 2004. Supplementary data for "Character-state space versus rate of evolution for phylogenetic inference." (Cladistics 20: 191-204.)
  • Simmons, M. P., 2005. Supplementary data for "Amino acid versus nucleotide characters for phylogenetic inference of the 'basal' angiosperms." Pages 1-27 in Plant genome biodiversity and evolution, volume 1B: phanerogams. (A.K. Sharma and A. Sharma, eds.). Science Publishers, Inc., Enfield, New Hampshire.
  • Simmons, M. P. and J. V. Freudenstein, 2003. Supplementary data for "The effects of increasing genetic distance on alignment of, and tree construction from, rDNA internal transcribed spacer sequences." (Molecular Phylogenetics and Evolution 26:444-451.)
  • Baer, C.F., 1999. Appendix to "Among-locus variation in Fst: fish, allozymes, and the Lewontin-Krakauer test revisited." (Genetics 152: 653-659.)
  • Simmons, M. P., L.-B. Zhang, C. T. Webb, A. Reeves and J. A. Miller, 2006 Supplementary data for " The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters." (Cladistics 22: 171-185.)
Computer programs
  • Condense, a program for condensing results from multiple different simulation replicates. (See Simmons, M. P., A. Reeves, and J. I. Davis, 2004. Character-state space versus rate of evolution for phylogenetic inference. Cladistics 20: 191-204.)
  • Concat, a program for concatenating simulated data matrices. (See Simmons, M. P., L.-B. Zhang, C. T. Webb and A. Reeves, Accepted. How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants. Systematic Biology.)
  • Maxclique, a program for finding maximal cliques and maximal independent sets. (See Simmons, M. P., T. G. Carr, and K. O'Neill, 2004. Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters.)
  • MicroMeasure, a scientific image analysis application for cytogeneticists and cytologists. (See Reeves, A., 2001. MicroMeasure: A new computer program for the collection and analysis of cytogenetic data. Genome 44: 439 - 443.)
Web sites
CSU Herbarium
The Colorado State University Herbarium is one of the few in the country which has developed a database (PICEA) for its collection. At present we have about 50,000 specimens in the database and are in the process of computerizing the entire collection.
Optical Coherence Microscopy for Plant Development
Optical coherence microscopy (OCM) is a relatively new, noninvasive, nondestructive in vivo imaging technology. Researchers in CSU Biology, together with colleagues at Harvey Mudd College, are the first to have applied this technology to follow the changes that occur in plants over time.
The sites listed above represent only a small portion of the research conducted by department personnel. For more information about research in CSU Biology, please see the profiles of our faculty.