As a systematic botanist, my research program consists of two interrelated components: phylogeny and taxonomy of the Celastraceae (spindle-tree family), and conceptual aspects of phylogenetic analysis of sequence-based molecular characters.
Empirical Research. In my empirical research, I work on the Celastraceae sensu lato (including the Hippocrateaceae and the Stackhousiaceae). Although in Fort Collins we’re surrounded by Euonymus in the form of hedges (especially E. alatus, the “burning bush”), only one species, Paxistima myrsinites, is native to Colorado. The Celastraceae are a large family, primarily of woody lianas, shrubs, and trees with a subcosmopolitan distribution (from tropical to temperate regions; absent in arctic and antarctic regions). Members of the family exhibit substantial variation in stamen, fruit, and seed characters, which have been used to subdivide the family taxonomically. There are 98 currently-recognized genera and about 1,264 species within the Celastraceae sensu lato (Simmons, 2004).
Two other researchers and I have worked on phylogenetic analyses of the Celastraceae in collaborative projects. Jennifer Hedin (from the Missouri Botanical Garden) and I developed a morphology-based phylogenetic analysis of the Celastraceae (Simmons and Hedin, 1999). Vincent Savolainen (from the Royal Botanic Gardens, Kew) and I sampled molecular characters. Vincent Savolainen sampled the atpB and rbcL loci from the chloroplast genome (Savolainen et al., 2000a, 2000b). I sampled the phytochrome B locus and 26S ribosomal DNA from the nuclear genome (Simmons et al., 2001a, 2001b).
My goal is to gain an understanding of the intergeneric phylogenetic relationships for the whole family of 98 genera. Although the above-mentioned studies are the most comprehensive phylogenetic analyses for the Celastraceae and have addressed many important questions, only 55 genera from the family have been sampled in the most comprehensive analysis (Simmons et al., 2001b), which is inadequate to address my goal. Expanded sampling will be conducted using the morphological characters and the chloroplast and nuclear loci that have already been sampled. Further taxon sampling will focus on genera that have not yet been sampled, genera whose inclusion within the Celastraceae is questionable, and genera whose circumscription is problematic. This study will be used to track morphological character evolution within the Celastraceae, determine which genera are appropriately included within the Celastraceae, and resolve intergeneric relationships within the family. Furthermore, this phylogenetic analysis will be used to propose a new classification of the Celastraceae to replace the currently followed artificial classifications by Loesener (1942) and Hallé (1962).
As part of this project, I will examine the developmental anatomy of the aril among members of the Celastraceae. Within the family, the aril has undergone tremendous diversification and may be fleshy, fleshy with filamentous extensions, a basal wing with the funiculus vasculature along the wing, a basal wing with the funiculus vasculature attached above the wing, a wing surrounding the seed, or a mucilaginous pulp. With sarcotestal seeds and several lineages with fleshy fruits, the Celastraceae also serve as an excellent group to test Corner’s (1954, 1976) and van der Pijl’s (1955, 1972) competing hypotheses regarding evolution of the aril in flowering plants.
Conceptual Research. In my conceptual research, I work on the phylogenetic analysis of sequence data. The incorporation of sequence characters into phylogenetic analyses requires three steps: a priori hypotheses of homology by alignment, coding the a priori hypotheses of homology as characters, and phylogenetic analysis of these characters. Each of these steps requires that several issues be addressed. A priori hypotheses of homology that will be used for phylogenetic analysis require that the investigator have confidence in their alignment. Alignment, performed by the insertion of gaps that putatively represent insertion and deletion events, is not generally problematic for sequences that are minimally divergent from one another. However, widely divergent sequences are more problematic to align because of problems with conflation of substitutions with insertions and deletions (Simmons and Freudenstein, 2003). Coding a priori hypotheses of homology as characters requires the investigator to determine how their hypotheses are appropriately analyzed. Points to consider while coding characters include whether the sequence data should be coded as nucleotide or amino-acid characters (Simmons, 2000; Simmons and Freudenstein, 2002a; Simmons et al., 2002a, 2002b), whether gaps that were inserted during the alignment should be coded as characters (Simmons and Ochoterena, 2000; Simmons et al., 2001c), and which sequences should be compared with one another to infer the phylogeny (Simmons et al., 2000; Simmons and Freudenstein, 2002b). In phylogenetic analysis of sequence characters, a gene tree is constructed that is then used to infer the phylogeny, either by itself or by incorporation of other sources of characters (e.g., gross morphology, anatomy, other gene trees).
Corner, E. J. H. 1954. The durian theory extended--II. The arillate fruit and the compound leaf. Phytomorphology 4: 152-165.
Corner, E. J. H. 1976. The Seeds of Dicotyledons. Cambridge: Cambridge University Press.
Hallé, N. 1962. Monographie des Hippocratéacées d'Afrique occidentale. Mémoires de l'Institut Français d'Afrique Noire 64: 1-245.
Loesener, T. 1942. Celastraceae. In: A. Engler and K. Prantl (eds.), Die Natürlichen Pflanzenfamilien 20b: 87-197. Duncker & Humblot, Berlin.
Savolainen, V., Fay, M. F., Albach, D. C., Backlund, A., van der Bank, M., Cameron, K. M., Johnson, S. A., Lledó, M. D., Pintaud, J.-C., Powell, M., Sheahan, M. C., Soltis, D. E., Soltis, P. S., Weston, P., Whitten, M., Wurdack, K. J., and Chase, M. W. 2000a. Phylogeny of the eudicots: a nearly complete familial analysis based on rbcL gene sequences. Kew Bulletin 55: 257-309.
Savolainen, V., Chase, M. W., Hoot, S. B., Morton, C. M., Soltis, D. E., Bayer, C., Fay, M. F., De Brujin, A., Sullivan, S., and Qiu, Y.-L. 2000b. Phylogenetics of flowering plants based upon a combined analysis of plastid atpB and rbcL gene sequences. Systematic Biology 49: 306-362.
Simmons, M. P. 2000. A fundamental problem with amino-acid-sequence characters for phylogenetic analyses. Cladistics 16: 274-282.
Simmons, M. P. 2004. Celastraceae. Pages 29-64 in The families and genera of vascular plants, volume 6 (K. Kubitzki, ed.). Springer, Berlin.
Simmons, M. P. Accepted. Hippocrateaceae. In: P. Morat (ed.), Flore de la Nouvelle-Calédonie. Paris: Muséum National d’Histoire Naturelle, Laboratoire de Phanérogramie.
Simmons, M. P., C. C. Clevinger, V. Savolainen, R. H. Archer, S. Mathews, and J. J. Doyle. 2001a. Phylogeny of the Celastraceae inferred from phytochrome B gene sequence and morphology. American Journal of Botany 88: 313-325.
Simmons, M. P. and J. V. Freudenstein. 2002a. Artifacts of coding amino acids and other composite characters for phylogenetic analysis. Cladistics 18: 354-365.
Simmons, M. P. and J. V. Freudenstein. 2003. 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.
Simmons, M. P. and J. P. Hedin. 1999. Relationships and morphological character change among genera of Celastraceae sensu lato (including Hippocrateaceae). Annals of the Missouri Botanical Garden 86: 723-757.
Simmons, M. P. and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381.
Simmons, M. P., H. Ochoterena, and T. Carr. 2001c. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Systematic Biology 50: 454-462.
Simmons, M. P., H. Ochoterena and J. V. Freudenstein. 2002a. Conflict between amino acid and nucleotide characters. Cladistics 18: 200-206.
Simmons, M. P., V. Savolainen, C. C. Clevinger, R. H. Archer, and J. I. Davis. 2001b. Phylogeny of the Celastraceae inferred from 26S nuclear ribosomal DNA, phytochrome B, rbcL, atpB, and morphology. Molecular Phylogenetics and Evolution 19: 353-366.
van der Pijl, L. 1955. Sarcotesta, aril, pulpa and the evolution of the angiosperm fruit. II. Verhandelingen der koninklijke nederlandsche akademie van wetenschappen; afdeeling natuurkunde; tweede sectie 58: 307-312.
van der Pijl, L. 1972. Principles of Dispersal in Higher Plants. Berlin: Springer-Verlag.