RESEARCH
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).
Literature Cited
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. 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.
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.
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.