As a systematic botanist, I am interested in addressing questions regarding the evolutionary relationships of taxa and the evolution of specific traits associated with those taxa. I am currently working on members of the Brassicaceae, or mustard plant family, which encompass over 340 genera and 3500 species distributed around the world (Rollins, 1993). The family contains numerous important crop species, such as broccoli, brussels sprouts, cauliflower, kale, horseradish, mustards, watercress, as well as common horticultural species and the molecular biology model organism Arabidopsis thaliana.
Despite the economic and
scientific importance of the Brassicaceae, intrafamilial relationships
remain relatively uncertain. The problems associated with our current
understanding of the Brassicaceae are the result of taxonomic reliance
on a few morphological characters that appear to display high degrees of
convergence and parallelism, when compared to other data, in combination
with a general lack of discrete morphological variation available to resolve
intrafamilial relationships.
My ongoing projects and short-term research objectives involve the
systematics of a group of New World, mostly Mexican mustard species (referred
to here as the "Halimolobos clade"). These projects were initiated
as the focus of my dissertation research. They include collaborative
studies (with Dr. Robert Price; Athens, GA USA) at the family level along
with a more detailed study focused on relationships and species boundaries
of the poorly known genus Sphaerocardamum. The data for this
research have been generated from four DNA sequences, morphology, anatomy,
crossing studies, and cytology (both karyotypic and flow cytometric).
The current results indicate that the Halimolobos clade is represented
by approximately 40 species and four genera (Halimolobos, Mancoa, Pennellia,
and Sphaerocardamum).
Below is an overview of my long-term research objectives:
1) Phylogenetic studies: I am working to help resolve Brassicaceae systematic problems through the combination of studies at higher and lower taxonomic levels using data from molecular and morphological sources. In addition to working with the relationships among Brassicaceae taxa, I am also interested in using results from these studies to address questions regarding biogeography, morphological character evolution, genome size evolution, and species delimitation issues within the family.2) Morphological character evolution: Studies on morphological character evolution are important to Brassicaceae systematics for several reasons. Characters from fruit morphology are the key characteristics used to classify members of the family. However, given current phylogenetic results from both my research and that of others (e.g., Price, 1997), it appears that characters other than these “key” characters represent better taxonomic markers for the Brassicaceae. Only further research on Brassicaceae lineages will help to establish which characters, or combination of characters, will be most useful in Brassicaceae classification.
Beyond providing characters for classification of the family, results from these studies can reveal major and/or minor shifts in morphological character form. Phylogenetic studies directed at questions regarding morphological character evolution can identify groups where more in-depth molecular developmental studies may find shifts in control or function of genes that lead to new phenotypes. I am interested in establishing collaborative projects that would address these types of issues in character development and homology assessment.3) Genome size evolution is a particularly interesting area of research because of the many long-standing debates regarding the evolution of genome size in flowering plants. These debates have focused on polyploidy, hybridization, retrotransposons, repeat elements and their role(s) in the evolution of land plant genomes. At present, relatively few studies have been conducted on lineages of closely related taxa that share similar cytologies (i.e., the same chromosome numbers) but distinctive genome sizes (e.g., Brandham and Doherty, 1998). I am interested in combining information from phylogenetic studies and comparative genomics studies to address what these intragenic and intergenic non-coding sequences are contributing to differences in nuclear genome sizes among closely related species. These types of studies will help to resolve theoretical arguments over the potential effect of biased length mutation (e.g., Petrov, 1997) in the flowering plants and should help to produce a better overall understanding of the "C-value paradox" as it relates to plants (Thomas, 1971).
4) Developing and incorporating new sources of data: When conducting systematic research, I strive to incorporate as many applicable data sources as possible to develop well-supported hypotheses. In order to accomplish this, I have developed primers to test the potential phylogenetic utility of a DNA sequence not previously used in systematics studies (pistillata intron; Bailey and Doyle, 1999) in addition to investigating the theoretical implications that different character coding schemes can have on phylogenetic analyses. At present, I am particularly intrigued by the coding of individual-level allelic diversity and duplicate gene copies in simultaneous analyses with morphology or other data sources.
5) Field Studies: I am interested in working with plant groups that are not well collected. In general, these are the taxa that we know the least about and those whose systematics will benefit most from in-depth field and laboratory-based research. For this reason, I have selected Mexican mustards as my primary research focus. Many Mexican states remain poorly explored botanically, and numerous of their mustards grow in small easily overlooked populations. These mustards strike a strong contrast with the many cosmopolitan weedy Brassicaceae that are more familiar to biologists. In addition, Mexican mustards include a substantial portion of the family’s diversity (38 [11%] of the ca. 340 Brassicaceae genera are native to Mexico) and our lack of knowledge for these taxa is another problem in current Brassicaceae systematics. I have established strong working relationships with Mexican researchers (at UNAM) and I plan to continue working on Mexican Brassicaceae.
Bailey, C.D. and J.J. Doyle. 1999. Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Molecular Phylogenetics and Evolution 13: 20-30.Brandham, P.E. and M.J. Doherty. 1998. Genome size variation in the Aloaceae, and angiosperm family displaying karyotypic orthoselection. Annals of Botany 82: 67-73.
Donoghue, M.J. and S. Mathews. 1998. Duplicate genes and the root of angiosperms, with an example using phytochrome sequences. Molecular Phylogenetics and Evolution. 9: 489-500
Mathews, S. and M.J. Donoghue. 1999. The root of angiosperm phylogeny inferred from duplicate phytochrome genes. Science 286: 947-950.Petrov, D. 1997. Slow but steady: reduction of genome size through biased mutation. The Plant Cell 1900-1901.
Price, R. A. 1997. Multiple origins of the genus Arabis. American Journal of Botany 84S: 224.
Simmons, M.P., C.D. Bailey, and K.C. Nixon. accepted-a. Phylogeny reconstruction using duplicate genes. Molecular Biology and Evolution.
Simmons, M.P., C.D. Bailey, and K.C. Nixon. submitted-b. An evaluation of duplicate gene rooting as presented by Donoghue and Mathews (1998). Cladistics.
Thomas, C.A. 1971. The genetic organization of chromosomes. Annual Review of Genetics. 5: 237-256.