Randy Smallís Research Interests

Randy Small’s Research Interests

Plant Molecular Systematics

The field of molecular systematics uses data from DNA sequences to analyze relationships among species. An understanding of relationships among species allows systematists to produce useful taxonomic classification systems, as well as to study biologically important phenomena such as the evolution of morphological characters, biogeography, and speciation mechanisms.

Plant cells have three different genomes that contain information that could be exploited to analyze species relationships: the chloroplast, mitochondrial, and nuclear genomes. These three different genomes differ greatly in size, structure, and evolutionary rate. Thus, different genomes may be useful for different kinds of systematic studies. Plant molecular systematic studies have relied primarily on data from the chloroplast genome, as well as from ribosomal DNA sequences of the nuclear genome. The remainder of the nuclear genome, however, has been left relatively unexplored by molecular systematists, primarily because of the more complex genetic architecture of the nuclear genome.

Part of my research interests are in exploring the utility of nuclear genes for systematic studies. In particular, I am focusing on two gene families: the alcohol dehydrogenase (Adh) gene family; and the granule-bound starch synthase (GBSSI) gene family. The plant family I work in is Malvaceae, and in particular I am interested the cotton genus (Gossypium), and in the large and heterogeneous genus Hibiscus.

In Gossypium, Adh sequences have proven to be extremely useful in some cases, providing significantly more information than either chloroplast or ribosomal DNA sequences. In other cases, Adh sequences provide relatively similar levels of resolution when compared to other sequences. With funding from the National Science Foundation I am beginning to explore the phylogenetic utility of the Adh gene family in Hibiscus section Furcaria (a circumtropical section with 200+ species) as well.

Studies of the GBSSI gene family in Malvaceae are in the preliminary stages, but initial data from Gossypium and Hibiscus section Muenchhusia (the North American Rose Mallows) suggest that GBSSI is likely to be a good tool for unravelling species-level phylogenetic questions. I am in the process of characterizing the GBSSI gene family from a collection of species that represent all of the tribes of the Malvaceae to determine the generality and limits of its usefulness.

Systematics Papers

Cronn, R.C, R.L. Small, T. Haselkorn, and J.F. Wendel. 2002. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. American Journal of Botany 89:707-725

St. Hilaire, R., W.R. Graves, and R.L. Small. 2001. Variation in TaqI-digested DNA of Sugar and Black Maples is independent of taxon and plant origin. HortScience 36:1327-1328

Small, R.L. and R.J. Hickey. 2001. Systematics of the Northern Andean Isoetes karstenii complex. American Fern Journal 91:41-69

Small, R.L. and J.F. Wendel. 2000. Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium L.). Molecular Phylogenetics and Evolution 16:73-84

Small, R.L, J.A. Ryburn, R.C. Cronn, T. Seelanan, and J.F. Wendel. 1998. The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. American Journal of Botany 85:1301-1315

Baum, D.A., R.L. Small, and J.F. Wendel. 1998. Biogeography and floral evolution of Baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Systematic Biology 47:181-207

Small, R. and R.J. Hickey. 1997. Levels and patterns of genetic variation in Isoëtes karstenii with observations on I. palmeri. American Fern Journal 87:104-115

Molecular Evolution

Molecular evolutionary studies seek to understand the processes by which DNA sequences change and to infer historical genetic events from the patterns observed in contemporary data. In this field, my research interests are in the evolutionary dynamics of nuclear gene families, and in patterns of nucleotide diversity in nuclear-encoded genes.

Almost all nuclear genes exist in gene families - groups of genes with a common evolutionary origin that (usually) have similar functions. These gene families vary from just a few to hundreds of copies per genome. One of the central questions is why does gene copy number vary so considerably both across gene families and across species? New genes must be "born" (via gene duplication) and old genes must "die" (become pseudogenized or deleted) for such variation in copy number to occur, but as yet we have little empirical information on the frequency or underlying causes of these phenomena. I am using the phylogenetically well-characterized cotton genus Gossypium to examine rates and patterns of gene family evolution, with particular attention to the alcohol dehydrogenase (Adh) gene family.

I am also interested in levels and patterns of genetic diversity at the DNA sequence level ("nucleotide diversity"). Levels of nucleotide diversity can be used to infer what molecular evolutionary processes have been acting on a particular sequence, and to compare genes both within a given genome, as well as between species. Genes that are highly conserved are likely to be under strong purifying selection that maintains a particular gene function. At the other end of the spectrum, genes (especially duplicated genes) may undergo positive Darwinian selection resulting a new function or expression pattern. Comparisons of orthologous genes between species may provide clues as to how those species differ; comparisons of paralogous genes within species may provide clues as to how that particular gene family have evolved.

Finally, the phenomenon of polyploidy throws an interesting twist into studies of molecular evolution because whole genomes are immediately duplicated providing complete genetic redundancy and thus allowing for the possibility of divergence in function of the duplicated copies. The cotton genus (Gossypium) provides an excellent model system for studying polyploidy induced molecular evolutionary changes because it contains both allotetraploid species and good models of their diploid progenitors. Thus the null hypothesis of additivity and evolutionary stasis in the polyploid can be examined by comparing sequences of the diploid progenitors to sequences from the polyploid. To test this null hypothesis using diploid and tetraploid Gossypium as a model, I am continuing to explore the Adh gene family, and studies have also been initiated on the GBSSI gene family, and a group of floral homeotic MADS-box genes.

Molecular Evolution Papers

Small, R.L. and J.F. Wendel. 2002. Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Molecular Biology and Evolution 19:597-607
Small, R.L. and J.F. Wendel. 2000. Copy number lability and evolutionary dynamics of the Adh gene family in diploid and tetraploid cotton (Gossypium) Genetics 155:1913-1926
Small, R.L. and J.F. Wendel. 2000. Phylogeny, duplication, and intraspecific variation of Adh sequences in New World diploid cottons (Gossypium L.). Molecular Phylogenetics and Evolution 16:73-84
Wendel, J.F., R.L. Small, R.C. Cronn, and C. L. Brubaker. 1999. Genes, jeans, and genomes: Reconstructing the history of cotton. In: Plant evolution in man-made habitats. Proceedings of VIIth international symposium of the international organization of plant biosystematists (L.W.D. van Raamsdonk and J.C.M. den Nijs, eds.) Hugo de Vries Laboratory, Amsterdam, The Netherlands
Cronn, R.C., R.L. Small, and J.F. Wendel. 1999. Duplicated genes evolve independently after polyploid formation in cotton. Proceedings of the National Academy of Sciences, USA 96:14406-14411
Small, R.L., J.A. Ryburn, and J.F. Wendel. 1999. Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Molecular Biology and Evolution 16:491-501