NYBG.org: Damon P. Little Profile


	Science Home ... About Us ... Scientists ... Profile


	Web Sites

	quantitative sequencing online key to Cupressaceae Barrington‘s Polystichum research gymnosperm database Adams‘ Juniperus research TNT (Tree analysis using New Technology)

Damon P. Little

Assistant Curator of Bioinformatics, Institute of Systematic Botany, Cullman Program for Molecular Systematic Studies
Ph.D., Cornell University
Ithaca, NY USA (2005)
"Evolution and circumscription of the true cypresses (Cupressaceae: Cupressus and Callitropsis): a combined molecular and morphological approach"
Expertise: conifers, phylogenetic analysis, information technology

dlittle@nybg.org

Little CV

Profile

My research interests can be divided into three intertwining areas: (1) Organismal studies focused on the systematics of gymnosperms; (2) the theory and practice of phylogenetic analysis; and (3) the application of information technology to morphological, anatomical, DNA barcoding, and molecular systematic studies (bioinformatics).

1. ORGANISMAL STUDIES. I am most interested in conducting research that integrates data from traditional (e.g., anatomical, developmental, morphological) and contemporary (e.g., DNA sequence, gene expression) sources to elucidate phylogenetic patterns and understand character evolution. Currently, much of my research focuses on Cupressaceae—a family of conifers that includes redwoods (Metasequoia, Sequoia, and Sequoiadendron), arborvitae (Thuja), junipers (Juniperus), and cypress (Callitropsis and Cupressus). Members of the family are widely cultivated for their attractive foliage and pleasant “cedar” scent. Their wood is of some economic importance due to its durability and resistance to rot (used in pencils, cedar chests, siding, decks, roofing shingles, etc.).

2. PHYLOGENETIC THEORY. The theory and practice of phylogenetic analysis is of great interest to me—particularly the properties of various tree search strategies/methods and support measures. I am in the process of testing the relative efficiency of several recently proposed methods (e.g., ratchet, tree fusion, Metropolis coupled Markov chain Monte Carlo, etc.) with the aim of developing general recommendations for search strategy. I have co–authored a forthcoming DNA sequence alignment program (with K. C. Nixon) that aligns sequences using an internally constant optimality criterion that is also consistent with the parsimony optimality criterion currently used for phylogenetic analysis. As a side benefit, our implementation of this criterion is much faster than other currently available algorithms.

3. INFORMATION TECHNOLOGY/BIOINFORMATICS. During my time in graduate school, I learned to program in C, C++, PERL, and SQL. To date, I have used this programing knowledge to undertake a performance evaluation of existing DNA barcoding algorithms as well as implement two novel barcoding procedures. In addition, I have produced a PERL script for automatically extracting peak area or height data from sequence chromatograms so that quantitative sequencing data can be more widely employed for the estimation of relative template frequency in pooled DNA samples. I am also interested in applying this programming knowledge to automate some of the menial tasks associated with the storage, analysis, and output of empirical data with which all systematists are saddled with. Thus far, I have written a series of PERL scripts that when operated in conjunction with a SQL database can be used to gather and store morphological and taxonomic data via a web browser interface. Additional scripts are used to generate and format taxonomic descriptions from these data. These scripts were used to generate range maps and write the taxonomic descriptions in my dissertation. After some modifications and improvements, I plan to make these scripts available to the botanical community.

Selected Publications

Tehler, A., D. P. Little, and J. S. Farris. 2003. The full–length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi. Mycological Research 107 (8): 901–916.

Little, D. P. and D. S. Barrington. 2003. Major evolutionary events in the origin and diversification of the fern genus Polystichum (Dryopteridaceae). American Journal of Botany 90 (3): 508–514.

Little, D. P. 2004. Documentation of hybridization between Californian cypresses: Cupressus macnabiana × sargentii. Systematic Botany 29 (4): 825–833.

Little, D. P., A. E. Schwarzbach, R. P. Adams, and C. F. Hsieh. 2004. The circumscription and phylogenetic relationships of Callitropsis and the newly described genus Xanthocyparis (Cupressaceae). American Journal of Botany 91 (11): 1872–1881.

Davis, J. I, K. C. Nixon, and D. P. Little. 2005. The limits of conventional cladistic analysis. Pp. 119–147 in V. A. Albert, ed. Parsimony, Phylogeny, and Genomics. Oxford: Oxford University Press.

Little, D. P. 2006. Evolution and circumscription of the true cypresses (Cupressaceae: Cupressus). Systematic Botany 31 (3): 461–480.

Little, D. P. and G. S. Hall. 2006. polySNP: an analysis tool for quantitative sequencing. Program distributed by the authors

Little, D. P. and D. Wm. Stevenson. 2007. A comparison of algorithms for identification of specimens using DNA barcodes: examples from gymnosperms. Cladistics 23 (1): 1–21. [cover illustration]

Little, D. P., R. C. Moran, E. D. Brenner, and D. Wm. Stevenson. 2007. Nuclear genome size in Selaginella. Genome 50 (4): 351–356. [cover illustration]