The New York Botanical Garden


Damon P. Little

Cullman Associate Curator of Bioinformatics, Cullman Program for Molecular Systematics

Ph.D., Cornell University
Ithaca, NY USA (2005)
Expertise: conifers, phylogenetic analysis, information technology


My research activities can be divided into two intertwining areas: (1) the application and development of novel bioinformatic tools to advance morphological, anatomical, DNA barcoding, and molecular systematic studies and (2) organismal studies focused on the systematics and character evolution of gymnosperms. Although one might view these two areas as disparate and unrelated, they inform and shape one–another—the needs of the organismal studies drive software development, the resulting software allows for efficient, novel, and innovative organismal research that in turn requires additional software development.

1. BIOINFORMATICS. During my time in graduate school, I learned to program in PERL and SQL. My initial goal was to automate the analysis, and output of large quantities organismal data. I wrote a suite of PERL scripts that operate in conjunction with a MySQL database. A web–based interface was used to collect and georeference specimen data; link individual morphological and molecular measurements to specimens; link photographs to specimens and character states; and output the data in the form of publication–ready text descriptions, tabular descriptions, summary graphics, identification keys, and distribution maps (chapter three of my dissertation was written by this software). The production of publication–ready output and the specimen–based nature of this package set it apart from other identification and monographic software packages (e.g. DELTA, Linnaeus II, TAXIS) which use taxa as the basic unit of description thereby preventing the user from easily tracking datum sources and changing species circumscriptions as new data become available. I am continuously refining this software.

DNA BARCODING. I have published a performance evaluation of existing DNA barcode identification procedures and I have designed and implemented several novel algorithms designed to produce more accurate results (Little and Stevenson 2007). I was tasked by the Plant Working Group of Consortium for the Barcode of Life (CBoL) to evaluate the relative merits of seven competing plant–specific DNA markers. I designed and implemented a software package that quantified relative identification success among these markers (PWG 2009). These data were used to select a pair of CBoL sanctioned markers for plant DNA barcoding. I have also developed an index of DNA sequence quality specifically tailored to the needs of DNA barcoding (Little 2010).

DNA SEQUENCE ANALYSIS. Another aspect of my research focuses on extracting additional data from automated Sanger sequence traces. I have produced a PERL script that calculates peak area from sequence chromatograms so that quantitative sequencing can be more widely employed for the estimation of relative template frequency in pooled DNA samples. Applications range from viral population genetics (e.g. Hall and Little 2007, Hall et al. 2010) to quantifying concerted evolution.

2. 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. Much of my research focuses on Cupressaceae.

Character Evolution. Within Callitropsis, Cupressus, and Juniperus, I am interested in the evolution of elaborations around the leaf transfusion tracheid pits. Currently, I am documenting the occurrence and size of vermiform thickenings in an attempt to understand the environmental and evolutionary factors that contributed to the phylogenetic distribution of this character. Preliminary data suggests that the size of the thickenings is positively correlated with summer climate—particularly factors relating to water availability and temperature. I also would like to undertake comparative studies of leaf organogenesis and pollination biology.

Population Level Studies. Within Callitropsis, nine to 25 New World taxa have been recognized. In several instances, commonly recognized wide–spread species are morphologically very similar to highly restricted populations that some, but not all, taxonomists consider to be distinct species, subspecies, or varieties. Nine of these endemics are included in the IUCN red list. Thus, it is important to determine if the endemics are genetically distinct from the wide–spread species for informed conservation and management decisions to be made. I have developed primers for simple sequence repeats (SSR a.k.a. microsatellite) that are single copy and cross amplify in all Callitropsis (tested on 95 individuals representing 46 populations). I intend to produce biologically–meaningful species delimitations within Callitropsis by sampling a large number of individuals (4,020) and populations (134) for these loci along with a suite of morphological measurements. The analysis of allele distributions in combination with morphological measurements will result in repeatable and robust species circumscriptions that will form the basis for a taxonomic monograph (with companion electronic species pages).

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.

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