Damon P. Little
Cullman Associate Curator of Bioinformatics, Cullman Program for Molecular Systematics
Ph.D., Cornell University
Ithaca, NY USA, 2005
Gymnosperms and Bioinformatics
conifers, phylogenetic analysis, information technology
North America, worldwide
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).
Clugston, J. A. R., M. P. Griffith, G. J. Kenicer, C. E. Husby, M. A. Calonje, D. P. Little, and D. W. Stevenson. 2018. Reproductive Phenology of Zamia L.: a comparison between wild cycads and their cultivated counterparts. Memoirs of The new York Botanical Garden 117 (1): 433–462.
Rousseau, P. P. J. Vorster, D. P. Little, and M. van der Bank. 2018. DNA barcoding Africa’s endemic cycads. Memoirs of The new York Botanical Garden 117 (1): 297–334.
Hernández–León, S., D. P. Little, O. Acevedo–Sandoval1, D. S. Gernandt, R. Rodríguez–Laguna, M. Saucedo–García, O. Arce–Cervantes, R. Razo–Zárate, and J. Espitia–López. 2018. Plant core DNA barcode performance at a local scale: identification of the conifers of the state of Hidalgo, Mexico. Systematics and Biodiversity. 16: 791–806.
Forest, F., E. Baloch, N. A. Brummitt, S. Bachman, J. Moat, S. Ickert–Bond, P. M. Hollingsworth, A. Liston, D. P. Little, S. Mathews, H. Rai, C. Rydin, D. W. Stevenson, P. Thomas, and S. Buerki. 2018. Gymnosperms on the EDGE. Scientific Reports. 8: 6053.
Clugston, J A. R., M. P. Griffith, G. J. Kenicer, C. E. Husby, M. A. Calonje, D. Wm. Stevenson, and D. P. Little. 2016. Zamia (Zamiaceae) phenology in a phylogenetic context: does in situ reproductive timing correlate with ancestry? Edinburgh Journal of Botany 73 (3): 345–370.
Meyer, R. S., B. D. Whitaker, D. P. Little, S.–B. Wu, E. J. Kennelly, C.–L. Long, and A. Litt. 2015. Parallel reductions in phenolic constituents resulting from the domestication of eggplant. Phytochemistry 115: 194–206.
Little, D. P. 2014. Authentication of Ginkgo biloba herbal dietary supplements using DNA barcoding. Genome 57 (9): 513–516.
Gorelick, R., D. L. Fraser, B. J. M. Zonneveld, and D. P. Little. 2014. Cycad (Cycadales) chromosome numbers are not correlated with genome size. International Journal of Plant Sciences 175 (9): 986–997.
Little, D. P. 2014. A DNA mini–barcode for land plants. Molecular Ecology Resources 14 (3): 437–446.
Salinas, N. R. and D. P. Little. 2014. 2matrix: a utility for indel coding and phylogenetic matrix concatenation. Applications in Plant Sciences 2 (1): 1300083.
Salinas, N. R. and D. P. Little. 2013. 2matrix: a utility for indel coding and phylogenetic matrix concatenation. Program distributed by the authors.
Little, D. P. and M. L. Jeanson. 2013. DNA barcode authentication of saw palmetto herbal dietary supplements. Scientific Reports 3: 3518.
Little, D. P., P. Knopf, C. Schulz. 2013. DNA barcode identification of Podocarpaceae—the second largest conifer family. PLoS ONE 8 (11): e81008.
Okunji, C. O., G. I. Giancaspro, N. Sarma, D. H. Reynaud, and D. P. Little. 2013. DNA–based methods for authentication of articles of botanical origin. Pharmacopeial Forum 39 (5) [free registration required].
Meyer, R. S., S. Knapp, A. Litt, K. G. Karol, D. P. Little, and M. Nee. 2013. Reply to J. Samuels: Taxonomic notes on several wild relatives of Solanum melongena L. Molecular Phylogenetics and Evolution 69 (1): 306–307.
Hall, G. S. and D. P. Little. 2013. Within–host competition between barley yellow dwarf–PAV and –PAS. Virus Research 174 (1–2): 148–151.
Salinas, N. R. and D. P. Little. 2012. Electric LAMP: virtual Loop–mediated isothermal AMPlification. ISRN Bioinformatics 2012: 696758.
Salinas, N. R. and D. P. Little. 2012. eLAMP: virtual Loop–mediated isothermal AMPlification. Program distributed by the authors.
Baker, D. A., D. Wm. Stevenson, and D. P. Little. 2012. DNA barcode identification of black cohosh herbal dietary supplements. The Journal of AOAC International 95 (4): 1023–1034.
Knopf, P., C. Schulz, D. P. Little, T. Stützel, and D. Wm. Stevenson. 2012. Relationships within Podocarpaceae based on DNA sequence, anatomical, morphological, and biogeographical data. Cladistics 28 (3): 271–299.
Meyer, R. S., K. G. Karol, D. P. Little, M. H. Nee, and A. Litt. 2012. Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication. Molecular Phylogenetics and Evolution 63 (3): 685–701.
Griffith, M. P., M. A. Calonje, D. Wm. Stevenson, C. E. Husby, and D. P. Little. 2012. Time, place, and relationship: cycad phenology in phylogenetic and biogeographic context. Memoirs of The New York Botanical Garden 106 (1): 59–81.
Little, D. P. 2012. BRONX: Barcode Recognition Obtained with Nucleotide eXposés 2.0. Program distributed by the author.
Lee, E. K., A. Cibrian–Jaramillo, S.–O. Kolokotronis, M. S. Katari, A. Stamatakis, M. Ott, J. C. Chiu, D. P. Little, D. Wm. Stevenson, W. R. McCombie, R. A. Martienssen, G. Coruzzi, and R. DeSalle. 2011. A functional phylogenomic view of seed plants. PLoS genetics 7 (12): e1002411.
Jeanson, M. L., J.–N. Labat, and D. P. Little. 2011. DNA Barcoding: a new tool for palm taxonomists? Annals of Botany 108 (8): 1445–1451.
Nagalingum, N. S., C. R. Marshall, T. B. Quental, H. S. Rai, D. P. Little, and S. Mathews. 2011. Recent synchronous radiation of a living fossil. Science 334 (6057): 796–799.
Little, D. P. 2011. DNA barcode sequence identification incorporating taxonomic hierarchy and within taxon variability. PLoS ONE 6 (8): e20552.
Stoeckle, M. Y., C. C. Gamble, R. Kirpekar, G. Young, S. Ahmed, and D. P. Little. 2011. Commercial teas highlight plant DNA barcode identification successes and obstacles. Scientific Reports 1: 42.
Little, D. P., P. Thomas, H. T. Nguyễn, and L. K. Phan. 2011. Before it had a name: diagnostic characteristics, geographic distribution, and the conservation of Cupressus tonkinensis (Cupressaceae). Brittonia 63 (2): 171–196. [erratum: Brittonia 64 (1): 102.]
Hollingsworth, P. M., S. W. Graham, and D. P. Little. 2011. Choosing and using a plant DNA barcode. PLoS ONE 6(5): e19254.
Schulz, C., D. P. Little, D. Wm. Stevenson, A. Nowogrodzki, and D. Paquiot. 2010. Growth and care instructions of a new model species—the lycophyte Selaginella apoda. American Fern Journal 100 (3): 167–171.
Hall, G. S., J. S. Peters, D. P. Little, and A. G. Power. 2010. Plant community diversity influences vector behaviour and Barley yellow dwarf virus population structure. Plant Pathology 59 (6): 1152–1158.
Little, D. P. 2010. A unified index of sequence quality and contig overlap for DNA barcoding. Bioinformatics 26 (21): 2780–2781.
Little, D.P. 2010. B: an index of sequence quality and contig overlap for DNA barcoding. Program distributed by the author.
Schulz, C., D. P. Little, D. Wm. Stevenson, D. Bauer, C. Moloney, and T. Stützel. 2010. An overview of the morphology, anatomy, and life cycle of a new model species―the lycophyte Selaginella apoda (L.) Spring. International Journal of Plant Sciences 171 (7): 693–712. [cover illustration]
Cibrián–Jaramillo, A., J. E. De la Torre–Bárcena, E. K. Lee, M. S. Katari, D. P. Little, D. W. Stevenson, R. Martienssen, G. M. Coruzzi, and R. DeSalle. 2010. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution. Genome Biology and Evolution 2: 225–239.
Little, D. P. 2009. BRONX: Barcode Recognition Obtained with Nucleotide eXposés. Program distributed by the author.
Hollingsworth P. M., L. L. Forrest, J. L. Spouge, M. Hajibabaei, S. Ratnasingham, M. van der Bank, M. W. Chase, R. S. Cowan, D. L. Erickson, A. J. Fazekas, S. W. Graham, K. E. James, K.-J. Kim, W. J. Kress, H. Schneider, J. van Alphen Stahl, S. C. H. Barrett, C. van den Berg, D. Bogarin, K. S. Burgess, K. M. Cameron, M. Carine, J. Chacón, A. Clark, F. Conrad, D. S. Devey, J. J. Clarkson, C. S. Ford, T. A. J. Hedderson, M. L. Hollingsworth, B. C. Husband, L. J. Kelly, P. R. Kesanakurti, J. S. Kim, Y. D. Kim, R. Lahaye, H.-L. Lee, D. G. Long, S. Madriñán, O. Maurin, I. Meusnier, S. G. Newmaster, C.-Wu Park, D. M. Percy, G. Petersen, J. E. Richardson, G. A. Salazar, V. Savolainen, O. Seberg, M. J. Wilkinson, D.-K. Yi, and D. P. Little. 2009. A DNA Barcode for Land Plants. Proceedings of the National Academy of Sciences 106 (31): 12794–12797.
Little, D. P. 2009. Simple pairwise matching for DNA barcoding. Program distributed by the author.
Martin, C. V., D. P. Little, R. Goldenberg, and F. A. Michelangeli. 2008. A phylogenetic evaluation of Leandra (Miconieae, Melastomataceae): a polyphyletic genus where the seeds tell the story, not the petals. Cladistics 24 (3): 315–327.
Hall, G. S. and D. P. Little. 2007. Relative quantitation of virus population size in mixed genotype infections using sequencing chromatograms. The Journal of Virological Methods 146 (1–2): 22–28.
Sass, C., D. P. Little, D. Wm. Stevenson, and C. D. Specht. 2007. DNA Barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of cycads. PLoS ONE 2 (11): e1154.
Douglas, A. Wm., D. Wm. Stevenson, and D. P. Little. 2007. Ovule development in Ginkgo biloba L. with emphasis on the collar and nucellus. International Journal of Plant Sciences 168 (9):1207–1236. [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]
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. 2007. degenbar: a simple SIDE (sequence identification engine). Program distributed by the author.
Little, D. P. 2007. DOME ID (Diagnostic Oligo Motifs for Explicit IDentification): a simple SIDE (sequence identification engine). Program distributed by the author.
Little, D. P. 2007. ATIM (Alignment-free Tree-based Identification Method): a simple SIDE (sequence identification engine). Program distributed by the author.
Little, D. P. and G. S. Hall. 2006. polySNP: an analysis tool for quantitative sequencing. Program distributed by the authors.
Little, D. P. 2006. Evolution and circumscription of the true cypresses (Cupressaceae: Cupressus). Systematic Botany 31 (3): 461–480.
Little, D. P. 2005. 2xread: a simple indel coding tool. Program distributed by the author.
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., 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.
Little, D. P. 2004. Documentation of hybridization between Californian cypresses: Cupressus macnabiana × sargentii. Systematic Botany 29 (4): 825–833.
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.