Cullman Curator of Bioinformatics, Cullman Program for Molecular Systematics
Ph.D., Cornell University
Ithaca, NY USA, 2005
gymnosperms and bioinformatics
conifers, phylogenetic analysis, information technology
My ongoing research program includes a multitude of projects spanning biodiversity informatics, phylogenomics, floristics, molecular systematics, monography, bioinformatics, and Artificial Intelligence (AI). The four projects I am most intensely working on at the moment are: a floristics project in northern Myanmar, a webapp for documenting biodiversity called Monographia, a gymnosperm phylogenomics project, and a herbarium specimen AI called iCurate.
As part of Kate Armstrong’s project to produce a checklist for Myanmar’s Northern Forest Complex, I have been on major collecting trips to Htamanthi Wildlife Sanctuary (Sagaing Region), Hponganrazi Wildlife Sanctuary (Kachin State), and Hkakaborazi National Park (Kachin State) resulting in more than 16.6 thousand specimens. My role in this project has largely been in the field (collecting, pressing, and drying) and in–country specimen handling (sorting and packing).
Monographia is a web app that automates descriptive systematic studies. It is designed to facilitate wide–scale collaborative research and increase efficiency via automation and data reuse: Monographia can collect, view, aggregate, and curate specimen data; link specimen data to individual morphological and molecular observations; and provide dynamically compiled data summaries in multiple formats and technical levels along with diagnostic interactive graphics and cross references to other data types.
I am part of a New York Plant Genomics Consortium team that is sequencing five gymnosperm genomes. Using these genomes and existing public data, we are making five pairs of genome comparisons: each pair consists of a “living fossil” and a more recently evolved relative in order to identify how these massive and complex genomes function, adapt, and evolve. Darwin first used the term “living fossils” to describe a group of gymnosperms that had apparently survived morphologically unchanged for hundreds of millions of years—we hope that these genome comparisons will illuminate underlying reasons for such resilience in the face of massive environmental changes. My role in the project is largely analytical: I am part of a team that is working out the best way to build and quickly analyze massive phylogenomic datasets. I am also working on an AI that will produce functional annotations for genes that are not similar to any well–annotated genes.
Along with collaborators, I have recently begun to work intensely on a project that seeks to produce an easy–to–use online tool, iCurate, that will provide species–level identification of herbarium specimen images. It is hoped that iCurate will be used by herbaria world–wide to automatically identify their own specimen images allowing for the curation of plant groups for which they lack expertise. The iCurate tool will be built, optimized, and expanded through a stepwise process that uses crowd–sourced AI models submitted to a series of online Kaggle competitions. The competitions will use an ever increasing number of species and images for model training eventually including all public vascular plant specimen images in GBIF and iDigBio (ca. 84% of species). A major research aim of this project is to design an AI architecture capable of both identifying known species but also capable of indicating that a specimen image is highly dissimilar to any of the species known to the AI and thus potentially a new species.
de Lutio, R., J.Y. Park, K.A. Watson, S. D’Aronco, J.D. Wegner, J.J. Wieringa, M. Tulig, R.L. Pyle, T.J. Gallaher, G. Brown, G. Guymer, A. Franks, D. Ranatunga, Y. Baba, S.J. Belongie, F.A. Michelangeli, B.A. Ambrose, and D.P. Little. 2022. The Herbarium 2021 Half–Earth challenge dataset and machine learning competition. Frontiers in Plant Science 12: 787127.
Zumajo–Cardona, C., D.P. Little, D. Stevenson, B.A. Ambrose. 2021. Expression analyses in Ginkgo biloba provide new insights into the evolution and development of the seed. Scientific Reports 11: 21995.
Paradiso, L. and D.P. Little. 2021. Authentication of garlic (Allium sativum L.) supplements using a trnLUAA mini–barcode. Genome 64 (11): 1021–1028.
Diaz–Silveira, G. L., J. Deutsch, and D. P. Little 2021. DNA Barcode authentication of devil’s claw herbal dietary supplements. Plants 10 (10): 2005.
de Lutio, R., D. Little, B. Ambrose, and S. Belongie. 2021. The Herbarium 2021 half–earth challenge dataset. FGVC8 Workshop at CVPR 2021. arXiv:2105.13808.
Little, D.P. 2020. Recognition of Latin scientific names using artificial neural networks. Applications in Plant Sciences 8 (7): e11378.
Little, D.P., M. Tulig, K.C. Tan, Y. Liu, S. Belongie, C. Kaeser–Chen, L.M. Kelly, F.A. Michelangeli, B.M. Thiers, K. Panesar, R.V. Guha, and B.A. Ambrose. 2020. An algorithm competition for automatic species identification from herbarium specimens. Applications in Plant Sciences 8 (6): e11365.
Little, D.P. 2019. QUAESITOR: a tool to locate Latin scientific names in vernacular text. Program distributed by the author.
Meyer, R.S., D.P. Little, Whitaker B.D., and A. Litt. 2019. The genetics of eggplant nutrition. Pp. 23–32 in M. Chapman, ed. Eggplant Genome.
Peng, H., R.S. Meyer, T. Yang, B.D. Whitaker, F. Trouth, L. Shangguan, J. Huang, A. Litt, D.P. Little, H. Ke, and W.M. Jurick II. 2019. A novel hydroxycinnamoyl transferase for synthesis of hydroxycinnamoyl spermine conjugates in plants. BMC Plant Biology 19: 261.
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–Sandoval, 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.