Rockefeller University

Program for the Human Environment

DNA Barcoding

A Klee diagram indicating correlations among indicator vectors for 12 animal groups

Ever since Carl Linnaeus began systematically classifying living things 250 years ago, biologists have looked at various features—color, shape, even behavior—to identify animals and plants. From insects and birds to trees and grasses, evidence now shows that short DNA sequences from a uniform locality on the genome can be a barcode of life for distinguishing species. First proposed by Paul Hebert, DNA barcoding offers a simple, standardized approach to species identification. DNA barcoding democratizes access to the storehouse of biological knowledge about organisms, helps solve identification mysteries that puzzle experts, and speeds writing the Encyclopedia of Life. Beginning with the early DNA barcode workshops in 2003, we are involved in helping apply this new tool to explore and understand biodiversity.

For an emphasis on the earlier period of barcode science, see the Barcode of Life homepage at https://phe.rockefeller.edu/barcode.

We continue to be keenly interested in understanding and visualizing the totality of DNA sequence space, as if looking at stars and galaxies, for which our work on Klee diagrams may prove valuable.

While DNA barcoding typically involves collecting tissue from which one extracts relevant DNA, we have become increasingly interested in the loose DNA in water, aquatic eDNA, and especially the loose DNA in seawater, marine eDNA. For more information see our pages about aquatic environmental DNA.

We also help out from time to time with the efforts of revive@restore to enhance biodiversity through the genetic rescue of endangered and extinct species.

About the icon – A Klee diagram indicating correlations among indicator vectors for 12 animal groups; see https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100755

edna

Details on our Aquatic DNA project (a collaboration with Monmouth University) are at https://phe.rockefeller.edu/barcode/blog/nycnj-aquatic-vertebrate-edna-project/ This project aims to detect fish and other vertebrates in freshwater and marine habitats by analyzing the traces of DNA they leave behind in the water.

Publications about DNA Barcoding

Matthew C. Yates, Taylor M. Wilcox, M. Y. Stoeckle, Daniel D. Heath. Interspecific allometric scaling in eDNA production among northwestern Atlantic bony fishes reflects physiological allometric scaling (PDF). Environmental DNA 2022 DOI: 10.1002/edn3.381 abundance, allometric scaling, allometry, biomass, eDNA, fishes

Mark Y Stoeckle, Jason Adolf, Jesse H Ausubel, Zach Charlop-Powers, Keith J Dunton, Greg Hinks. Current laboratory protocols for detecting fish species with environmental DNA optimize sensitivity and reproducibility, especially for more abundant populations [external link]. ICES Journal of Marine Science vol. fsab273, 2022 https://doi.org/10.1093/icesjms/fsab273

Mark Y. Stoeckle, Jesse H. Ausubel, Michael Coogan. 12S gene metabarcoding with DNA standard quantifies marine bony fish environmental DNA, identifies threshold for reproducible detection, and overcomes distortion due to amplification of non-fish DNA (PDF). , Environmental DNA, (eds.). DOI: 10.1002/edn3.376 (11 November): 2022 bottom trawl survey, coastal ecosystem, eDNA, environmental DNA, marine fish, metabarcoding, quantitative metabarcoding

Alan Curry and Jesse H. Ausubel. Biological information for the new blue economy and the emerging role of eDNA (PDF). Chapter 13 (pp. 249-258) in Preparing a Workforce for the New Blue Economy: People, Products, and Policies, Liesl Hotaling and Richard W. Spinrad, (eds.). Elsevier, 2021 https://doi.org/10.1016/B978-0-12-821431-2.00030-5 aquatic eDNA

JH Ausubel and DS Thaler. Plant and Animal Diversity Is Declining, But What About Microbial Diversity? [external link]. Pp. 11 May in RealClear Science 2021 biodiversity

MY Stoeckle, MD Mishu and Z Charlop-Powers. Improved Environmental DNA Reference Library Detects Overlooked Marine Fishes in New Jersey, United State [external link]. Frontiers in Marine Science 7 (226): 2020 edna

MY Stoeckle , MD Mishu, Z Charlop-Powers. GoFish: A versatile nested PCR strategy for environmental DNA assays for marine vertebrates [external link]. Plos One 2018

MY Stoeckle, DS Thaler. Why Should Mitochondria Define Species? (PDF). Human Evolution 33 (1-2): 1-30, 2018 Species evolution, mitocondrial evolution, speciation, human evolution

MY Stoeckle, L Soboleva, Z Charlop-Powers. Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary [external link]. PLoS ONE 12 (4): 2017 e0175186. https://doi.org/10.1371/journal.pone.0175186

MS Stoeckle. Fishing for DNA: Free-floating eDNA identifies presence and abundance of ocean life [external link]. The Conversation 2017

DS Thaler, MY Stoeckle. Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies [external link]. Ecology and Evolution 6 (19): 6824–6835, 2016

C von Beeren, MY Stoeckle, J Xia , G Burke, DJC Kronauer. Interbreeding among deeply divergent mitochondrial lineages in the American cockroach (Periplaneta americana). [external link]. Pp. 8297 in Scientific Reports vol. 5, 2015

MY Stoeckle, DS Thaler. DNA Barcoding Works in Practice but Not in (Neutral) Theory [external link]. Plos One 9 (7): e100755, 2014 barcode, dna barcode, barcoding, dna barcoding

MY Stoeckle. Barcoding Life Highlights 2013. Barcoding Life Highlights, 2013 barcode, dna barcode, barcoding, dna barcoding

Stoeckle, MY. DNA Barcoding ready for breakout [external link]. GeneWatch 26 (5): 2013 barcode, dna barcode, barcoding, dna barcoding

MY Stoeckle, C Coffran. TreeParser-Aided Klee Diagrams Display Taxonomic Clusters in DNA Barcode and Nuclear Gene Datasets [external link]. Nature Scientific Reports 3 (2635): 2013 barcode, dna barcode, barcoding, dna barcoding

DA Lijtmaer, KCR Kerr, MY Stoeckle, and PL Tubaro. DNA Barcoding Birds: From Field Collection to Data Analysis (PDF). Chapter 7 (pp. 127–152) in Methods in Molecular Biology (Methods and Protocols), WJ Kress and DL Erickson, (eds.). vol. 858, Humana Press, Totowa, NJ, 2012 https://doi.org/10.1007/978-1-61779-591-6_7 barcode, dna barcode, barcoding, dna barcoding

MY Stoeckle, KCR Kerr. Frequency Matrix Approach Demonstrates High Sequence Quality in Avian BARCODEs and Highlights Cryptic Pseudogenes [external link]. PLoS ONE 7 (8): e43992, 2012 barcode, dna barcode, barcoding, dna barcoding

MY Stoeckle, J Chenery, and D Schindel. Barcoding Life Highlights 2011 (PDF). Barcoding Life Highlights, 2011 barcode, dna barcode, barcoding, dna barcoding

MY Stoeckle, CC Gamble, R Kirpekar, G Young, S Ahmed and DP Little. Commercial Teas Highlight Plant DNA Barcode Identification Successes and Obstacles [external link]. Nature Scientific Reports 1:42 2011 BIOINFORMATICSEARTH AND ENVIRONMENTALSCIENCESPLANT SCIENCESBIODIVERSITYbarcode, dna barcode, barcoding, dna barcoding

DE Schindel, MY Stoeckle, CM Milensky, M Trizna, BK Schmidt, CA Gebhard, GR Graves. Project Description: DNA Barcodes of Bird Species in the National Museum of Natural History, Smithsonian Institution, USA [external link]. Pp. 87–91 in ZooKeys vol. 152, 2011 Barcode, Birds, dna barcode, barcoding, dna barcoding

A Johnsen, E Rindal, PGP Ericson, D Zuccon , KCR Kerr, MY Stoeckle, JT Lifjeld. DNA barcoding of Scandanavian birds reveals divergent lineages in trans-Atlantic species (PDF). J Ornithol 151 (3): 565–578, 2010 Birds, barcode, dna barcode, barcoding, dna barcoding

MJ Raupach, JJ Astrin, K Hannig, MK Peters, MY Stoeckle, JW Waegele. Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes [external link]. Front Zool 7 (26): 2010 barcode, dna barcode, barcoding, dna barcoding

L Sirovich, MY Stoeckle, Y Zhang. Structural analysis of biodiversity [external link]. PLoS ONE 5 (2): e9266, 2010 barcode, dna barcode, barcoding, dna barcoding

JH Ausubel. A botanical macroscope [external link]. Proc Natl Acad Sci U S A 106 (31): 12569–12570, 2009 barcode, dna barcode, barcoding, dna barcoding, taxonomy, biodiversity, Horizontal Genomics, species

MY Stoeckle, K Winker. A global snapshot of avian tissue collections: state of the enterprise (PDF). Auk 126 (3): 684–687, 2009 barcode, dna barcode, barcoding, dna barcoding, taxonomy, biodiversity

L Sirovich, MY Stoeckle, Y Zhang. A scalable method for analysis and display of DNA sequences [external link]. PLoS ONE 4 (10): e7051, 2009 DNA Barcoding, Klee diagram

MY Stoeckle, PDN Hebert. Barcode of life (PDF). Pp. 82–88 in Sci Am vol. 299, 2008 barcode, dna barcode, barcoding, dna barcoding

K Stoeckle, L Strauss. High school students track down fish fraud (PDF). Pp. 34 in Pacific Fishing September, 2008 barcode, dna barcode, barcoding, dna barcoding

NS Sodhi, D Astuti, AC Diesmos, P Ericson, N Fernandopulle, S Kotagama, E Kudavidanege, HC Lim, B Lee, SLH Lim, Y Lin, DJ Lohman, W Meckvichai, H Miranda, RG Moyle, P Ong, KA Pan, D Prawiradilaga, MA Rahman, A Rahmani, FH Sheldon, MY Stoeckle, S Sulandari. Barcoding Indo-Malayan birds (PDF). Pp. 397–398 in Raffles Bull Zool vol. 55, 2007 barcode, dna barcode, barcoding, dna barcoding, birds

KCR Kerr, MY Stoeckle, CJ Dove, LA Weigt, CM Francis, PDN Hebert. Comprehensive DNA barcode coverage of North American birds [external link]. Pp. 535–543 in Mol Ecol Notes vol. 7, 2007

MY Stoeckle, PE Waggoner, JH Ausubel. Barcoding Life, Illustrated: Goals, rationale, results (PDF). Consortium for the Barcode of Life (CBOL) 2005 barcode, dna barcode, barcoding, dna barcoding

MY Stoeckle, PE Waggoner, JH Ausubel. Barcoding Life: Ten Reasons (PDF). Consortium for the Barcode of Life (CBOL) 2004 Brochure barcode, dna barcode, barcoding, dna barcoding

PDN Hebert, MY Stoeckle, T Zemlak, CM Francis. Identification of birds through DNA barcodes [external link]. PLoS Biology 2 (10): 312, 2004 DNA Barcoding, biodiversity, taxonomy, species

MY Stoeckle. Taxonomy, DNA, and the bar code of life (PDF). BioScience 53 (9): 2–3, 2003 barcode, dna barcode, barcoding, dna barcoding, biodiversity, taxonomy, species