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.

See the Barcode of life homepage at https://phe.rockefeller.edu/barcode

About the icon – A Klee diagram indicating correlations among indicator vectors for 12 animal groups see http://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

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

Mark Y. Stoeckle , Mithun Das Mishu, Zachary Charlop-Powers. GoFish: A versatile nested PCR strategy for environmental DNA assays for marine vertebrates [external link]. Plos One 2018

Stoeckle MY, Soboleva L, Charlop-Powers Z. 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 DS, MY Stoeckle. Bridging 2 scholarly islands enriches both:COI DNA barcodes for species identification v human mitochondrial variation study of migrations pathologies [external link]. Ecology and Evolution 6 (19): 6824–6835 2016

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

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

Stoeckle, MY. 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

Stoeckle, MY, Coffran, C. 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. W. John Kress and David L. Erickson. DNA Barcoding Birds: From Field Collection to Data Analysis (PDF). Chapter 7 in DNA Barcodes: Methods and Protocols 127–152 2012 barcode, dna barcode, barcoding, dna barcoding

MY Stoeckle and 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, CC Gamble, R Kirpekar, G Young, S Ahmed & Damon P. 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]. ZooKeys : 87–91 2011 Barcode, Birds, dna barcode, barcoding, dna barcoding

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

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

MJ Raupach, JJ Astrin, K Hannig, MK Peters, MY Stoeckle, JW Wägele. 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. A scalable method for analysis and display of DNA sequences [external link]. PLoS ONE 4 (10): e7051 2009 DNA Barcoding, Klee diagram

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

Stoeckle MY, Winker K. 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

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

K Stoeckle, L Strauss. High school students track down fish fraud (PDF). Pacific Fishing September: 34 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). Raffles Bull Zool : 397–398 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]. Mol Ecol Notes : 535–543 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

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

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