Plant DNA barcodes: Applications today and in the future

DNA barcodes have provided a new biological tool for organismal biologists to increase their understanding of the natural world. Over the last decade four plant DNA barcode markers, rbcL, matK, trnH‐psbA, and ITS2, have been developed, tested, and used to address basic questions in systematics, ecology, evolutionary biology and conservation, including community assembly, species interaction networks, taxonomic discovery, and assessing priority areas for environmental protection. Forensic investigators have also applied these plant DNA barcodes in the regulatory areas of traffic in endangered species and monitoring commercial products, such as foods and herbal supplements. Major challenges ahead will focus on building the global plant DNA barcode library and adopting genomic sequencing technologies for a more efficient and cost‐effective workflow in applying these genetic identification markers to additional fields of biological and commercial endeavors.

[1]  M. Donoghue,et al.  Maximising Synergy among Tropical Plant Systematists, Ecologists, and Evolutionary Biologists. , 2017, Trends in ecology & evolution.

[2]  W. DeKeseredy,et al.  Future directions , 2005, Psychiatric Quarterly.

[3]  W. Kress,et al.  Comparing Floristic Diversity and Conservation Priorities across South East Queensland Regional Rain Forest Ecosystems Using Phylodiversity Indexes , 2017, International Journal of Plant Sciences.

[4]  H. D. de Boer,et al.  DNA Barcoding Reveals Limited Accuracy of Identifications Based on Folk Taxonomy , 2014, PloS one.

[5]  A. Widmer,et al.  DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species , 2016, PloS one.

[6]  Steven G Newmaster,et al.  DNA barcoding detects contamination and substitution in North American herbal products , 2013, BMC Medicine.

[7]  N. Pitman,et al.  The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa , 2016, Scientific Reports.

[8]  P. Taberlet,et al.  Towards next‐generation biodiversity assessment using DNA metabarcoding , 2012, Molecular ecology.

[9]  Xiaohua Jin,et al.  Evaluation of DNA barcodes in Codonopsis (Campanulaceae) and in some large angiosperm plant genera , 2017, PloS one.

[10]  Campbell O. Webb,et al.  Phylomatic: tree assembly for applied phylogenetics , 2005 .

[11]  N. Swenson Phylogenetic analyses of ecological communities using DNA barcode data. , 2012, Methods in molecular biology.

[12]  Nathan G. Swenson,et al.  The assembly of tropical tree communities – the advances and shortcomings of phylogenetic and functional trait analyses , 2013 .

[13]  N. Baeshen,et al.  Biological Identifications Through DNA Barcodes , 2012 .

[14]  D. Janzen,et al.  Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[15]  David L. Erickson,et al.  Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly. , 2010, Ecology letters.

[16]  W. Kress,et al.  Wood nitrogen concentrations in tropical trees: phylogenetic patterns and ecological correlates. , 2014, The New phytologist.

[17]  Subramanyam Ragupathy,et al.  DNA Barcode Authentication of Wood Samples of Threatened and Commercial Timber Trees within the Tropical Dry Evergreen Forest of India , 2014, PloS one.

[18]  P. Taberlet,et al.  DNA barcoding for ecologists. , 2009, Trends in ecology & evolution.

[19]  J. Terborgh,et al.  Hyperdominance in the Amazonian Tree Flora , 2013, Science.

[20]  David L. Erickson,et al.  Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests , 2016, PloS one.

[21]  D. Janzen,et al.  Use of DNA barcodes to identify flowering plants. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Nancy Knowlton,et al.  DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity , 2015, Proceedings of the National Academy of Sciences.

[23]  David L. Erickson,et al.  Exploring Tree-Habitat Associations in a Chinese Subtropical Forest Plot Using a Molecular Phylogeny Generated from DNA Barcode Loci , 2011, PloS one.

[24]  David L. Erickson,et al.  Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China , 2015, Molecular ecology resources.

[25]  David L. Erickson,et al.  The Roots of Diversity: Below Ground Species Richness and Rooting Distributions in a Tropical Forest Revealed by DNA Barcodes and Inverse Modeling , 2011, PloS one.

[26]  David L. Erickson,et al.  Phylogenetic Analysis of Local-Scale Tree Soil Associations in a Lowland Moist Tropical Forest , 2010, PloS one.

[27]  D. Baird,et al.  Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers , 2016, PloS one.

[28]  David L. Erickson,et al.  Tropical Plant–Herbivore Networks: Reconstructing Species Interactions Using DNA Barcodes , 2013, PloS one.

[29]  David L. Erickson,et al.  Change in community phylogenetic structure during tropical forest succession: evidence from New Guinea , 2012 .

[30]  J. Conran,et al.  Application of DNA Barcodes in Asian Tropical Trees – A Case Study from Xishuangbanna Nature Reserve, Southwest China , 2015, PloS one.

[31]  D. Stevenson,et al.  DNA barcode identification of black cohosh herbal dietary supplements. , 2012, Journal of AOAC International.

[32]  Kelly M. McManus,et al.  Phylogenetic Structure of Foliar Spectral Traits in Tropical Forest Canopies , 2016, Remote. Sens..

[33]  M. Harrington,et al.  Plant DNA Barcodes Can Accurately Estimate Species Richness in Poorly Known Floras , 2011, PloS one.

[34]  E. C. Smidt,et al.  ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests , 2015, PloS one.

[35]  De‐Zhu Li,et al.  Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants , 2011, Proceedings of the National Academy of Sciences.

[36]  Pierre Taberlet,et al.  From barcodes to genomes: extending the concept of DNA barcoding , 2016, Molecular ecology.

[37]  Mehrdad Hajibabaei,et al.  DNA mini-barcodes. , 2012, Methods in molecular biology.

[38]  María Uriarte,et al.  The relationship between tree biodiversity and biomass dynamics changes with tropical forest succession. , 2014, Ecology letters.

[39]  David L. Erickson,et al.  Temporal turnover in the composition of tropical tree communities: functional determinism and phylogenetic stochasticity. , 2012, Ecology.

[40]  Kyle G. Dexter,et al.  Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities , 2012 .

[41]  David L. Erickson,et al.  Variation of tropical forest assembly processes across regional environmental gradients , 2016 .

[42]  David L. Erickson,et al.  A Well-Resolved Phylogeny of the Trees of Puerto Rico Based on DNA Barcode Sequence Data , 2014, PloS one.

[43]  Peter M Hollingsworth,et al.  Telling plant species apart with DNA: from barcodes to genomes , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

[44]  David L. Erickson,et al.  Advances in the Use of DNA Barcodes to Build a Community Phylogeny for Tropical Trees in a Puerto Rican Forest Dynamics Plot , 2010, PloS one.

[45]  David L. Erickson,et al.  Closely-related taxa influence woody species discrimination via DNA barcoding: evidence from global forest dynamics plots , 2015, Scientific Reports.

[46]  T. Itioka,et al.  Wide Host Ranges of Herbivorous Beetles? Insights from DNA Bar Coding , 2013, PloS one.

[47]  S. Graham,et al.  Spatial patterns of plant diversity below‐ground as revealed by DNA barcoding , 2011, Molecular ecology.

[48]  Nicolas Salamin,et al.  Land plants and DNA barcodes: short-term and long-term goals , 2005, Philosophical Transactions of the Royal Society B: Biological Sciences.

[49]  M. Pärtel,et al.  Plant species richness belowground: higher richness and new patterns revealed by next‐generation sequencing , 2012, Molecular ecology.

[50]  Shilin Chen,et al.  Plant DNA barcoding: from gene to genome , 2015, Biological reviews of the Cambridge Philosophical Society.

[51]  David L. Erickson,et al.  Patterns of Phylogenetic Diversity of Subtropical Rainforest of the Great Sandy Region, Australia Indicate Long Term Climatic Refugia , 2016, PloS one.

[52]  E. Bužan,et al.  20 years since the introduction of DNA barcoding: from theory to application , 2013, Journal of Applied Genetics.

[53]  David L. Erickson,et al.  DNA barcodes for ecology, evolution, and conservation. , 2015, Trends in ecology & evolution.

[54]  Generating plant DNA barcodes for trees in long-term forest dynamics plots. , 2012, Methods in molecular biology.

[55]  J. Chave,et al.  Shifts in species and phylogenetic diversity between sapling and tree communities indicate negative density dependence in a lowland rain forest , 2010 .

[56]  Sylvie Duthoit,et al.  DNA barcoding the floras of biodiversity hotspots , 2008, Proceedings of the National Academy of Sciences.

[57]  David L. Erickson,et al.  The Contribution of Rare Species to Community Phylogenetic Diversity across a Global Network of Forest Plots , 2012, The American Naturalist.

[58]  Alfried P Vogler,et al.  DNA barcoding insect–host plant associations , 2009, Proceedings of the Royal Society B: Biological Sciences.

[59]  Ting Gao,et al.  Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species , 2010, PloS one.

[60]  T. Stuessy,et al.  Monographic plant systematics : fundamental assessment of plant biodiversity , 2011 .

[61]  Thomas W. A. Braukmann,et al.  Testing the Efficacy of DNA Barcodes for Identifying the Vascular Plants of Canada , 2017, PloS one.

[62]  C. Cruaud,et al.  How Effective Are DNA Barcodes in the Identification of African Rainforest Trees? , 2013, PloS one.

[63]  David L. Erickson,et al.  DNA metabarcoding illuminates dietary niche partitioning by African large herbivores , 2015, Proceedings of the National Academy of Sciences.

[64]  Christopher Baraloto,et al.  Identification of Amazonian Trees with DNA Barcodes , 2009, PloS one.

[65]  M. A. Smith,et al.  Barcoding a Quantified Food Web: Crypsis, Concepts, Ecology and Hypotheses , 2011, PloS one.

[66]  A. Oliveira,et al.  Local plant species delimitation in a highly diverse Amazonian forest: do we all see the same species? , 2013 .

[67]  C. Cunningham,et al.  Using DNA to assess errors in tropical tree identifications: How often are ecologists wrong and when does it matter? , 2010 .

[68]  A. Vogler,et al.  DNA profiling of host–herbivore interactions in tropical forests , 2010 .

[69]  W. John Kress,et al.  300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants , 2006 .

[70]  P. Jordano,et al.  Who dispersed the seeds? The use of DNA barcoding in frugivory and seed dispersal studies , 2014 .

[71]  A. Fazekas,et al.  Testing candidate plant barcode regions in the Myristicaceae , 2008, Molecular ecology resources.

[72]  James Haile,et al.  Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland , 2007, Science.

[73]  Norman A. Bourg,et al.  CTFS‐ForestGEO: a worldwide network monitoring forests in an era of global change , 2015, Global change biology.

[74]  P. Hebert,et al.  Identification of Birds through DNA Barcodes , 2004, PLoS biology.

[75]  W. John Kress,et al.  A DNA barcode for land plants , 2009, Proceedings of the National Academy of Sciences.

[76]  R. Lahaye,et al.  Evaluation of candidate DNA barcoding loci for economically important timber species of the mahogany family (Meliaceae) , 2011, Molecular ecology resources.

[77]  Damon P. Little,et al.  Choosing and Using a Plant DNA Barcode , 2011, PloS one.

[78]  Campbell O. Webb,et al.  Plant DNA barcodes, taxonomic management, and species discovery in tropical forests. , 2012, Methods in molecular biology.

[79]  P. Hollingsworth Refining the DNA barcode for land plants , 2011, Proceedings of the National Academy of Sciences.

[80]  W. Kress,et al.  Using a comprehensive DNA barcode library to detect novel egg and larval host plant associations in a Cephaloleia rolled-leaf beetle (Coleoptera: Chrysomelidae) , 2013 .

[81]  J. G. Burleigh,et al.  What Makes a Leaf Tough? Patterns of Correlated Evolution between Leaf Toughness Traits and Demographic Rates among 197 Shade-Tolerant Woody Species in a Neotropical Forest , 2011, The American Naturalist.

[82]  Damon P. Little,et al.  Commercial Teas Highlight Plant DNA Barcode Identification Successes and Obstacles , 2011, Scientific reports.

[83]  Stephen J. Wright,et al.  Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities , 2012 .

[84]  P. Peres‐Neto,et al.  Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead , 2014, Molecular ecology resources.

[85]  W. John Kress,et al.  DNA Barcoding—a Windfall for Tropical Biology? , 2008 .

[86]  David L. Erickson,et al.  DNA barcodes: Genes, genomics, and bioinformatics , 2008, Proceedings of the National Academy of Sciences.

[87]  David L. Erickson,et al.  DNA barcodes: methods and protocols. , 2012, Methods in molecular biology.

[88]  W. Kress,et al.  Limited tolerance by insects to high temperatures across tropical elevational gradients and the implications of global warming for extinction , 2016, Proceedings of the National Academy of Sciences.

[89]  Edward O. Wilson,et al.  Half-Earth: Our Planet's Fight for Life , 2016 .

[90]  W. Kress,et al.  DNA Barcodes Confirm the Taxonomic and Conservation Status of a Species of Tree on the Brink of Extinction in the Pacific , 2016, PloS one.

[91]  J. E. Rawlins,et al.  Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity , 2009, Molecular ecology resources.

[92]  L. Weigt,et al.  Using DNA Barcodes to Identify Bird Species Involved in Birdstrikes , 2008 .

[93]  David L. Erickson,et al.  Mapping Biodiversity and Setting Conservation Priorities for SE Queensland’s Rainforests Using DNA Barcoding , 2013, PloS one.

[94]  David L. Erickson,et al.  Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach , 2014, Front. Genet..

[95]  R. Francis,et al.  A critical review on the utility of DNA barcoding in biodiversity conservation , 2012, Biodiversity and Conservation.

[96]  W. Kress,et al.  DNA barcoding as a reliable method for the authentication of commercial seafood products. , 2012 .

[97]  J. Chave,et al.  Habitat specialization and phylogenetic structure of tree species in a coastal Brazilian white-sand forest , 2014 .

[98]  Rolando Perez,et al.  Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama , 2009, Proceedings of the National Academy of Sciences.