DNA barcoding - taxon identification using a standardized DNA region - has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism's remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.

https://www.cell.com/trends/ecology-evolution/pdf/S0169-5347(08)00344-3.pdf

DNA barcoding for ecologists

SYSTEMATIC BIOLOGY that accompany this article, Will and Hebert respond to 10 questions selected by V.S. to reflect the balance of issues raised by the PEET audience (Hebert and Gregory, 2005; Will et al., 2005). Alternatively, you can follow the original debate as all 2 hours of the complete symposium are available to watch as a streaming video from http:// streamer.cen.uiuc.edu/seminars/peet/peet2-3-4.wmv (Windows Media Player required). A CKNOWLEDGEMENTS R EFERENCES Anonymous. 2003. What’s in a name? Economist 366:62. Blaxter, M. 2003. Counting angels with DNA. Nature 421:122– Godfray, H. C. J., and S. Knapp. 2004. Introduction [to a theme issue ’Taxonomy for the twenty-first century’]. Phil. Trans. R. Soc. Lond. B Gotelli, N. J. 2004. A taxonomic wish-list for community ecology. Phil. Trans. R. Soc. Lond. B 359:585–597. Hebert, P. D. N., A. Cywinska, S. L. Ball, and J. R. deWaard. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270:313–322. Hebert, P. D. N., and T. R. Gregory. 2005. The promise of DNA barcoding for taxonomy. Syst. Biol. 54:852–859. Hebert, P. D. N., M. Y. Stoeckle, T. S. Zemlak, and C. M. Francis. 2004. Identification of birds through DNA barcodes. PLoS Biol. 2:1657– Holmes, B. 2004. Barcode me. New Scientist 182:32–35. Kurosawa, O., and M. Washizu. 2004. Acquisition and amplification of targeted position of electrostatically stretched DNA. J. Inst. Electro- stat. Jpn. 28:59–64. Lipscomb, D. L., N. Platnick, and Q. D. Wheeler. 2003. The intellectual content of taxonomy: a comment on DNA taxonomy. TREE 18:65–66. May, R. M. 2004. Tomorrow’s taxonomy: Collecting new species in the field will remain the rate-limiting step. Phil. Trans. R. Soc. Lond. B Moritz, C., and C. Cicero. 2004. DNA barcoding: Promise and pitfalls. PLoS Biol. 2:1529–1531. NCBI. 2005. National Center for Biological Information. Gen- Bank statistics available at http://www.ncbi.nlm.nih.gov/About/ tools/restable stat.html. Nicholls, H. 2003. DNA: The barcode of life? Originally published on behalf of Elsevier by BioMedNet. Now available at http://www. uoguelph.ca/∼phebert/media/BioMedNet%20News%20article. pdf. Pennisi, E. 2003. Modernizing the tree of life. Science 300:1692–1697. Rodman, J. E., and J. H. Cody. 2003. The taxonomic impediment over- come: NSF’s Partnerships for Enhancing Expertise in Taxonomy (PEET) as a model. Syst. Biol. 52:428–435. Schindel, D. E., and S. E. Miller. 2005. DNA barcoding a useful tool for taxonomists. Nature 435:17. Tautz, D., P. Arctander, A. Minelli, R. H. Thomas, and A. P. Vogler. 2003. A plea for DNA taxonomy. TREE 18:70–74. Taylor, R. W. 1983. Descriptive taxonomy: Past, present, and future. Pages 93–134 in Australian systematic entomology: A bicentenary perspective (E. Highley, and R. W. Taylor, eds.). CSIRO, Canberra. Vincent, M., Y. Xu, and H. Kong. 2004. Helicase-dependent isothermal DNA amplification. EMBO Rep. 5:795–800. Will, K. W., B. D. Mishler, and Q. D. Wheeler. 2005. The perils of DNA barcoding and the need for integrative taxonomy. Syst. Biol. 54:844– First submitted 23 March 2005; reviews returned 9 June 2005; final acceptance 12 July 2005 Associate Editor: Vincent Savolainen Syst. Biol. 54(5):844–851, 2005 c Society of Systematic Biologists Copyright ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150500354878 The Perils of DNA Barcoding and the Need for Integrative Taxonomy K IPLING W. W ILL , 1 B RENT D. M ISHLER , 2 AND Q UENTIN D. W HEELER 3 ESPM Department—Insect Biology and 2 Department of Integrative Biology, University of California, Berkeley, California 94720, USA Natural History Museum, Cromwell Road, London, SW7 5BD, UK “Your work, Sir, is both new and good, but what’s new is not good and what’s good is not new.” Samuel Johnson We argue that DNA barcoding has both new and good elements, but unfortunately no elements that are both. We are strongly in favor of the good idea of using DNA for identification, but that is old hat—the use of DNA for identification goes back to the beginning of molecular systematics. The DNA barcoders cannot take any credit for that. Their new idea that DNA barcoding can replace normal taxonomy for naming new species and studying their relationships is worse than bad, it is destructive. Statements by some barcoding proponents suggest an in- evitable replacement of taxonomic research rather than augmentation of technology to taxonomic science, e.g., “a COI-based identification system will undoubtedly Downloaded from http://sysbio.oxfordjournals.org/ at UNIVERSITY OF CALIFORNIA BERKELEY on August 29, 2013 I thank Kipling Will and Paul Hebert for taking part in the de- bate, Mike Irwin and Gail Kampmeier for organizing the fifth biennial PEET conference, and the National Science Foundation for financially supporting this meeting. Kevin Cummings, Martin Hauser, Andrew Miller, Mark Wetzle, and Kazunori Yoshizawa provided specimens and in some cases unpublished DNA sequences that were used dur- ing the species identification demonstration in this session. Martin Hauser, Mathys Meyer, Floyd Shockley, Daniela Takiya, and Jamie Zahniser assisted in the running of the debate. The symposium video was filmed and edited by Ritch Strom on behalf of the office of con- tinuing education at the University of Illinois. Rasplus Jean-Yves, Kevin Johnson, Rod Page, Diana Percy, Vincent Savolainen, Jason Weckstein, and an anonymous reviewer provided comments on an earlier (and considerably different) version of this manuscript. This work was supported by a grant from the National Science Foundation (DEB-0107891). VOL. 54

/pdf/the-perils-of-dna-barcoding-and-the-need-for-integrative-4ag0mt6f70.pdf

The Perils of DNA Barcoding and the Need for Integrative Taxonomy

The evolutionarily conserved p53 protein and its cellular pathways mediate tumour suppression through an informed, regulated and integrated set of responses to environmental perturbations resulting in either cellular death or the maintenance of cellular homeostasis. The p53 and MDM2 proteins form a central hub in this pathway that receives stressful inputs via MDM2 and respond via p53 by informing and altering a great many other pathways and functions in the cell. The MDM2-p53 hub is one of the hubs most highly connected to other signalling pathways in the cell, and this may be why TP53 is the most commonly mutated gene in human cancers. Initial or truncal TP53 gene mutations (the first mutations in a stem cell) are selected for early in cancer development inectodermal and mesodermal-derived tissue-specific stem and progenitor cells and then, following additional mutations, produce tumours from those tissue types. In endodermal-derived tissue-specific stem or progenitor cells, TP53 mutations are functionally selected as late mutations transitioning the mutated cell into a malignant tumour. The order in which oncogenes or tumour suppressor genes are functionally selected for in a stem cell impacts the timing and development of a tumour.

p53: 800 million years of evolution and 40 years of discovery

An oligonucleotide barcode for species identification in Trichoderma and Hypocrea.

DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. The field is transitioning from barcoding individuals to metabarcoding communities. This revolution involves new sequencing technologies, bioinformatics pipelines, computational infrastructure, and experimental designs. In this dynamic genomics landscape, metabarcoding studies remain insular and biodiversity estimates depend on the particular methods used. In this opinion article, I discuss the need for a coordinated advancement of DNA-based species identification that integrates taxonomic and barcoding information. Such an approach would facilitate access to almost 3 centuries of taxonomic knowledge and 1 decade of building repository barcodes. Conservation projects are time sensitive, research funding is becoming restricted, and informed decisions depend on our ability to embrace integrative approaches to biodiversity science.

/pdf/from-barcoding-single-individuals-to-metabarcoding-2hw68096pt.pdf

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciparum circumsporozoite gene can genetically barcode isolates

Two sets of three replicate lines of Drosophila melanogaster were artificially selected by reproduction at either a 'young' or an 'old' age. The pure lines, the hybrids between the lines within a selection regimen and the base stock from which the lines were derived were compared for longevity, early and late fertility, development time, larval viability and adult thorax length. Comparison of hybrid with pure lines showed some evidence for inbreeding depression in the lines from both selection regimes. Comparison of hybrid lines with the base stock did not provide evidence for any trade-off in either males or females between early fertility on the one hand and late life fertility and longevity on the other. Nor was there any clear evidence of a trade-off between pre-adult and adult fitness components. There was evidence of inadvertent selection for rapid development in both selection regimens, especially in the females of the 'young' lines, and this complicated the interpretation of the responses and correlated responses to selection. An improvement in adult performance in the 'old' line males relative to the base stock appeared to be attributable to reversal of mutation accumulation. Comparison of the hybrid 'young' and 'old' lines with the base stock did not support the idea that the superior longevity and late life fertility of the 'old' lines relative to the 'young' lines could be accounted for by the effects of mutation accumulation in the 'young' lines. The results point to the need to compare selected lines with their base stock when deducing responses and correlated responses to selection and to avoid unintentional selection. In this type of experiment, larval density should be standardized during selection, and adults should not be under pressure for rapid maturation.

Evolutionary effects of selection on age at reproduction in larval and adult: drosophila melanogaster.

The study examined the effects of evolution at two different larval densities on pre-adult and adult fitness traits. Five replicate selection lines each were cultured at either 50 or 150 larvae per vial, avoiding selection on development time, age at breeding or for adaptation to adult density, one or more of which factors has been a confounding variable in previous studies. Low density selection lines evolved extended development times at both growth densities. The extended development times were associated with greater adult body size at the lower growth density only, and particularly in females. The lines did not differ significantly in larval competitive ability at either growth density. At neither growth density did the early adult fertility of females or the lifespan of either sex differ between the lines from the two selection regimes, but at the lower growth density the late fertility of low density line females was significantly enhanced. The results suggest that larval density does have important effects on the expression and resolution of life history trade-offs in Drosophila melanogaster, but that these may be somewhat different from those reported in previous studies.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1420-9101.1996.9050609.x

Evolutionary responses of Drosophila melanogaster life history to differences in larval density

Nanotechnology-based approaches have demonstrated encouraging results for sustainable agriculture production, particularly in the field of fertilizers and pesticide innovation. It is essential to evaluate the economic and environmental benefits of these nanoformulations. Here we estimate the potential revenue gain/loss associated with nanofertilizer and/or nanopesticide use, calculate the greenhouse gas emissions change from the use of nanofertilizer and identify feasible applications and critical issues. The cost–benefit analysis demonstrates that, while current nanoformulations show promise in increasing the net revenue from crops and lowering the environmental impact, further improving the efficiency of nanoformulations is necessary for their widescale adoption. Innovating nanoformulation for targeted delivery, lowering the greenhouse gas emissions associated with nanomaterials and minimizing the content of nanomaterials in the derived nanofertilizers or pesticides can substantially improve both economic and environmental benefits. Nanotechnology has the potential to increase the net revenue from agricultural products and alleviate the environmental impact of conventional fertilizers and pesticides. Further improving the efficiency of nanoformulations is necessary for their wide adoption. 

/pdf/cost-benefit-analysis-of-nanofertilizers-and-nanopesticides-eb8r4j6z.pdf

Cost-benefit analysis of nanofertilizers and nanopesticides emphasizes the need to improve the efficiency of nanoformulations for widescale adoption.

'Candidatus Liberibacter' Pathosystems at the Forefront of Agricultural and Biological Research Challenges.

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