DNA Barcodes pp 459-465 | Cite as

Future Directions

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 858)

Abstract

It is a risky task to attempt to predict the direction that DNA barcoding and its applications may take in the future. In a very short time, the endeavor of DNA barcoding has gone from being a tool to facilitate taxonomy in difficult to identify species, to an ambitious, global initiative that seeks to tackle such pertinent and challenging issues as quantifying global biodiversity, revolutionizing the forensic identifications of species, advancing the study of interactions among species, and promoting the reconstruction of evolutionary relationships within communities. The core element of DNA barcoding will always remain the same: the generation of a set of well-identified samples collected and genotyped at one or more genetic barcode markers and assembled into a properly curated database. But the application of this body of data will depend on the creativity and need of the research community in using a “gold standard” of annotated DNA sequence data at the species level. We foresee several areas where the application of DNA barcode data is likely to yield important evolutionary, ecological, and societal insights, and while far from exclusive, provide examples of how DNA barcode data will continue to empower scientists to address hypothesis-driven research. Three areas of immediate and obvious concern are (1) biodiversity inventories, (2) phylogenetic applications, and (3) species interactions.

Key words

DNA barcode Biodiversity Phylogenetics Ecology Trophic CO1 Next-generation sequencing 

References

  1. 1.
    Hebert PDNH, Cywinska A, Ball S, deWaard J (2003) Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci 270: 313–321CrossRefGoogle Scholar
  2. 2.
    Vernooy R, Haribabu E, Muller MR et al (2010) Barcoding life to conserve biological diversity: beyond the taxonomic imperative. PLoS Biol 8:e1000417PubMedCrossRefGoogle Scholar
  3. 3.
    Radulovici AE, Archambault P, Dufresne F (2010) DNA barcodes for marine biodiversity: moving fast forward? Diversity 2:450–472CrossRefGoogle Scholar
  4. 4.
    Dinca V, Zakharov EV, Hebert PD, Vila R (2010) Complete DNA barcode reference library for a country’s butterfly fauna reveals high performance for temperate Europe. Proc R Soc Lond B Biol Sci 278:347–355. doi:10.1098/rspb.2010.1089 CrossRefGoogle Scholar
  5. 5.
    McLaughlin JF, Hellmann JL, Boggs CL, Ehrlich PL (2002) Climate change hastens population extinctions. Proc Natl Acad Sci USA 99:6070–6074. doi:10.1073/pnas.052131199 PubMedCrossRefGoogle Scholar
  6. 6.
    Ezard THG, Aze T, Pearson PN et al (2011) Interplay between changing climate and species’ ecology drives macroevolutionary dynamics. Science 332:349–351PubMedCrossRefGoogle Scholar
  7. 7.
    Kelly AE, Goulden ML (2008) Rapid shifts in plant distribution with recent climate change. Proc Natl Acad Sci USA 105:11823–11826PubMedCrossRefGoogle Scholar
  8. 8.
    Dukes JS, Mooney HA (1999) Does global change increase the success of biological invaders? TREE 4:135–139Google Scholar
  9. 9.
    Simberloff D (2000) Global climate change and introduced species in United States forests. Sci Total Environ 262:253–261PubMedCrossRefGoogle Scholar
  10. 10.
    Armstrong KF, Ball SL (2005) DNA barcodes for biosecurity: invasive species identification. Philos Trans R Soc Lond B Biol Sci 360: 1813–1823. doi:10.1098/rstb.2005.171 PubMedCrossRefGoogle Scholar
  11. 11.
    Dawnay N, Ogden R, McEwing R et al (2007) Validation of the barcoding gene COI for use in forensic genetic species identification. Forensic Sci Int 173:1–6PubMedCrossRefGoogle Scholar
  12. 12.
    Pfrender ME, Hawkins CP, Bagley M et al (2010) Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches. Q Rev Biol 85:319–340PubMedCrossRefGoogle Scholar
  13. 13.
    Stribling J (2006) Environmental protection using DNA barcodes or taxa? Bioscience 56:878–879CrossRefGoogle Scholar
  14. 14.
    Pilgrim EM, Jackson SA, Swenson S et al (2011) Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls. J N Am Benthol Soc 30:217–231CrossRefGoogle Scholar
  15. 15.
    Barber P, Boyce SL (2006) Estimating diversity of Indo-Pacific coral reef stomatopods through DNA barcoding of stomatopod larvae. Proc R Soc Lond B Biol Sci 273:2053–2061CrossRefGoogle Scholar
  16. 16.
    Kesanakurti PR, Fazekas AJ, Burgess KS (2011) Spatial patterns of plant diversity below-ground as revealed by DNA barcoding. Mol Ecol 20:1289–1302PubMedCrossRefGoogle Scholar
  17. 17.
    Floyd R, Abebe E, Papert A, Blaxter M (2002) Molecular barcodes for soil nematode identification. Mol Ecol 11:839–850PubMedCrossRefGoogle Scholar
  18. 18.
    Soininen EM, Valentini A, Coissac E et al (2009) Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Front Zool 6:16. doi:10.1186/1742-9994-6-16 PubMedCrossRefGoogle Scholar
  19. 19.
    Ficetola GF, Coissac E, Zundel S et al (2010) An in silico approach for the evaluation of DNA barcodes. BMC Genomics 11:434PubMedCrossRefGoogle Scholar
  20. 20.
    Janzen DH, Hajibabaei M, Burns JM et al (2005) Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Proc R Soc Lond B Biol Sci 360:1835–1845CrossRefGoogle Scholar
  21. 21.
    Hebert PDN, Penton EH, Burns JM et al (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–14817PubMedCrossRefGoogle Scholar
  22. 22.
    DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos Trans R Soc Lond B Biol Sci 360:1905–1916. doi:10.1098/rstb.2005.1722 PubMedCrossRefGoogle Scholar
  23. 23.
    Seberg O, Humphries CJ, Knapp S, Stevenson DW, Peterson G, Scharff N et al (2003) Shortcuts in systematics? A commentary on DNA-based taxonomy. TREE 18:63–65Google Scholar
  24. 24.
    Miller SE (2007) DNA barcoding and the renaissance of taxonomy. Proc Natl Acad Sci USA 104:4775–4776. doi:10.1073/pnas.0700466104 PubMedCrossRefGoogle Scholar
  25. 25.
    Chase MW, Fay MF (2009) Barcoding of plants and fungi. Science 325:682–683PubMedCrossRefGoogle Scholar
  26. 26.
    Kress WJ, Erickson DL, Jones FA et al (2009) Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc Natl Acad Sci USA 106:18621–18626PubMedCrossRefGoogle Scholar
  27. 27.
    Schreeg LA, Erickson DL, Kress WJ, Swenson NG (2011) Phylogenetic analysis of local-scale tree soil associations in a lowland moist tropical forest. PLoS One 5:e13685. doi:10.1371/journal.pone.0013685 CrossRefGoogle Scholar
  28. 28.
    Uriarte M, Swenson NG, Robin L, Chazdon RL et al (2011) Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly. Ecol Lett 13:1503–1514CrossRefGoogle Scholar
  29. 29.
    Pisani D, Wilkinson M (2002) Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst Biol 51:151–155PubMedCrossRefGoogle Scholar
  30. 30.
    Thompson JN (1999) The evolution of species interactions. Science 284:2116–2118. doi:10.1126/science.284.5423.2116 PubMedCrossRefGoogle Scholar
  31. 31.
    Novotny V et al (2002) Low host specificity of herbivorous insects in a tropical forest. Nature 416:841–844PubMedCrossRefGoogle Scholar
  32. 32.
    Novotny V, Drozd P, Miller SE et al (2007) Why are there so many species of herbivorous insects in tropical rainforests? Science 313: 1115–1118CrossRefGoogle Scholar
  33. 33.
    Norton DA, Didham RK (2007) Comment on “Why are there so many species of herbivorous insects in tropical rainforests?”. Science 315:1666bCrossRefGoogle Scholar
  34. 34.
    Leray M, Agudelo CN, Mills CM, Meyer CP (2011, submitted) Trophic interactions from COI fragment amplification of gut contents: methodological guidelines and case studies of two omnivorous reef fish species. PLoS ONEGoogle Scholar
  35. 35.
    Glenn TC (2011) Field guide to purchasing and using next-generation DNA sequencers. Mol Ecol Notes 11:759–769Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of BotanySmithsonian Institution, National Museum of Natural HistoryWashingtonUSA

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