Review
DNA barcodes for ecology, evolution, and conservation

https://doi.org/10.1016/j.tree.2014.10.008Get rights and content

Highlights

  • DNA barcodes are becoming an integral tool for the identification of species and the understanding of the evolution and ecology of biodiversity.

  • Although the specification of a single short DNA region as a universal identifier for all of biodiversity has not materialized, a few genetic markers have now been identified to assist in the DNA barcode endeavor.

  • DNA barcodes are providing resolved local phylogenies of plant taxa to aid understanding of the principles of how species are assembled into communities and the evolution of functional traits in these assemblages.

  • Previous attempts to resolve multispecies interactions have been enhanced through use of DNA barcodes in investigations of trophic interactions and ecological forensics.

The use of DNA barcodes, which are short gene sequences taken from a standardized portion of the genome and used to identify species, is entering a new phase of application as more and more investigations employ these genetic markers to address questions relating to the ecology and evolution of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms are proving invaluable for understanding species boundaries, community ecology, functional trait evolution, trophic interactions, and the conservation of biodiversity. The application of next-generation sequencing (NGS) technology will greatly expand the versatility of DNA barcodes across the Tree of Life, habitats, and geographies as new methodologies are explored and developed.

Section snippets

DNA barcodes: what, why, and how

In reference to the universal coded labels found on commercial products, the term ‘DNA barcode’ is now commonly applied by biologists to a standardized short sequence of DNA that can be recovered and characterized as a unique identification marker for all species on the planet [1] (see Glossary). For many users of DNA barcodes, identification of an unknown sample by correctly matching a specific genetic marker to a reference sequence library is the primary goal (Box 1). However, DNA barcodes

Taxonomy, systematics, and species discovery

A primary goal of evolutionary biologists and ecologists is to understand the origin of species and the factors causing the disparity in species richness in different biomes across the globe. In many cases, the full diversity of species in a given region is still unknown, especially in the most biodiverse habitats [16]. DNA barcodes have been particularly useful in the discovery of cryptic and previously unrecognized species of animals [17]. For insects, it has been demonstrated that new

Concluding remarks and future contributions of DNA barcodes

Here, we have focused mainly on the basic scientific applications of DNA barcodes to increase our understanding of species relations and boundaries, community ecological processes and networks, and the assessment of biodiversity for effective conservation. In addition, the forensic use of DNA barcodes for identification of endangered species and commercially useful plants and animals is being expanded by local, state, and national governments. DNA barcodes are proving useful as evidence in

Acknowledgments

We are grateful to Susanne Renner and two anonymous reviewers of this manuscript for their constructive suggestions. Authors were supported by grants from the NSF-RCN program for ‘Tropical Forests in a Changing World’ (Award ID: 0741956) to D. McClearn, the Smithsonian Institution Postdoctoral Fellowship Program, Global Earth Observatories Program, and the Office of the Under Secretary for Science, and the National Geographic/Waitt Institute Grant (W149-11) to C.G-R. M.U. acknowledges support

Glossary

Alpha and beta species diversity
alpha diversity is calculated as the total species diversity in any single site or unit. Beta diversity quantifies site-to-site variability in community composition.
Community assembly
ecological communities are created through the arrival, reproduction, and local extinction of individual species. Community assembly processes drive colonization and extinction dynamics, and range from entirely stochastic to entirely deterministic (e.g., competition or environmental

References (99)

  • U. Eberhardt

    Methods for DNA barcoding of fungi

  • N. Evans et al.

    DNA barcoding methods for invertebrates

  • M. Vences

    DNA barcoding amphibians and reptiles

  • D.M. Spooner

    DNA barcoding will frequently fail in complicated groups: an example in wild potatoes

    Am. J. Bot.

    (2009)
  • M. Elias

    Limited performance of DNA barcoding in a diverse community of tropical butterflies

    Proc. R. Soc. B

    (2007)
  • A.J. Fazekas

    Are plant species inherently harder to discriminate than animal species using DNA barcoding markers?

    Mol. Ecol. Resour.

    (2009)
  • C. Moritz et al.

    DNA barcoding: promise and pitfalls

    PLoS Biol.

    (2004)
  • S.G. Razafimandimbison

    Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: a case study from Naucleeae (Rubiaceae)

    Syst. Biol.

    (2004)
  • W.J. Kress et al.

    DNA barcodes: genes, genomics, and bioinformatics

    Proc. Natl. Acad. Sci. U.S.A.

    (2008)
  • S. Joly

    Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead

    Mol. Ecol. Resour.

    (2014)
  • C. Chakraborty

    DNA barcoding to map the microbial communities: current advances and future directions

    Appl. Microbiol. Biotechnol.

    (2014)
  • A. Purvis et al.

    Getting the measure of biodiversity

    Nature

    (2000)
  • M.A. Smith

    Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections

    Proc. Natl. Acad. Sci. U.S.A.

    (2008)
  • P.R. Shashank

    DNA barcoding reveals the occurrence of cryptic species in host-associated population of Conogethes punctiferalis (Lepidoptera: Crambidae)

    Appl. Entomol. Zool.

    (2014)
  • C. Bertrand

    Mitochondrial and nuclear phylogenetic analysis with Sanger and next–generation sequencing shows that, in Area de Conservacion Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologically cryptic species

    BMC Evol. Biol.

    (2014)
  • P.D.N. Hebert

    Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator

    Proc. Natl. Acad. Sci. U.S.A.

    (2004)
  • C. García-Robledo

    Using a comprehensive DNA barcode library to detect novel egg and larval host plant associations in Cephaloleia Rolled-leaf Beetles (Coleoptera: Chrysomelidae)

    Biol. J. Linn. Soc.

    (2013)
  • M.A. Smith

    DNA barcoding and the taxonomy of Microgastrinae wasps (Hymenoptera, Braconidae): impacts after 8 years and nearly 20 000 sequences

    Mol. Ecol. Resour.

    (2012)
  • E.D. Silva

    Alona iheringula Sinev & Kotov, 2004 (Crustacea, Anomopoda, Chydoridae, Aloninae): life cycle and DNA barcode with implications for the taxonomy of the Aloninae subfamily

    PLoS ONE

    (2014)
  • S.E. Hamsher et al.

    A floristic survey of marine tube-forming diatoms reveals unexpected diversity and extensive co-habitation among genetic lines of the Berkeleya rutilans complex (Bacillariophyceae)

    Eur. J. Phycol.

    (2014)
  • R. Winterbottom

    A cornucopia of cryptic species: a DNA barcode analysis of the gobiid fish genus Trimma (Percomorpha, Gobiiformes)

    Zookeys

    (2014)
  • C. Costion

    Plant DNA barcodes can accurately estimate species richness in poorly known floras

    PloS ONE

    (2011)
  • W.J. Kress

    Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

    Proc. Natl. Acad. Sci. U.S.A.

    (2009)
  • C.O. Webb

    Exploring the phylogenetic structure of ecological communities: an example for rain forest trees

    Am. Nat.

    (2000)
  • N.J.B. Kraft

    Functional traits and niche-based tree community assembly in an amazonian forest

    Science

    (2008)
  • N.G. Swenson et al.

    Opposing assembly mechanisms in a Neotropical dry forest: implications for phylogenetic and functional community ecology

    Ecology

    (2009)
  • C.H. Graham et al.

    Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

    Ecol. Lett.

    (2008)
  • N.G. Swenson

    Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities

    Ecology

    (2012)
  • O.J. Hardy et al.

    Characterizing the phylogenetic structure of communities by an additive partitioning of phylogenetic diversity

    J. Ecol.

    (2007)
  • M. Uriarte

    Trait similarity, shared ancestry and the structure of neighbourhood interactions in a subtropical wet forest: implications for community assembly

    Ecol. Lett.

    (2010)
  • D.L. Erickson

    Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

    Front. Genet.

    (2014)
  • M.A. Smith

    DNA barcode accumulation curves for understudied taxa and areas

    Mol. Ecol. Resour.

    (2009)
  • C.O. Webb

    Phylogenies and community ecology

    Annu. Rev. Ecol. Syst.

    (2002)
  • J. Cavender-Bares

    The merging of community ecology and phylogenetic biology

    Ecol. Lett.

    (2009)
  • J. Cavender-Bares

    Phylogenetic overdispersion in Floridian oak communities

    Am. Nat.

    (2004)
  • H. Qian et al.

    A latitudinal gradient in large-scale beta diversity for vascular plants in North America

    Ecol. Lett.

    (2007)
  • P.H. Harvey et al.

    The Comparative Method in Evolutionary Biology

    (1991)
  • A.R. Ives et al.

    Generalized linear mixed models for phylogenetic analyses of community structure

    Ecol. Monogr.

    (2011)
  • M.M. Mayfield

    Traits, habitats, and clades: identifying traits of potential importance to environmental filtering

    Am. Nat.

    (2009)
  • Cited by (0)

    View full text