Rockefeller University

Program for the Human Environment

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“Taxonomy for the twenty-first century” and “DNA barcoding of life”: special theme issues of Philosophical Transactions of the Royal Society available online

“Taxonomy for the twenty-first century” the 29 April 2004 special theme issue of Philosophical Transactions of the Royal Society Biological Sciences is available online. Allen Herre recommends this compilation as “an extremely useful source of information and ideas on what taxonomy is, what its needs are (and our needs of it), and where it is going.”

Introduction by H. C. J. Godfray and S. Knapp
Taxonomic triage and the poverty of phylogeny by Quentin D. Wheeler
A taxonomic wish-list for community ecology by Nicholas J. Gotelli
Protist taxonomy: an ecological perspective by Bland J. Finlay
Stability or stasis in the names of organisms: the evolving codes of nomenclature by Sandra Knapp, Gerardo Lamas, Eimear Nic Lughadha, et al.
Prokaryote diversity and taxonomy: current status and future challenges by Aharon Oren
Taxonomy and fossils: a critical appraisal by Peter L. Forey, Richard A. Fortey, Paul Kenrick, et al.
Automated species identification: why not? by Kevin J. Gaston and Mark A. O’Neill
The promise of a DNA taxonomy by Mark L. Blaxter
Towards a working list of all known plant species by Eimear Nic Lughadha
Biodiversity informatics: managing and applying primary biodiversity data by Jorge Soberón and Townsend Peterson
Unitary or unified taxonomy? by Malcolm J. Scoble
The role of taxonomy in species conservation by Georgina M. Mace
Taxonomy and environmental policy by Cristián Samper
Taxonomy: where are we now? by Peter H. Raven
Now is the time: by Daniel H. Janzen
Tomorrow’s taxonomy: collecting new species in the field will remain the rate-limiting step by Robert M. May
Documenting plant diversity: unfinished business by Peter R. Crane
Taxonomy as a fundamental discipline by Edward O. Wilson

“DNA barcoding of life” the 29 October 2005 issue of Philosophical Transactions of the Royal Society Biological Sciences is devoted to papers presented at the First International Barcode Conference held at The Natural History Museum, London, 7-9 February 2005, a gathering that included 220 participants from 44 countries. By special arrangement with The Royal Society, this issue is available to members and visitors to the Consortium of the Barcode of Life site.

Towards writing the encyclopaedia of life: an introduction to DNA barcoding by Vincent Savolainen, Robyn S. Cowan, Alfried P. Vogler, et al.
DNA barcodes for biosecurity: invasive species identification by K.F. Armstrong and S.L. Ball
DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar by M. Alex Smith, Brian L. Fisher, Paul D.N. Hebert
Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding by Daniel H. Janzen, Mehrdad Hajibabaei, John M. Burns, et al.
DNA barcoding Australia’s fish species by Robert D. Ward, Tyler S. Zemlak, Bronwyn H. Innes, et al.
Deciphering amphibian diversity through DNA barcoding: chances and challenges by Miguel Vences, Meike Thomas, Ronald M. Bonett, et al.
The problems and promise of DNA barcodes for species diagnosis of primate biomaterials by Joseph G. Lorenz, Whitney E. Jackson, Jeanne C. Beck, et al.
Applying DNA barcoding to red macroalgae: a preliminary appraisal holds promise for future applications by Gary W. Saunders
Land plants and DNA barcodes: short-term and long-term goals by Mark W. Chase, Nicolas Salamin, Mike Wilkinson, et al.
Microcoding: the second step in DNA barcoding by R.C. Summerbell, C.A. Lévesque, K.A. Seifert, et al.
The unholy trinity: taxonomy, species delimitation and DNA barcoding by Rob DeSalle, Mary G. Egan, Mark Siddall
Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences by Melanie Markmann and Diethard Tautz
DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers by Michael T. Monaghan, Michael Balke, T. Ryan Gregory, et al.
Defining operational taxonomic units using DNA barcode data by Mark Blaxter, Jenna Mann, Tom Chapman, et al.
An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding by Paul De Ley, Irma Tandingan De Ley, Krystalynne Morris, et al.
Critical factors for assembling a high volume of DNA barcodes by Mehrdad Hajibabaei, Jeremy R. deWaard, Natalia V. Ivanova, et al.
A likelihood ratio test for species membership based on DNA sequence data by Mikhail V. Matz and Rasmus Nielsen
TaxI: a software tool for DNA barcoding using distance methods by Dirk Steinke, Miguel Vences, Walter Salzburger, et al.

Some Fret Over Exceptions to Barcoding

The springboard for a recent news@nature.com item by Hannah Hickey “Butterflies poke holes in DNA barcodes” is a report by Gompert et al in press in Mol. Ecology on genetic differences between two subspecies of Melissa blue butterfly, Lycaeides melissa melissa and L. m. samuelis. The latter subspecies is commonly known as “Karner blue” and is listed under the USA Endangered Species Act. Analysis of mitochondrial DNA revealed some populations of Karner blue have distinct COI sequences but those populations adjacent to the range of L. m. melissa subspecies do not. This result is not surprising. For one, DNA barcoding does not aim to separate subspecies. Subspecies are geographic variants within species whose differences shade into one another so it would be surprising if any single gene showed a sharp demarcation between populations. Most subspecies do not show diagnostic genetic differences, and when such differences are found, it has often led to proposals to elevate them to species status.

Regarding the utility of DNA barcoding, the findings with Melissa blues are unremarkable, as there are cases in all animal groups studied so far in which barcoding narrows identification to a few closely-related species, but no further. For example, see my earlier entry on comparing barcode performance. It may be helpful to point out that DNA barcoding is an instrument, not a theory. Cases of partial resolution do not “disprove” barcoding or invalidate its use. In fact, one application of DNA barcoding will be to quickly highlight such cases which may be biologically interesting as they likely represent recent speciation, ongoing hybridization, or synonymy.

A more relevant Nature article that Ms. Hickey might have cited is Als et al study of Maculinea large blues, a related group morphologically similar, taxonomically confusing, and highly endangered butterflies. Large blues have “extraordinary parasitic lifestyles…later instars live in ant nests where they either devour the brood (predators), or are fed mouth-to-mouth by adult ants (cuckoos)”. Genetic analysis using mitochondrial and nuclear DNA uncovered numerous cryptic species with unsuspected host specificity, thereby both multiplying the challenge and providing the key to conservation, the need to conserve both ant hosts and butterflies.

As highlighted by the large blue study, the larger and more exciting challenge for biodiversity science will be how to incorporate the enormous number of genetically and biologically distinct forms whose discovery is facilitated by large-scale barcoding.

Photo of Rebel’s large blue Maculinea rebeli and phylogeny showing cryptic species among predatory Maculinea from Nature article by Als et al.

Norway Convenes Barcoding Collections Symposium

Representatives from 15 natural history museums and research institutions in Norway, Sweden, and Denmark gathered at Oslo Natural History Museum on 20-21 March 2006 to discuss the role genetic resource collections in the Barcoding of Life Initiative. Lutz Bachmann, Arild Johnsen, Jan T. Lifjeld, and Jon Lonnve organized an enjoyable and productive meeting, including many well-timed coffee breaks! There was general enthusiasm about museums joining in a collective effort, the public and scientific importance of genetic collections and natural history museums in understanding and preserving biodiversity, and the Barcoding of Life Initiative. As an initial step, the Natural History Museum in Oslo plans to barcode Norwegian birds, drawing on its 10,000+ samples of avian tissues. For more information contact Jan T. Lifjeld (j.t.lifjeld@nhm.uio.no).

Locations of natural history museums represented at Oslo meeting

DNA barcoding helps resolve tropical biodiversity

Tropical fauna challenge taxonomy because species richness is greater in the tropical than in temperate zones, most tropical species are as yet undescribed, and within-species genetic variation appears to be greater.

World Terrestrial Biodiversity https://www.nhm.ac.uk/research-curation/projects/worldmap/
Land Animal and Plant Biodiversity World Map

Two recent papers show DNA barcoding aids species identification and discovery in tropical fauna. In January 24, 2006 Proceedings of the National Academy of Sciences USA, Hajibabaei et al examine 4260 specimens representing 521 (71%) of hesperiids (skipper butterflies), sphingids (sphinx moths), and saturniid moths of the of the ACG conservation area in Costa Rica. 510 (98%) of recognized species have distinct barcodes, 11 (2%) have barcodes that overlap with another closely-related species, and 13 recognized species have 2 or more distinct barcode clusters. Associated co-variation in habitat, food plant, and adult and caterpillar morphology indicate these clusters represent cryptic species, a total of 27 new species whose discovery was facilitated by barcoding.

In a similar vein, DNA barcoding revealed cryptic species with unsuspected host-specificity in a genus of presumed generalist tropical parasitoid tachinid flies. Insect parasitoids are a major cause of natural insect mortality and are used as biological control agents. They are thought to represent 8%-25% of all insect species, but understanding species richness and biology is hampered by the very large number of morphologically similar species. A published commentary by Herre emphasizes “…the value of DNA barcoding in uncovering hidden diversity…especially when coupled with traditional taxonomy and a keen appreciation of the fascinating details of basic natural history.”

All Birds Barcoding Initiative (ABBI) flight update

Bird barcodes fly in. So far, researchers have deposited 3308 avian COI barcodes from about 800 species, which represents 8% of world birds, to the Barcode of Life Database (BOLD) www.barcodinglife.org. Sequences from outside North America are flocking in, including a recent set from western Australian parrots, contributed by Peter Spencer, Murdoch University. Quoting P. Spencer “these species are generally high profile, expensive (some >AUD50K) and charismatic (aka people like to steal and display them!).” The barcode database may assist with wildlife forensics in preventing illegal taking and export.

Specimen locations for avian barcodes deposited in BOLD as of 12 march 2006

ABBI on tour, internationally. A 2 day meeting “Museum Collections and the Barcoding of Life” will be held at the Oslo Natural History Museum on March 20-21, 2006, and is heavily oversubscribed! ABBI-related presentations include talks by Per Ericson, Swedish Museum of Natural History; Jon Fjeldsa, Zoological Museum, Copenhagen; Arild Johnsen, Oslo Natural History Museum; and myself.

On April 7-8, 2006, a Consortium for the Barcode of Life (CBOL) meeting will be held in Capetown, South Africa. David Schindel, Executive Secretary of CBOL, will present a summary of ABBI progress and plans.

A workshop on “DNA barcoding of Palearctic bird species at Naturalis” will be held at National Museum of Natural History, Leiden, on 20-21 April 2006, organized by Per Ericson, Swedish Museum of Natural History. There may be additional space; if interested, please contact Per Ericson Per.Ericson@nrm.se

Where is that barcoder? An excellent site with remarkable photos of pelagic birds www.oceanwanderers.com/, sometimes features ID puzzles, such as this unidentified petrel that landed on a cruise ship coming into Hawaii. Despite being held and photographed, its identify remains uncertain. A single breast feather collected before releasing and we might know the answer!

Comparing barcoding performance

Suggested metric, terminology, and standard graphic

How well do barcodes distinguish among species? A standardized, simple quantitative method and terminology for comparing barcoding performance among different data sets will be helpful.

In trying to answer this question, I aim to promote terminology that does not include “error”. In my view, it generally does not make sense to talk about the error rate of barcoding. Barcoding is an instrument akin to a telescope, except that it is designed to resolve species, not stars. A telescope that does not resolve a double star is not wrong, it simply lacks sufficient resolution. Also, the term error rate implies there is an accurate reference standard in species identification. As systematists emphasize, species definitions are hypotheses and frequently undergo revision. Thus in this view barcoding performance, effectiveness, and resolution are useful descriptive terms and are more informative than barcoding error rate.

What we want is an approach that quantitatively compares barcoding with current taxonomy. In the future, taxonomy may incorporate some of the groups discovered through barcoding as recognized species, perhaps will combine some of the recognized species with overlapping barcodes into single species, and additional sequence data may enable resolution of species with overlapping barcodes. To start, a 2 x 2 table comparing recognized species to distinct barcode groups:

Barcode groups and species

Suggested terminology:

Barcode group (or cluster): the shallowest branch in a neighbor-joining tree that corresponds to one or more recognized species or potential split within a recognized species.

Distinct barcodes: a barcode group that corresponds to a recognized species or a potential split within a recognized species. This definition can incorporate whatever criteria are used for recognizing splits (such as criteria that have been used to define provisional species, ESUs).

Barcode resolution: #barcode groups/total #species, in which total #species includes recognized species plus provisional species/ESUs.

This definition of barcode resolution incorporates “partially-resolved” species, so that if, for example, 8 species are resolved into 4 barcode groups, then resolution for that set would be 4/8 = 50%. Alternatively, if idea of partial resolution is not helpful, resolution could be defined more simply as a + b (green + yellow)/total #species.

Suggested graphic: Applying this to recent barcode data sets:

Suggested standard graphic comparing barcode performance

Suggested color scheme: As in table, green (=good!) matches current taxonomy; yellow represents novel species/provisional species/ESUs (yellow like an early bud that lacks chlorophyll), and gray (as in a gray indeterminate zone) represents recognized species with overlapping barcodes. By definition, all potential splits/ESUs have distinct barcodes, so d) in the 2 x 2 table is blank. As barcode findings are incorporated into taxonomy, I expect that the proportion that is green will increase—the greening of barcoding and taxonomy!

Mark Stoeckle

China’s 2nd MagLev

China confirmed its leadership in new transport technology with an announcement 13 March 2006 that it will build the world’s 2nd commercial maglev between Shanghai and Hangzhou, 175 km apart. The round trip will take less than 1 hour, fitting the journey into the human daily travel time budget and assuring massive traffic, as we explain in our papers Toward Green Mobility and The Evolution of Transport.