Rockefeller University

Program for the Human Environment

Area of Research: DNA Barcoding

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

ABBI issues Inaugural Workshop Report

The All Birds Barcoding Initiative (ABBI) issued its Inaugural Workshop Report. The meeting was attended by 48 participants from 23 countries. At the close of the meeting, co-chair Allan Baker drew a comparison with the Human Genome Project. There was early resistance to and skepticism of the Genome Project that gave way to collaboration and success. Based on his experience and research results to date, Baker predicted that the ornithological community would come to accept and support barcoding and that ABBI would be highly successful.

CBOL and Natural History host International Barcode Conference in London

The conference, held on 10 Feb 2005, brought together over 200 participants from a wide range of disciplines. The Natural History Museum has this news item regarding the event.

Out of this conference comes three new initiatives: one to count all birds in the world, one to count all fishes in the world (Fish-BOL), and one to count all plant life in Costa Rica. The Fish-BOL group held a workshop in Guelph on 5 June 2005 (see the progam)