BARCODING life HIGHLIGHTS 2011

STICHODACTYLA ANEMONE

AMPHIPRION PERCULA ORANGE CLOWNFISH

BUILDING THE DNA BARCODE SYSTEM FOR THE WORLD’S , PLANTS, AND FUNGI THE BIODIVERSITY CHALLENGE

Understanding life on Earth—what lives

where, how life interacts, and how life is

changing—begins with identifying species.

DNA barcodes—short DNA sequences from

a uniform location on the genome—

distinguish , plant, and fungal species.

A simple, standardized identification system,

DNA barcoding assists researching,

monitoring, and appreciating Earth’s

changing biodiversity.

XYLOCOPA VIRGINICA EASTERN CARPENTER BEE

SALVIA OFFICINALIS GARDEN SAGE M. STOECKLE BARCODE-BASED DISCOVERIES

Cataloguing hidden diversity. Some groups Safeguarding public health. In East Africa, Untangling names. Every scientific name is with simple external features may seem researchers analyzed blood meals of tsetse based on a particular type specimen archived lacking in diversity, but DNA tells another flies (Glossina swynnertoni), the vector of in a museum or herbarium, which serves story. In red (Phylum Rhodophyta), trypanosomiasis, documenting geographic as a permanent reference for the species common seaweeds around the world, COI differences in animal hosts, helping inform name. When the type specimen degrades barcodes point to dozens of unrecognized local control strategies. over time or is damaged, diagnostic species hidden among the 1,200 analyzed (CN MUTURI ET AL, PLOS ONE 2011) features may be lost. This makes difficult so far. The widespread and invasive classifying similar-looking specimens, common earthworm, Lumbricus terrestris, sometimes resulting in misidentifications named by Linnaeus and studied by Darwin, or multiple names assigned to the same is revealed by barcoding to be two distinct species. Researchers are barcoding type species, previously unrecognized due to specimens, like the moth shown above, overlapping variation in size and shape. anchoring the species name to a DNA code, (GW SAUNDERS ET AL, BOTANY 2010; SW JAMES ET AL, PLOS ONE 2011) widely-accessible even when morphologic features of the defining original are lost.

(PDN HEBERT, BIODIVERSITY INSTITUTE OF ONTARIO; P12 P11 P30 P38 P21 P1 P3 P40 P2 P44 P45 P13 P41 P37 P34 PHOTO: STUART HUMPHREYS, AUSTRALIAN MUSEUM)

LEFT: LITTLE BROWN BAT (MYOTIS LUCIFUGUS) RIGHT: PARTS IN BAT GUANO Finding facts from fragments. Gut contents and feces reveal hidden predator-prey relationships and help trace the network of interactions that make up a food web.

H3 H16 H15 H28 H36 H2 H1 H4 H17 H5 Researchers in Africa and Canada used DNA sequences from bat guano to reveal Targeting pests naturally. Barcoding speeds unanticipated diversity of prey and roosts the search for natural insect predators by specializing in different hunting grounds. accurately identifying potential biocontrol (BOHMANN ET AL, PLOS ONE 2011; EL CLARE ET AL, MOL ECOL 2011; agents, usually tiny, otherwise-hard-to-iden- PHOTOS: EL CLARE, UNIVERSITY OF BRISTOL) Discovering diagnostic differences. DNA tify parasitic wasps or flies, including those barcodes sort specimens into unequivocal still developing inside larvae. This approach categories, helping experts discover revealed unexpected parasitic insect distinguishing features. This approach diversity for spruce budworm moth prompted recognition of a new European (Choristoneura fumiferana), the most liverwort, Herbertus norenus, from speci- economically destructive insect in North mens previously misclassified under two America. Parasitic , or parasitoids, other names. Correcting classifications are also key components of natural enabled taxonomists to discern diagnostic ecosystems. In New Guinea, barcodes features for H. norenus and its once identified 93 hitherto unknown connec- confusing close relatives, strengthening tions among lepidopteran hosts and their species descriptions for the entire group. Rediscovering lost species. The Barcoding multiple parasitoids. (D BELL ET AL, MOL ECOL RES 2011) Fauna Bavarica project () turned up (MA SMITH ET AL PLOS ONE; HRCEK ET AL, MOL ECOL RES 2011) several rarely-seen species, including the predatory water bilineatus, thought locally extinct for 26 years.

(A HAUSMANN, BARCODING FAUNA BAVARICA) HELPING SOCIETY AND SCIENCE

SUNDAY OCT 23, 2011 SPECIAL REPORT FISHY BUSINESS

BAIT AND SWITCH: Protecting consumers. In the past year, Helping threatened species. Illegal fishing Improving environmental monitoring. barcode surveys in Canada, Ireland, Spain, practices threaten sharks and rays (Class Finding out what lives in the water is the , and United States Elasmobranchii). Many species are protected most accurate way to measure the health of documented 10 –50 percent mislabeling of by law, but enforcement of regulations rests streams, rivers, lakes, wetlands and oceans. fish products, including those sold at on recognizing dried fins and other frag- Traditional bioassessment with microscopes prominent restaurants and stores. In all mentary specimens. The Pew Ocean and morphologic keys often takes months studies, inaccuracies involved substitution Environment Group highlighted DNA and often identifies only to genus or family with less expensive or less desirable species. barcoding as a “rapid, reliable, inexpensive level. Barcoding of invertebrates in marine Mislabelings include selling imported, method of identifying shark body parts in and freshwater samples is accelerating farmed fish as locally caught, and selling trade.” As of September 2011, researchers identifications and improving accuracy. The species at risk of decline as sustainably have barcoded nearly 9,000 specimens Southern California Coastal Water Research harvested fish. Responding to calls for from over 500 elasmobranch species, Project (SCCWRP) together with US improved monitoring, the US Food and establishing ineffaceable identifiers for 50 Environmental Protection Agency, Stroud Drug Administration (FDA) formally percent of the world’s sharks and rays. Water Research Center (SWRC), and adopted DNA barcoding for seafood (PEW ENVIRONMENTAL GROUP OCEAN SCIENCE REPORT, Canadian Centre for DNA Barcoding, is MARCH 2010; D STEINKE, MARBOL). identification in October 2011. developing standardized barcoding methods (CONSUMER REPORTS, DECEMBER 2011; BOSTON GLOBE, OCTOBER 23, for bioassesment. 2011; R HANNER ET AL, PLOS ONE 2011; D MILLER ET AL, FISH FISHERIES 2011; OCEANA, REPORT MAY 25, 2011; PEW CENTER FOR (B SWEENEY ET AL, J N AMER BENTHOL SOC 2011; PUBLIC INTEGRITY, REPORT JULY 12, 2011; WWW.FDA.GOV/FOOD/ PHOTOS: B SWEENEY, SWRC; P MILLER, SCCWRP) FOODSAFETY/PRODUCT-SPECIFICINFORMATION/SEAFOOD/ DNASPECIATION)

Exciting educators. The TeaBOL student investigators helped inspire Cold Spring Harbor’s Urban Barcode Project, a science competition open to all public and private Inspiring artists. A video installation on Engaging young minds. At Coastal Marine school students in New York City, with species and barcodes was chosen for Biolabs, Ventura, California, high school $10,000 prizes. Here teachers attend an “Unnamed,” an exhibition of unsung students are collecting reference barcodes Urban Barcode workshop at GenSpace, a design. The exhibition, curated by the for marine life in the kelp forest and community science laboratory in Brooklyn, Chinese artist and political activist Ai near-shore areas in a federally-funded New York. Weiwei, was part of the Gwangju Design project. In New York City, high school (D MICKLOS, COLD SPRING HARBOR LABORATORY (CSHL); PHOTO: CSHL) Biennale in South Korea in October 2011. students found 35 percent of commercial (NEW YORK TIMES, OCTOBER 2, 2011) herbal teas contained unlisted ingredients, ranging from chamomile to common weeds. The TeaBOL students co-authored an article in Nature’s Scientific Reports in June 2011, sparking global news coverage and inquiries from tea manufacturers.

(R IMONDI, COASTAL MARINE BIOLABS (CMB); MY STOECKLE ET AL, SCIENTIFIC REP 2011; PHOTOS: CMB, COLD SPRING HARBOR LABORATORY) BUILDING THE LIBRARY

Collecting in collections. Natural history Establishing accessible, permanent identifiers. Spawning new expeditions. A group of museums and herbaria are organized Translating specialist knowledge into the Argentine and Bolivian scientists is hotspots of biodiversity, thanks to decades simple language of DNA helps share collecting Bolivian insect and bird speci- of expeditions and countless hours of taxonomic expertise with a broad audience. mens for traditional and barcode study. curating. Demonstrating their enormous Recording identifications in DNA may be Many of these will become part of local value, a team of researchers barcoded particularly critical for the less charismatic biorepositories and the rapidly growing 28,000 moth and butterfly specimens in groups with few taxonomic experts. Research- research infrastructure for barcoding. just ten weeks at CSIRO’s Australian ers recently barcoded 2,334 marine annelid Springtime in South Africa launches the National Insect Collection (ANIC) in worms at eight locations in the Atlantic, annual Toyota Enviro Outreach expedition Canberra, representing about 65 percent of Arctic, and Pacific oceans ranging from tidal —researchers with a fleet of specially the country’s 10,000 known species. Even flats to ocean floor sediments at 60 meters— equipped 4x4 vehicles head to remote though many were older than 20 years, over some of the incredible diversity is shown biodiversity hotspots to gather specimens 80 percent of the ANIC specimens pro- above. 145 named and 200 provisional for DNA barcoding. The 2011 expedition duced barcode records. In the past year, marine annelid species are now firmly linked collected fish, molluscs, insects, spiders, researchers at Smithsonian Institution’s to barcodes. and plants in iSimangaliso Wetland Park, a National Museum of Natural History (CM CARR ET AL, PLOS ONE 2011) 332,000 hectare World Heritage Site (NMNH) in Washington, DC, have barcod- containing most of South Africa’s remaining ed more than 3,000 frozen bird tissues, swamp forests. each backed up by a permanent voucher (PHOTOS: P TUBARO, TOYOTA ENVIRO OUTREACH) specimen like those shown above, from over 1,400 species, adding more than 1,000 new species to the global avian barcode library.

(PHOTOS: ANIC; C DOVE, NMNH)

Making headway on hyperdiverse groups. Many groups are too populous and too Completing regional inventories. For most diverse for any specialist to know in detail. applications, a regional barcode library DNA barcodes provide the specialist and answers the question “what organism is LEFT: EIMERIA, A PATHOGENIC PROTIST generalist alike with a standardized this?” Researchers recently completed a RIGHT: AMINITA MUSCARIA, A FATAL FUNGUS identification tool of unlimited capacity. library that characterizes 1,264 of the 1,338 Mapping two of the largest, darkest realms Butterflies and moths (order Lepidoptera) species (94 percent) of butterflies and large of biodiversity. Protista (single-celled are the largest well-analyzed group so far, moths of Germany. Local agricultural pests animals) and Fungi are comprised of many with over 500,000 barcode records from and invasive species can now be identified deeply divergent evolutionary lineages—for from 60,000 named and provisional by DNA and distinguished from non-harm- example, two fungi may relate more species, a large fraction of the world’s ful relatives. In Japan, botanists established distantly than a fish to an insect. The 170,000 total. (www.lepbarcoding.org; a library of rbcL barcodes for 689 of the 783 communities of researchers that work on iBOL Working Group 1.9—Terrestrial local ferns and horsetails (94 percent), these phyla have identified a single gene Bio-Surveillance). creating a naming tool that works for all life region that promises to document the vast (WWW.LEPBARCODING.ORG) stages, including gametophyte forms often unstudied diversity, opening new research indistinguishable by appearance. areas, ranging from rapid assessment of (A HAUSMANN ET AL, SPIXIANA 2011; A EBIHARA ET AL, PLOS ONE 2010; PHOTOS: A HAUSMANN, JESMOND DENE). water quality to diagnosis of disease caused by indoor mold.

(BTM DENTINGER, PLOS ONE 2011; JD OGEDENGBE ET AL, INT J PARASITOL 2011; PHOTOS: M MAGGS, JD OGEDENGBE) THE BIODIVERSITY CHALLENGE

The global map shows the wide distribution of collection locations for the 1.3 million specimens representing 114 thousand known and 53 thousand provisional species recorded in Barcode of Life Data Systems (BOLD) as of September 2011. Red indicates the highest density of sampling and orange indicates lower density. (WWW.BOLDSYSTEMS.ORG)

"SUISPQPEB JOTFDUT TQJEFST DSBCTBOESFMBUJWFT $IPSEBUB WFSUFCSBUFT spiders .BHOPMJPQIZUB GMPXFSJOHQMBOUT and kin

.PMMVTDB NPMMVTDTJODMVEJOHDMBNT TOBJMT TRVJE

3IPEPQIZUB SFETFBXFFET insects molluscs

"OOFMJEB TFHNFOUFEXPSNTJODMVEJOHFBSUIXPSNT MFFDIFT vertabrates

&DIJOPEFSNBUB TUBSGJTI TFBVSDIJOT other )FUFSPLPOUPQIZUB CSPXOTFBXFFET EJBUPNT animals /FNBUPEB SPVOEXPSNT

1MBUZIFMNJOUIFT GMBUXPSNT flowering plants fungi              

BOJNBMT QMBOUT 1 square = 10,000 species other plants Building a biodiversity macroscope. Just as How big is the challenge? About 1.9 Top Ten Phyla. Number of barcoded telescopes help see the Very Far and micro- million species of animals, plants, and specimens in Barcode of Life Data scopes the Very Small, barcoding can be a fungi are known and about 167 thousand Systems (BOLD). macroscope that helps see the Very Large— named or provisional species have been (WWW.BARCODINGLIFE.ORG) patterns in the enormous diversity of life barcoded so far. The International Barcode on Earth. The ‘Klee diagram’ above con- of Life Project (iBOL) aims to expand the denses 3,000 barcodes from 1,400 bird library to 500 thousand species, including species into a ‘heat map.’ The lighter most of those of established importance to blocks along the diagonal indicate groups society such as food sources, endangered of species with similar barcodes, and cor- and threatened species, disease vectors, respond to evolutionary divisions that biol- and invasive species. ogists have recognized through 250 years (ATLAS OF LIVING AUSTRALIA) of study. Focusing the barcoding macro- scope on the growing Library promises to reveal structural patterns across the diver- sity of animal, plant, and fungal life.

(SIROVICH ET AL, PLOS ONE 2010; FIGURE: MY STOECKLE). GROWING ORGANIZATIONS

IBOL PARTICIPANTS CENTRAL NODES Canada, China, European Union (, , Germany, , Portugal, Spain, United Kingdom), and United States REGIONAL NODES Argentina, Australia, Brazil, India, Mexico, New Zealand, , , Saudi Arabia and South Africa NATIONAL NODES iBOL and CBOL join forces with UN. Colombia, Costa Rica, Kenya, Korea, Madagascar, Panama, Ahmed Djoghlaf, Executive Secretary of Papua New Guinea and Peru the UN Convention on Biological Diversity (CBD) Secretariat and Christian Burks, former board chair of iBOL, signed a memorandum of cooperation at the October 2010 CBD conference in Nagoya, Japan. iBOL supports CBD’s work to protect and enhance biodiversity at national and international levels. CBOL’s involvement in the CBD Working Group on Access “free and open access “providing access to “global access to and Benefit Sharing is helping to develop to biodiversity data” biomedical and genomic knowledge about life information” on Earth” an international regime that differenti- ates commercial and non-commercial research, simplifying access to specimens Opening access and linking to e-Biosphere. The acceleration of biomedical for public-good projects like barcoding. science during the past decade owes much to adoption of policies and practices

(PHOTO: UNCBD) of promptly sharing observations and data. Barcoders and others interested in biodiversity are taking similar steps to share knowledge about life on Earth. Publishing in open access journals, promptly uploading genetic data to NCBI’s GenBank, and establishing links among major biodiversity databases are putting on an global information platform and speeding the process of documenting biodiversity for society and science.

(WWW.GBIF.ORG; WWW.NCBI.NLM.NIH.GOV; WWW.EOL.ORG) TWO GLOBALORGANIZATIONS WITHSHAREDGOALS Smithsonian Institution University ofGuelph CONACYT andCONABIO(Mexico) Ministry ofScienceandTechnology (Brazil) German Federal MinistryofEducationandResearch(BMBF) Natural SciencesandEngineeringResearchCouncil (Canada) International DevelopmentResearchCentre (Canada) Richard LounsberyFoundation Gordon andBettyMooreFoundation Alfred P.SloanFoundation Ontario MinistryofResearchandInnovation Ontario GenomicsInstitute Genome Canada SPONSORS include Highlights 2011. a publicDNABarcodeLibrary. Theyjointlysponsorproductionanddistributionof CBOL andiBOLsharethegoalsofbuilding,disseminating,promotinguse Life socialnetwork. and informationsharingthroughConnect (http://connect.barcodeoflife.net),theBarcodeof general awarenessofbarcodingthroughaninformationwebsite(www.barcodeoflife.org) training opportunities,andinternationalconferencesheldeverytwoyears.CBOLpromotes community standards,organizesandsupportsworkinggroups,workshops,networks, organizations frommorethan50countries,CBOLbuildsglobalparticipation,sets barcoding asaglobalstandardforspeciesidentification.With morethan200member The Consortium fortheBarcodeofLife(CBOL), freeandopentoall,developsDNA HIGHLIGHTS (D STEINKEETAL,BARCODINGNEMO:DNA-BASED IDENTIFICATIONS FORTHEORNAMENTAL FISHTRADE.PLOSONE, COVER resources—financial support,humaneffort,andspecimens—towardthe5M/500K goal. from Genome Canada andOntarioGenomics Institute.iBOLparticipantscommit more than100scientistsfrom20countries.Launchedin2010withsupport quarter ofallknownspeciesonEarth.Headquartered inCanada, iBOListhecreationof standardized DNAsequencescapableofidentifying500thousandspecies,morethana launched. By theendof2015,iBOLaimstobuildareferencelibrary5million The InternationalBarcodeofLife(iBOL)isthelargestbiodiversitygenomicsinitiativeever DNA barcodeshelpprotectmarine life. 2011 Compiled andedited byMarkStoeckle,JohnChenery, andDavidSchindel. 2009 )

GRAPHIC DESIGN: ROSSIGNOL & ASSOCIATES DESIGN www.rossignoldesign.com